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Introduction Mimics interfaces between scanner data (CT, MRI, Technical scanner, ...) and Rapid Prototyping, STL file format, CAD and Finite Element analysis. The Mimics software is an image-processing package with 3D visualization functions that interfaces with all common scanner formats. Additional modules provide the interface towards Rapid Prototyping using STL or direct layer formats with support. Alternatively, an interface to CAD (design of custom made prosthesis and new product lines l ines based on image data) or to Finite Element meshes is available. Materialise's Interactive Medical Image Control System (MIMICS) is an interactive tool for the visualization vi sualization
and segmentation of CT images as well as MRI images and 3D rendering of objects. Therefore, in the medical field Mimics can be used for diagnostic, operation planning or rehearsal purposes. A very flexible interface to rapid prototyping systems is included for building buil ding distinctive segmentation objects. The software enables the user to control and correct the segmentation of CT-scans and MRI-scans. For instance, image artifacts coming from metal implants can easily be removed. The object(s) to be visualized visuali zed and/or produced can be defined exactly by medical staff. No technical knowledge is needed for creating on screen 3D visualizations of medical objects (a cranium, pelvis, etc.) Separate software is available to define and calculate the necessary data to build buil d the medical object(s) created within Mimics on all rapid prototyping systems. Mimics is a general-purpose segmentation program for gray value images. It can process any number of 2D image slices (rectangular images are allowed). allow ed). The only restriction is the physical memory of your computer. The interface created to process the images provides several segmentation and visualization tools.
Overview Mim Mimics ics mod modules ules Mimics consists of five modules. The image below shows the links between the main program and its modules.
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Mimics Mimics interactively read CT/MRI data in the DICOM format. format. Segmentation and editing tools enable the the user to manipulate the data to select bone, soft tissue, skin, etc. Once an area of interest is separated, it can be visualized in 3D. After this visualization, a file can be made to interface with STL+ or MedCAD. CAD data, imported as STL files, can be visualized in 2D and 3D for design validation based on the anatomical geometry.
Import Module Import module imports CT and MRI data from a wide variety of scanner formats. The data can be accessed from CD, optical disk, DAT tapes, 4 mm tapes, etc.
RP Slice Modu le RP Slice module provides an interface to Rapid Prototyping systems via sliced files with patented support structure generation. The perforated support structures are generated in no time and use less material. Supported formats:
Introduction
Common Layer Interface Files (*.cli)
3D Systems Layer Interface Files (*.sli)
3D Systems Contour Files (*.slc)
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STL+ Module STL+ module provides interface options via triangulated formats. Supported formats:
STL (ASCII and Binary)
DXF
VRML
PLY
MedCAD Module MedCAD module provides a direct interface to CAD systems via surfaces, curves, and objects exported as IGES files. Supported files:
B-Spline (NURB) curves and surfaces exported as IGES
Point Cloud
Simulation Module The Simulation module is an open platform for surgical simulations. You can perform a detailed analysis of your data using the anthropometric analysis, plan osteotomies and distraction surgeries or simulate and explain a surgical procedure for your implant design.
FEA FE A Modul Mod ule e The FEA module provides an interfacing to FEA (Finite Element Analysis) and CFD (Computational Fluid Dynamics). Supported formats:
Patran Neutral
Abaqus
Ansys
Fluent
Nastran
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What's W hat's new Basic Mimics mod ule Upgraded User Interface With the well-organized, intuitive user interface, you can quickly access all relevant tools and functions. Changes to the user interface include a redesign of the graphical elements to conform to “Windows XP” style, as well as a clearer organization of related functions and options.
Ad ju just st Gray Graysc scale ale The Adjust Gray Scale toolbar is replaced with a Contrast Histogram. This histogram allows you to do windowing like before by dragging the two points on the graph horizontally and vertically with the left mouse button. Windowing with the right mouse button is still possible.
Volume Rendering You can visualize a dataset in 3D without segmentation efforts. efforts . This powerful visualization tool instantly gives you a 3D view of your dataset’s content.
Enhanced Enhance d Rotation and Translation to ols New tools for Rotating and Translating STL’s and 3D objects enable straightforward positioning of the objects in your project. All you have to do is grab the rotation or translation tool.
New Ne w Shortcu ts New shortcuts were added to the software General Shortcuts SPACE
CTRL +I
Scroll wheel
If you hover with the mouse over a view and press the spacebar, that view is put to full screen. To unzoom to full screen, press the spacebar again. If you want to make all masks invisible, press CTRL+I. To make all previous visible masks visible again, press CTRL+I again. With the scroll wheel you can zoom in on the active view.
Navigation s hortcuts for the 3D view Navigation Rotate the 3D view left/right and up/down Arrows keys Rotate the 3D view 30 degrees up PageUp Rotate the 3D view 30 degrees down PageDown Rotate the 3D view with 30 degrees left Home End Rotate the 3D view with 30 degrees right SHIFT + keys above ALT + left/right left/right
Pan the 3D view Do washing machine rotation
Extended Extende d Clippin g functionality lity enables you to manipulate several clipping planes at the same time. It also The extended clipping functiona gives you greater input on the actual clipping action. These new visualization options expand the possibilities for
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displaying your 3D images
Convert MedCAD MedCAD object to mask MedCad Object like spheres, cylinders and nerves can be converted to a mask.
Add Ad d Ann A nnot otati ation on s With Mimics 10 you can make annotations directly on any object and save this additional information in the dataset. This new functionality ensures efficient communication among all parties involved in the project.
3D Mask Editing The new 3D mask editing too l allows users to display the 2D mask information in the 3D view and edit that mask in 3D. This tool is very helpful when removing scatter and for easily separating complex structures like vessels.
Delete De lete unselected unselected im age ages s fr om p roject After you’ve imported the images, you can still choose to delete unselected unselected images in the organize image dialog.
MedCAD Module Fit Ce Centerlines nterlines Using Mimics 10 you can calculate and measure the centreline of 3D object , for example of a vessels. This information can then be used for clinical cl inical trials, diagnostic purposes or for the design of new or custom devices.
FEA FE A Modul Mod ule e New Ne w Ans ys Form at You can now export you optimized surface mesh as an Element Based Ansys mesh. Starting from this mesh format you can immediately generate your volume mesh in Ansys.
Simulation Module New Ne w Cuttin g Tool A new cutting tool was added to the the simulation module. By drawing a curve on a 3D object, you can separate the the enclosed object from the original 3D object.
Soft-Tissue Module The Soft-Tissue tool predicts the behavior of the facial tissue with regard to the surgical bone repositioning. The Soft-Tissue module is based on a biomechanical model of the soft-tissue and it runs on top of the simulation module.
Inst nsta alli lling ng Mimics
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We recommend that you close all other applications before installing Mimics. You must have administrative privileges to install the software. s oftware. Place the Mimics CD into your CD-ROM drive. Make sure the artwork faces up. The autorun starts automatically. If the autorun does not start automatically, browse to your CD-drive and choose autoplay or double-click on ‘MimicsSetup.exe’ in the Mimics folder. During the installation the following dialogs will be shown:
STEP 1:
Wait until the progress bar is finished. You will automatically go to step 2.
STEP 2:
Click Next to proceed.
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STEP 3:
After reading the license agreement, agreement, select the “I accept the terms of the license agreement” bullet and click on the Next button.
STEP 4:
Select your region and click Next .
STEP 5:
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Choose for the Complete or Custom setup type and select where Mimics will be installed. Mimics will be installed in C:\Program Files\Materialise\Mimics 10.0\ by default. If you prefer another directory, click on the Browse button and select an existing directory out of the list. Click Next to proceed. If you have chosen the Complete setup, you will immediately go to Step 7. If you have chosen the Custom option, you will go to Step 6.
STEP 6:
Select if you want to install the Demo Files or not and click on Next .
STEP 7:
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If you have chosen to install the Demo Files, you can choose where these demo files should be installed. Mimics will store the studies in a folder C:\MedData by default. If you want to change this directory, select Browse and go to the folder where you want to store your data.
STEP 8:
Program icons will be added to the Programs Folder > Materialise Software. If you want another folder name, then type a new name or select one from the existing folder list.
STEP 9:
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When everything is filled in like you want, click Next to proceed. If you want to change or review something, click Back.
STEP 10:
The Mimics software gets installed. This can take a few moments. This window will close automatically when the progress bar is finished.
STEP 11:
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Mimics will then ask you if you want to see an overview of what the new features are in Mimics.
STEP 12:
The software is successfully installed. Click Finish to close the installation dialog. It’s recommended to reboot your computer to finalize the installation. To uninstall Mimics, go to Start > Settings > Control panel > Add/Remove programs . Select Mimics 10.0 and click the Remove button. All Mimics folders and the desktop icon will be removed. Note: The installation of the DICOM Input Application and of the Distractor and Anthropometric template libraries
are separate processes. The libraries have to be installed separately in order for the Simulation module to function correctly.
Registration To start Mimics, double click the Mimics icon Materialise and choose to start Mimics.
on your desktop or go via the Start button to Programs,
Materialise Software is password protected. When you start Mimics for the first time or when your password has expired, a registration dialog will appear. Mimics can be registered with a local license or a floating license. In the Registration dialog you can display your current license situation, display contact information, request passwords and register new modules. To display the Registration dialog, go to the Options menu and choose
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Licenses.
There are two sections in this dialog: the Register new modules section and the System Information section.
Register new modules There are three different steps when registering new modules:
Step 1: Request password You can request password via the Password request wizard. To start this wizard, click on the Request password button. When you click on the Contact information button, you will see contact information so you can contact Materialise if needed.
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Step 2: Enter password When you have generated a password via the Password request wizard, you can enter this in the Password edit box. Passwords that have been copied to the clipboard can be pasted in the edit box by clicking on the Paste button.
Step 3: Register When the password has been entered in the edit box, you can register the password by clicking on the Register button. You will then see a message that gives you feedback about the registered passwords.
System Information In the System Information section of the register dialog you can find your SystemID, your CCKey (if filled in) and you can specify floating license servers.
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System ID Your SystemID is a unique identifier for your pc. This id is dependant on your hardware and will be used to generate a password.
CCKey The CCKey is a unique identifier for your software license. You can use this key for generating passwords with our on-line password generation system. The CCKey can be found on your Certificate of Authenticity that you will receive when you buy the software (so evaluators don't have a CCKey). It is optional to fill in the CCKey, but we advice you to do this because this will facilitate the password generation process.
Floating license server Via the specify button you can enter floating license servers if needed. This function should only be used when you have floating passwords. You can add or change floating license servers by clicking on the Specify button in the System information section. This will open following dialog:
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In this dialog, all the floating license servers that are used by the software are listed. For each floating license server the IP Address (or hostname), the port and a description are displayed. To remove a floating license server from the list, select the server and click on the Delete button. To change a floating license server, select the server in the list and click on the Change button. To add a new floating license server, click on the Ad d button. These buttons will open following dialog:
In this dialog you can fill in the IP Address or hostname, IP Port and Description for the floating license server. You can also Browse for a server by clicking on the Browse button. With the browse function you can browse your Network Places, select the appropriate floating license server and by clicking on the OK button, the name of this server will be filled in automatically.
Show Modules When you click on the Show Modules button, you will see a list of all the modules that are available for your software. The name, version, type of license, days left and a comment is displayed for each module. If you haven't got a password for a certain module, there will appear n/a as number of days left and "no license found for this module" will be displayed under the comments section.
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Password Request Wizard When you start the password request wizard, you can choose how you want to request your passwords. You can choose between Online password request, Request passwords via E-Mail and Request passwords via Fax. If you have bought our software, if you have already received your Card of Authenticity and if you are connected to the Internet, we advice you to use the Online password generation. This way you will receive your passwords instantly.
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Online Password Request When you have chosen to generate passwords online, you will be asked to fill in your CCKey and E-Mail address if this data hasn't been entered before. You can find your CCKey on your Certificate of Authenticity. You will receive this Certificate of Authenticity when you buy the software. This card contains a unique CCKey that identifies the license you have bought. This CCKey can be used to generate your own passwords via the online password system.
If you have filled in the required information you can click on the Finish button and you will automatically be directed to the correct webpage. First you will have to choose your language by clicking on one of the flags.
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You can find more information about web passwords by clicking on the How does it work? link. When you have chosen your language you will go to the second screen where you have to fill in your CCKey. If you have entered your CCKey in your software when asked, this key will already be filled in automatically.
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To continue click on the Login link. In the next screen you will have to fill in information about the software you are requesting passwords for. When this is done, you can request a regular password or an emergency password. This password will be sent to you by E-Mail. If you request a regular password and you receive a message that some of the information was not correct and that you will be contacted by Materialise, you can generate an emergency password if needed. This password can be used for a week and should be requested when your password has expired and you really need to continue working with the software.
Request Passwords via E-Mail When you choose to request a password via E-Mail, you will see a window where you have to fill in your contact data. Fields with an exclamation mark behind them have to be filled in. When you have filled in the correct information and click on the Finish button, your E-Mail software will start and a new mail will be shown with all the information needed for us to generate a password. Once you have filled in your contact data, this information will be saved. So next time you request a password, you won't have to fill in your contact data again.
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Request Password via Fax When you choose to request a password via Fax, you will see a window where you have to fill in your contact data. Fields with an exclamation mark behind them have to be filled in. When you have filled in the correct information and click on the Finish button, a document will be shown with all the information needed for us to generate a password. This document can then be printed and faxed to us. Once you have filled in your contact data, this information will be saved. So next time you request a password, you won't have to fill in your contact data again.
Using help Mimics provides Help so that you can get useful information while you are working. The help pages contain a description of each command and dialog box, and explains procedures for most tasks. To get help, press F1 or select Help | General Help from the menu bar. The Help window consists of a tabbed window showing a tree of topics at the left side and a preview window at the right side. If the page is not displayed completely, maximize the help window or scroll with the scroll bars.
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You can search for the correct help page in 4 different ways:
Browse through the tree by clicking on the book icons and page icons. Click on an underlined item in the preview page to jump to the help page about that item. The tree will be updated accordingly. Select the Index tab and type the first few letters of the topic you're looking for. The corresponding items will be highlighted in the list while typing. Click the Display button to view the item that is highlighted. To search very quickly all pages about a specific topic, click on the Search tab and fill in the name of the topic. Click the List topics button to show a list of all help pages about the topic. Click on an item in the list to view the page. To hide the contents window. Once it's hidden you can show it again by clicking again on this button. To display the previous page. To display the page that was shown before clicking the Back button. To print the current page.
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The different views In the default configuration the images appear in a four-dimensional engineering view. The images in the top right view are called the axial images (XY-view or Top-view) and are surrounded by a red border. The upper left view (surrounded by an orange border) shows the coronal images that are the images resliced in the XZ-direction (Front-view). The lower left view (surrounded by a green border) shows the sagittal images that are the images resliced in the YZ-direction (Side-view). The lower right view (surrounded by a light-green border) shows the 3D view. These windows can be resized by moving the edge between the images (Click and drag to move this edge).
Image Axial Sagittal Coronal 3D view Parallel Cross-sectional
Color
Red Green Orange Light-green Yellow (these images are only visible after performing an online reslice) Blue (these images are only visible after performing an online reslice)
The other images that can be shown are:
Alignment image (if available) X-ray image
Title Bar The title bar displays some information about the project:
The name of the project is displayed first (unless you have chosen to hide the patient name) and after the patient name, the compression of the project is displayed. There are several different types of compression possible:
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Displayed in title bar:
Case:
Lossless Compression
No compression was used while importing and JPEG compression was not used during saving CT compression was used while importing and JPEG compression was not used during saving MR compression was used while importing and JPEG compression was not used during saving No compression was used while importing and project was saved with JPEG compression CT compression was used while importing and project was saved with JPEG compression MR compression was used while importing and project was saved with JPEG compression
CT Compressed MR Compressed Lossy JPEG Compressed Lossy JPEG & CT Compressed Lossy JPEG & MR Compressed
Menu Bar Almost all functions can be accessed via the menus of the menu bar. Corresponding to some of these functions, you will find buttons on the toolbars.
3D Toolbar The 3D toolbar is displayed at the right side of the 3D view.
Toggle transparency You can show the 3D object opaque or transparent. Click on the button opaque and transparent view.
in the 3D toolbar to toggle between
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Transparency off Transparency on You can change the transparency of the 3D object and make objects transparent. Drag the Transparency slider at the bottom of the 3D properties dialog. If the slider is all the way to the right, the 3D surface is opaque and nothing below the surface can be visualized. If the slider is all the way to the left, the 3D surface is completely transparent.
Clipping Clipping allows you to visualize the section in which you are interested. It can be used, to evaluate the gray values on the section boundaries or to look inside the model to get a better comprehension of the geometry. The section can be made along the different planes, axial, coronal and sagittal. Several clipping planes can be activated at the same enabling you to isolate the part of interest. To enable clipping click on the Enable/Disable clipping button in the clipping tab:
. The settings of the clipping can be changed
Acti ve By default one axial clipping plane is active. To make more planes active, make sure to check the active icon
.
Clipping in the Axial Clipping in the Sagittal Combined axial and Plane Plane sagittal clipping plane The position of the clipped plane in the 3D view corresponds with the position of the active axial, sagittal or coronal image. Scrolling through the 2D images updates the clipped plane in 3D. Also navigation on the clipped 3D is possible by clicking on visible parts on the 3D. When you rotate the 3D along the clipped plane, the visibility
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automatically reverses.
Type As stated above you can select multiple clipping planes. For each view you can define two clipping planes. For each of the clipping planes, you can choose which objects need to be clipped. You can choose this by selecting the clipping plane in the list and changing the selections in the dropdown menu selected by default.
. All objects are
Clipping along two axial and a sagittal Clipping along the axial and sagittal plane plane
Clip By default the direction of the clipping plane is defined by the viewing angle. The direction of the clipping plane can be locked by selecting a clip direction. Click on the clip icon
to lock to a clipping direction or to unlock.
Lock The location of the clipping plane is locked to the slice position. To unlock the clipping plane from the slice position, disable the lock icon . When the lock icon is disabled, you can determine the location of the clipping plane with the slider at the bottom of the clipping tab.
Texturing You can also choose between three texturing methods:
No texturing Object texturing Full slice texturing When choosing No texturing, only the 3D Object is clipped and you can see inside the 3D Object. When choosing Object Texturing, a texture corresponding with the 2D slice is placed in the contours of the 3D Objects. When choosing Full slice texturing, the 3D Object is not clipped, but the whole 2D slice is visible in the 3D window. Note: This technique is only available in OpenGL and direct3D rendering (not in software). To check your rendering option, go to Option | Preferences and select the OpenGL or Direct3D rendering option in the 3D
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settings. To accelerate the performance of clipping, activate the hardware acceleration in the same dialog.
Volume rendering Volume rendering allows you to quickly visualise your 2D image data as a 3D object without any segmentation. The 3D object is build up out of the voxels representing the dataset. The transparency of the voxels i s determined based on their grey value.Volume rendering is a pure visualisation tool and cannot be used for anything else (e.g. exporting). You can find the interface for the volume rendering in the volume rendering project management tab:
Defini ng the opacity This interface shows a histogram which represents the gray values or Hounsfield units of the dataset. The transparency of the gray values is set by the opacity lines on the histogram. The higher a line is positioned the more opaque the voxels within that range will be visualised. In the first column the line representing the low Hounsfield values is positioned to the bottom. Subsequently the voxels are represented transparent. In the second column the line is positioned higher which makes the voxels opaque.
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Move a point
Position a point click left and drag the point to its new position
Add a point
Click left on a line to add an extra point
Delete a point
Right click on a point and select delete to delete a point
Defining the color The graph below the histogram defines the color of the rendered voxels. You can choose a color for each point in the graph by right-clicking on the points and choosing Change Color. Mimics will then create an interpolated shading between the different control points. The same system for adding, moving and deleting bullets is available as for the opacity line.
Predefined settings On the bottom of the volume rendering interface you find a dropdown list with predefined settings. The predefined settings are optimized for CT image and allow you to quickly select bone, soft-tissue or both You can save your current setting as a predefined setting by clicking on the save button. To delete your predefined setting, select it from the dropdown box and click on the delete button.
Show reference planes It is possible to show in the 3D view the reference planes of the current position by clicking on the Show Reference Plane button
. The reference planes take over the colors that belong to the different views:
Axial Red Coronal Orange Sagittal Green Cross Sectional Blue Parallel Yellow The reference planes that have to be shown can be selected in the 3D tab of the Preference settings. Only the reference planes of the views that are displayed can be shown in the 3D view.
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Select 3D view When you click on Select 3D View button , a list with all possible default views is displayed. Selecting an item from this list will position the 3D object according to the selected position.
Rotate view The rotate function is only available on a 3D object. There are different ways to select the rotate function:
right-drag with your mouse button
use the arrows-keys for precise rotation
use Home / End to rotate 10 degrees Left / Right
use Page Up / Page Down to rotate 10 degrees Up / Down
right-click in the 3D view and select Rotate View from the context menu
click on the Rotate View button
in the toolbar
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select View > Rotate View from the menu bar
Toggle visibility By toggling the colored cubes in the 3D toolbar, you can make the 3D objects, with the corresponding color, visible or invisible. For every 3D object in the project there is a corresponding cube.
Indicators in the views On the different views you can see intersection lines, tick marks, slice positions and orientation strings. To hide the intersection lines, tick marks or slice positions, select its entry in View menu > Indicators . Select again its entry to show it again. If you never want to see one or more indicators when loading a project, select Preferences from the Options menu and go to the Visualization tab. In this dialog you can make your selection of these indicators.
Tick Marks The set of red tick marks to the left of the sagittal and coronal images reference the position of each axial image in the study. The set of green tick marks below the axial images reference the position of each sagittal image in the study. The set of orange tick marks to the left of the axial images reference the position of each coronal image in the study.
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tick marks on tick marks off In the View menu , the preference setting for tick marks can be temporarily overruled. If you prefer another setting permanently, go to Options > Preferences > Visualization .
Intersection Lines In the View menu , the preference setting for intersection lines can be temporarily overruled. If you prefer another setting permanently, go to Options > Preferences > Visualization . The relation between the different views is indicated by the colors of the intersection lines (dashed or full colored lines over the view). When you move to a new position, the intersection lines will be updated and show you your current position in the data set. They are in the matching color of the corresponding view. Notice the red horizontal line across the sagittal and coronal images. It references the exact location of the axi al image. When you move to a new position, the intersection lines will be updated and show you your current position in the data set. After performing an online reslice, you will see 3 blue dashed or full lines and a yellow dashed or full line in the axial image. The middle blue line references the exact location of the cross-sectional image (surrounded by a blue border). The most left blue line reference the exact location of the cross-sectional image at the left top corner of the cross-sectional grid. The most right blue line reference the exact location of the cross-sectional image at the right bottom corner of the cross-sectional grid. The yello w line reference the exact location of the parallel image that is displayed. Color Table Axial Cross-section Parallel Sagittal Coronal
Red Blue (only visible if the project is resliced in Reslice Layout) Yellow (only visible if the project is resliced in Reslice Layout) Green Orange
Note: You can choose between dashed or full lines in the Visualization tab of the Preference window.
Slice Position In the view that contains the scanner images, the slice position is indicated in the lower left corner and the image number is indicated in the lower right corner. In the other views, the slice position is indicated in the lower right corner. Image Axial Sagittal Coronal
Numbering
Increasing from bottom to top Increasing from the right to the left side of the patient Increasing from posterior to anterior
Orientation strings
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The colored letters located on each view shows the orientation of the images. P : Posterior A : Anterior L : Left R : Right T : Top B : Bottom
Looking at the images you can verify if they are correct, if not you can easily change them in the Change Orientation window going to File > Change Orientati on .
The Context Menu If you right-click with your mouse on any of the views, you will see the context menu. The functions in the context menu can differ, depending on the location you click on: if you right-click on an image, on the 3D view, on a 3D object, a STL, a CAD object, ...
There are several easy shortcuts available from the default context menu: Pan View Zoom Unzoom Zoom to full screen 3D Window
Enables the panning mode Enables the zoom mode Unzooms the view Zooms the view to full screen Enables the 3D view in the window
1-Click Navigation 1-click navigation is very easy. By clicking once on an image (e.g. the axial image) with your left mouse button all images are immediately updated to show the same point. Navigation is also possible from the 3D image.
Pan view Every image and 3D view can be panned or moved. When you select the pan function, the cursor will change to a cross-shaped double arrow. There are different ways to select the pan function:
hold down the SHIFT key, right-drag your mouse button
right-click in an image or in the 3D view and select Pan View from the context menu
click on the Pan View button in the toolbar
hold down the SHIFT key in combination with the arrows-keys for precise rotation
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Hold down the SHIFT key in combination with Home / End for quick Left / Right panning
select View > Pan View from the menu bar
Rotate view The rotate function is only available on a 3D object. There are different ways to select the rotate function:
right-drag with your mouse button
use the arrows-keys for precise rotation
use Home / End to rotate 10 degrees Left / Right
use Page Up / Page Down to rotate 10 degrees Up / Down
right-click in the 3D view and select Rotate View from the context menu
click on the Rotate View button in the toolbar
select View > Rotate View from the menu bar
There are two different modes when rotating the 3D view. When your mouse cursor is in the middle of the 3D window and you then hold down the right mouse button, the 3D view turns about a vertical axis when you move the mouse left and right. The 3D view tilts around a horizontal axis if you move the mouse up and down. When your mouse cursor is at the side of the 3D window and you then hold down the right mouse button, the 3D view rotates around an axis perpendicular to your screen when moving the mouse.
Zoom Allows to Zoom in at a user defined rectangle. Click on the left mouse button to indicate a corner of the zoom rectangle, drag and release to indicate the opposite corner. Can be used on every image.
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There are different ways to select the zoom function:
hold down the CTRL key, right-drag your mouse button
right-click in an image or in the 3D view and select Zoom from the context menu
click on the Zoom button in the toolbar
select View > Zoom from the menu bar
Note: The behaviour of zooming is different in Reslice Layout.
Zoom to fixed factor Allows to Zoom in at a defined factor. Click on the arrow and choose from the drop-down list the factor you want to zoom with: your cursor becomes a lens.
Zoom to full screen Allows you to display a view on the whole screen. Click on the Zoom to full screen button and the cursor will change to a magnifying glass. Then click on an image. To return to a normal view, click again on the Zoom to full screen button. Zoom to full screen on axial view
When you hover with the mouse over a view and click on the spacebar the view is put to full screen. To unzoom press the spacebar again. You can also zoom to full screen by by invoking the context menu by right-clicking on the view.
Unzoom Changes the display scale to show the whole image. You need to select the function first and then left-click on the view on which you want to apply the function.
Project Management
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The project management gives you an overview of all the objects in the project. You can hide the project menu by toggling the project management button in the main toolbar
.
The project management consists out of containers which hold a number of tabs. Each tab stands for a kind of objects in Mimics. It lists the available objects in the project. On the bottom of a tab you have a toolbar with the most common functions. On the toolbar you typically find a create, a delete and a properties button. The last button on each toolbar is always the action button . This button lists all the functions that can be performed on the selected object. Besides object based tabs there are three different tabs on the bottom of the project management. The contrast tab allows you to adjust the gray scale of the images. The volume rendering tab shows a histogram of the dataset and a line which allows you to set the opacity of the voxels. The clipping tab lists the possible clipping planes and their settings. When the containers are docked in the project management they have a fixed size. To enlarge them you can undock them by left-clicking on the pointed top of the container and dragging the container outside the project management. The same counts for the different tabs. You can left-click on the tab and drag the tab outside the container. Tabs can as well be dragged to another container
Masks
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A mask is a collection of pixels where all actions (editing, region growing, ..) and calculations (3D calculations, STL, ..) are based on.
List of the created masks Name
Name of the mask. By clicking on the name of the mask, it can be renamed.
Visible
Lists if the mask is visible or not by means of glasses.
Lower Threshold
Lower Threshold setting of the mask.
Higher Threshold
Higher Threshold setting of the mask.
Functions on masks New
Creates a new mask with a default threshold
Delete
Deletes the selected mask
Properties
Gives numerical information of the selected mask
Duplicate
Duplicates the selected mask
Clear
Clears the contents of the selected mask, the threshold of the mask is kept
Calculate 3D
Opens the Calculate 3D window
Action
Lists the available function on the selected mask
Properties The mask properties gives numerical information about the gray values in the selected mask:
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Minimum value
Minimum gray value in the selected mask
Maximum value
Maximum gray value in the selected mask
Average value
Average gray value from the selected mask
Standard deviation
Number of pixels
Amount of pixels in the selected mask
Mask volume
The volume of the mask
Scale
The scale you are working in: GV (Grayvalues) or HU (Hounsfield Units).
3D objects
List o f the created 3D reconst ructi ons
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Name
Name of the 3D, by clicking on the name of the 3D, it can be renamed.
Visible
Lists if the 3D is visible or not by means of glasses.
Contour Visible
Lists if the contour of the 3D object is visible on the 2D images or not by means of glasses. You can change the visibility of the contours by clicking on the glasses.
Transparency
Lists the transparency settings of the 3D, possible options are: opaque (= not transparent), low, medium and high. Change the transparency by clicking on the icon in the transparency column. To see your objects transparent, the transparency button has to be enabled.
Quality
Quality which was set before calculation, possible options are: low, medium, high, custom.
Functions on 3D reconstructions New
Creates a new 3D. The Calculate 3D window appears.
Delete
Deletes a 3D.
Properties
Gives the properties of the calculated 3D object.
Move
Activates the handles to move the STL to a new positions
Rotate
Activates the handles to rotate the STL around its axis
Action
Lists the available functions on the selected 3D object
Properties of a 3D Object When you click on the Properties button in the 3D Objects list, following dialog box will open:
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Mimics displays the name, color and transparency of the object. The volume, surface, outer dimensional parameters and the number of points and/or triangles are also shown, which give a good idea if reducing of the file for further applications is needed. You can change the transparency of the 3D object and make objects transparent. Drag the Transparency slider at the bottom of the 3D properties dialog. If the slider is all the way to the right, the 3D surface is opaque and nothing below the surface can be visualized. If the slider is all the way to the left, the 3D surface is completely transparent. In order to see the 3D object transparent, you need to click the Toggle transparency button
in the 3D toolbar.
Opaque 3D Transparent 3D If the Details button on the 3D Properties dialog is selected, some measurements of the 3D object are displayed.
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Move and Rotate button When the simulation module is licensed, two new buttons will appear on the 3D tab of the project management: Move and Rotate. These buttons allow you to rotate and/or move one or more 3Ds.
Rotate When you select a 3D object and click on the Rotate button, rotation handles will appear around the 3D object. You can now rotate the 3D objects around the X, Y or Z axis of the project by grabbing one of the colored rotation handles. You can also rotate the object around an axis perpendicular to the camera by grabbing the outer ring of the rotation tool. To change the rotation center select the center of the tool and move it to its new position. The rotation value is shown in the status bar.
Move When you select a 3D object and click on the Move button, translations arrows appear. To translate the 3D object grab a translation arrow and move the mouse. To translate the object parallel to the viewing plane, grab and move the middle of the tool. The translation value is shown in the status bar.
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Polylines
List of the created Polylin e sets Sets
Name of the polyline. By clicking on the name of the polyline, it can be changed.
Visible
Lists if the polyline is visible or not by means of glasses.
Based On
Tells on which mask the polylines were calculated. If the set is grown out of another set, it is independent of a mask.
Functions on Polyline sets New
Creates a new polyline set. The Calculate Polylines window appears.
Delete
Deletes a polyline set
Duplicate
Duplicates the selected polyline set
Color
Changes the color of a polyline set
Polyline growing
The polyline Growing tool provides the capacity to create several sets of polylines.
Action
Lists the available functions on the select polyline set
STLs
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List of cr eated Objects Name
Name of the object. By clicking on the name of the object, it can be changed.
Visible
Lists if the object is visible or not by means of glasses.
Contour Visible
Lists if the contour of the object is visible on the 2D slices or not by means of glasses. You can change the visibility of the contours by clicking on the glasses.
Transparency
Lists the transparency settings of the STL, possible options are: opaque (= not transparent), low, medium and high. Change the transparency by clicking on the icon in the transparency column. To see your objects transparent, the transparency button has to be enabled.
Functions on Objects Load
Loads an STL file into the project.
Remove
Removes an STL file from the project.
Properties
Displays the properties of the selected STL file.
Export STL
Saves the selected STL file (with its current position).
Move
When the Move button is enabled, you can move the STL in the 2D views and the 3D view.
Rotate
When the Rotate button is enabled, you can rotate the STL in the 2D views and the 3D view.
Action
Lists the available functions you can perform on the selected STL
Transform
Opens the transformation dialog:
In this dialog, you can enter a transformation matrix, invert the transformation matrix if needed and apply it on the selected STL file. You can also load a transformation matrix file, written out by Mimics when reslicing or
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cropping a project or when doing an STL registration.
Measures
List of t he created Measurements Type
The type of measure, represented by its corresponding icon. Possible measures are: a 2D or 3D distance, a 2D or 3D angle or a density measure. These are the same measures that are available in the tools toolbar and are represented in the list with the same icon.
Visible
Lists if the measure is visible or not by means of glasses.
Value
Depending on the type of measure this value can represent a distance (mm), an angle (in degrees) or a mean density (HU or grey values).
Deviation
The deviation in Hounsfield units or grey values for a density measure.
Area
The area in mm² of a density measure.
Functions on Measurements New
Shows a menu from where you can choose the type of measure. Possible measures are: a 2D distance, a 3D distance, a 2D angle, a 3D angle or a density measure. These are the same measures that are available in the tools toolbar.
Delete
Deletes one or more measures.
Properties
Shows the properties of the selected measurement.
Locate
Updates all views to show to selected measure. Only angle and distance measures can be located.
Action
Lists the available function on the selected measurment
Curves
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A reslice curve allows you slice the images in a different direction. To draw a reslice curve, select Online Reslice from the File menu . The resliced images can only be viewed when the Reslice layout is chosen in the View menu.
List of th e created Curves Name Visible Cross-Section Length (mm)
Name of the reslice curve. By clicking on its name, it can be changed. The active reslice curve is indicated by means of glasses. In the Reslice layout the images corresponding the active reslice curve will be shown. The cross-section length determines the width of the cross-section images. This length is set to optimal by default, but can be altered by double-clicking on the Optimal text. This way you can specify an exact cross-section length. Note: To return to the Optimal setting after you have specified an exact length,
set 0 as the value of the cross-section length.
Functions on Curves New Delete
Opens the reslice curves toolbox to draw a new curve. Deletes one or more reslice curves.
Annotation
List of t he created Annotation Name
Name of the annotation. The name is generated automatically based on the object on which the annotation is attached
The different views
Visible Object Text
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The visibility of the annotations is set by means of the sunglasses Lists the object to which the annotation is attached Shows the content of the annotation
Functions on Annotations New
Activates the annotation cursor. Click with your mouse on the object on which you want to attach an annotation. The annotation properties dialog will open in where you can add your comments.
Delete Properties Locate Action
Deletes the selected annotation Opens the Annotation Properties dialog Updates all views to show to selected annotation. Lists the available actions on the selected annotation
Adjust grayscale The mapping of pixel values into gray levels is specified by the level and the width of the line on the histogram. The amount of available gray values levels is dependent on your display setting. When your display setting is set on true color (24-bit or 32-bit) you will be able to map the pixel values onto 128 gray levels. You can change the window by grabbing one of the points or the line and move it with the left mouse button. You can as well define the position of the points by filling in a value in the Minimum and Maximum field.
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Instead of defining the contrast yourself, you can choose one of the predefined scales from the dropdown box. You can change the gray scale also interactively by pointing at an image of interest and dragging the right mouse button. The cursor will change into . Move the mouse down to increase the width of the gray scale - this lowers the contrast within the soft tissue. Move the mouse up to decrease the width of the gray scale - this heightens the contrast within the soft tissue. Move the mouse to the right to increase the level of the gray scale this darkens the soft tissue. Move the mouse to the left to decrease the level of the gray scale - this lightens the soft tissue. When you are satisfied with your gray scale, release the mouse button. All the images are updated immediately with the new gray scale.
Volume rendering The volume rendering tab shows a histogram of the dataset and a line which allows you to set the opacity of the voxels. To visualize the volume rendered 3D select the volume render button in the 3D toolbar. You can find more information about volume rendering in the section about the 3D toolbar.
Clipping In the clipping tab you can define the different clipping planes and their options. To activate clipping select the clipping button in the 3D toolbar. You can find more information about clipping in the 3D toolbar section
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Shortcut Keys General Shortcuts F1 CTRL + Z CTRL + Y CTRL + F CTRL + I CTRL + SHIFT + M Alt + F4
SPACE
Open the Online Help Undo last action Redo last action Enable/Disable the Navigation Toolbar Makes all mask invisible Enable/Disable the Movie export Exit Mimics If you hover with the mouse over a view and press the spacebar; that view is put to full screen. To unzoom to full screen; press the spacebar
Shortcuts on files CTRL + O CTRL + P CTRL + S CTRL + N
Open a file Print a file Save a file Close a file
Shortcuts on the views ArrowUp ArrowDown PageUp PageDown CTRL + L Right mouse button
Go to next slice Go to previous slice Go 10 slices up Go 10 slices down Make slice indicators visible/invisible Adjust gray scale: Move the mouse horizontally while keeping the buttons pressed to change the level of the gray scale. Move the mouse vertically to change the width of the gray scale. Pan: Move the mouse while keeping the buttons pressed to pan.
SHIFT + Right mouse button CTRL + Right mouse button Zoom: Move the mouse vertically while keeping the buttons pressed to zoom in and
out.
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Shortcuts on the 3D view Arrow keys Page Up Page Down Home End SHIFT + keys above ALT + left/right
Rotate the 3D view left/right and up/down Rotate the 3D view 10 degrees down Rotate the 3D view 10 degrees up Rotate the 3D view 10 degrees left Rotate the 3D view 10 degrees right Pan the 3D view Do washing machine rotation
Shortcuts on t he layouts F2 F3 F4 F5
Image Layout 3D Layout Reslice Layout Simulation Layout (if the simulation module is licensed)
Shortcuts on Segmentation functions Region Growi ng CTRL + R
Start the Region growing function
Edit CTRL + E While in edit mode: D E T CTRL + drag left mouse button SHIFT + Left mouse button
Open the edit toolbar and go in edit mode Draw Erase Draw with local threshold Resize the edit cursor Temporarily release the edit-tool and do 1-click navigation.
Shortcuts on text fields in dialogs CTRL + C CTRL + X CTRL + V
Copy Cut Paste
Shortcuts on Movie Tool CTRL + SHIFT+ M SHIFT+ F8 SHIFT+ F9
Start the movie tool Start Recording / Stop Recording Pause Recording
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Shortcuts on Polylines CTRL + U
Update polylines
CT Gray scale CT images are a pixel map of the linear X-ray attenuation coefficient of tissue. The pixel values are scaled so that the linear X-ray attenuation coefficient of air equals -1024 and that of water equals 0. This scale is called the Hounsfield scale after Godfrey Hounsfield, one of the pioneers in computerized tomography. Using this scale, fat is around -110, muscle is around 40, trabecular bone is in the range of 100 to 300 and cortical bone extends above trabecular bone to about 2000.
The pixel values are shown graphically by a set of gray levels that vary linearly from black to white. Mimics displays the CT images using up to 256 gray levels if your display setting is true color (24-bit or 32-bit), 128 gray levels if your display setting is 256 color palette, but as few as 32 gray levels if your display setting is high color (16-bit). The mapping of pixel values into gray levels is specified by a level and a width. A gray scale is centered about its level.
For example, a level of 0 specifies that water will be displayed as mid-gray. The extent of the gray scale is specified by its width. The default gray scale used by Mimics allows you to see the full range of tissue from air in the maxillary sinus to the densest of cortical bone, but subtle differences in the soft tissue cannot be visualized. If you narrow the gray scale, you can better visualize subtle differences in the soft tissue or trabecular bone, but at the cost of forcing cortical bone to be in one gray level: white. Narrowing the gray scale can help you locate the mandibular canal if it is not easily seen with the default gray scale.
File Menu
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File Menu The file menu contains the following items:
You will also find the corresponding buttons in the toolbar.
Open project Open an existing project by selecting File > Open project from the menu bar or by clicking its button on the Main Toolbar. When you click on the black arrow on the Open project button, a list of previously opened projects appears. The Open project dialog displays your folders containing Mimics files (*.mcs) on the left side of the window. Folders for the floppy-, Compact Disc and zip-drive are also displayed when they are installed. Click on a folder to see the list of Mimics files in that folder. Use the arrows on the scroll bar if the patient you wish to view is not displayed. Open a study by clicking once its line in the list and then the Open button or by double-clicking its line. There are two different modes in the Open project window. The first mode allows you to easily browse on your harddisk. The second mode will show you more information for each project. You can switch between these modes with the
button.
Note: The first mode will be disabled when the Hipaa preference, Hide file name, is enabled. To change the Hipaa preferences go to
preferences, you can change the Hipaa settings in the General section
File Menu
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List of studi es Displays the browse tree Displays the patient name Shows the study ID Shows the study date Displays the file name
Browse tree Patient Study ID Study Date File
Functions Add directory to Favorites
Adds the current
Make default
Makes the selected folder your default
Delete folder
To delete the selected folder from the list of favorites.
Browse Delete study
To select a new directory in order to see the reformatted CT studies the folder contains. You will be asked if you want to add the folder to the list of favorites. To delete the selected study from your computer.
Search in Subfolders
Shows all the projects in the folder and subfolders
Switch view
Switches between the two browse modes.
Sort by column
Quickly sort the studies by a column by clicking on the column header
Change column order
Change the order of the columns by dragging the column header to the left or the right
Open
Click on the Open button after selecting a study or double-click on a study to open it
Cancel
Closes the Open dialog box
File Menu
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Help
Opens the help pages on the Open project subject
List of favorites Click on a folder to see the images within the folder. The path of the selected folder is shown at the top. Right-click on a folder to display the following context menu.
Rename Remove
To change the name of the folder To remove the folder only from the list of favorites. The folder will not be removed from your computer.
Reduce Images High-resolution images can contain a lot of noise and this means that a noisy 3D is obtained. When you want to filter the noise within the images or want to speed up the segmentation functions, use a voxel reduction. The reduce Images window (see picture) is shown when loading data sets that require more memory than available or when the preference setting “Always ask to reduce images when loading” (on the General tab page) is selected. Based on the amount of images and the pixel size, the necessary amount of memory is calculated and compared with the total amount of memory (RAM). If more memory is needed than available, a reduction is proposed.
This function groups voxels together when loading the study. A reduction value of 1 means no reduction; every single voxel will be loaded. A reduction of 2 will group 4 voxel together (2 in the X-direction and 2 in the Y-direction) as 1 voxel with as gray value the mean gray value of the 4 voxels. The maximum allowed reduction is 5. Since pixels are grouped together, the noise is filtered out and all segmentation tools work faster.
Save project Saves the Mimics project.
Save project As Allows you to save the project with another name.
File Menu
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When saving the project, you can choose to compress it. The compression algorithm used is a lossy JPEG compression. Using this option will reduce the size of the project. You can choose between three different quality presets for the JPEG compression: When saving a project, it is possible to compress the images in the project with a lossy JPEG compression. This way you can reduce the size of your projects. It is possible to choose between three quality presets:
High Quality – Low Compression
Medium Quality – Medium compression
Low Quality – High compression
The higher the compression factor is, the smaller your files will become, but the worse your image quality will be. When you have done a reduction on the images during loading or importing, you can also choose to keep the reduction when you are saving the project.
Close project Closes the Mimics project. If necessary, the program will prompt you to save it.
Import STL file Loads an STL file into the project. It will appear in the Project Management, STL tab and in the 3D window.
File Menu
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Note: You can only load an STL file if a project is open, the function is disabled if no project is opened.
STL Library The STL library allows you to create a library with STL files on your hard drive that is easily accessible from Mimics. The first time you use the STL Library, Mimics will ask where you want to create this library:
We recommend creating a new folder on a hard disk with a lot of free space. After you have selected the directory where the STL library will be located, you will see following interface:
File Menu
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The interface is divided in two parts: the le ft part will show a directory tree of your library. If you select an STL in the tree, you will see the properties for that STL in the right part. If you select a directory in the tree, you will see a list on the right of all the STL’s that are found in that directory.
You can extend the library in two ways:
You can copy STL files in the STL library folder via the Microsoft Explorer. You can also create new directories or remove files via this way. The changes will be visible the next time you open the STL library in Mimics or when you click on the Refresh button.
You can create new folders and import STL files in the library by clicking on the appropriate buttons in the STL library interface. When you select one or more STL’s in the tree or in the list on the right and click the Load button, the selected STL’s will be loaded in Mimics. You can also adjust the Name, Manufacturer, Product Line and Description when viewing the properties of an STL by clicking on the fields. These changes will be saved to a small XML file in the STL library.
Import im ages To start the Import Images wizard, first close all projects and than select Import images from the File menu. The wizard will start with STEP 1.
Selecting images to import The first step is to choose the source directory of the images to import. You can click immediately on the drive or folder in the favorites column or you can browse for the drive or folder in the Windows Explorer tree. When you look for images on an optical disk or tape, you need to browse to the folder “SCSI adaptor”. Click o n the + sign in front of “SCSI adaptor” to see the list of optical drives. Click on the optical drive and browse to the folder with the images. As soon as you select the source directory, all images within the directory are displayed at the right side and are immediately selected. Click Next to continue the conversion.
File Menu
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Favorites The following folders will be listed as favorites when starting the Import images wizard for the first time. To browse through the folders on your computer. To display the images received via a DICOM network (if the Dicom Input Application module is installed and licensed). To display the images stored on a floppy disk (if a floppy drive is available). To display the images stored on a CD (if a CD drive is available).
Browse DIA Floppy CD
To add a new folder as favorite you nee d to browse for that folder in the Windo ws Explorer tree and click the Add favorite button in the toolbar. Right-click on a favorite folder (except for the Browse folder) to delete or rename the folder. Each favorite folder can be dragged to another place in the list.
Filename This window displays all the files in the selected Source Directory. All images are automatically selected. To restrict the selection you can hold down
the CTRL key and left mouse button to select the images one by one
the shift key and left mouse button to select the first and the last image in your selection
Import Toolbar Add the selected folder to the Favorites column Select all the images/projects in the Filename window Displays a window with extra information about the images to import Rebuild the DIA database in order to display recently received images To merge 2 or more image sequences of one patient To delete images within the DIA folder When there is a DICOMDIR file available in the folder, you can toggle between viewing the studies as specified in the DICOMDIR or viewing the files. Select this button to display the images in the subfoldes To dump images from a tape
Manual import If Mimics does not recognize the image format, check the Manual import option before clicking the Next button. This option allows you to import any type of images by providing Mimics all the image information yourself. For more details, go to the Manual import page.
File Menu
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Selecting studies to convert In this window information is shown about the studies you are going to convert. All studies that are selected will be converted and for those studies, a Mimics file will be made in the default working folder. To unselect a study, click on the checkmark in front of each study. Click the Convert button to start the conversion. Notice that when you click the Back button, you are able to add some more studies to the list. In this way you can perform a batch conversion. If multiple image sequences of the same patient are displayed, this means that not all image parameters are equal. The differences are highlighted in bold. To merge one or more sequences to one Mimics project, select them by using the SHIFT key and left mouse button, and click the Merge button
. Merging sequences in not allowed when the patient name, pixel size or image orientation is different.
Note: Mimics checks for several parameters during the import of images. If one of these parameters are different, Mimics splits the data set
in different parts. The parameters that Mimics checks for are: height, width, pixel size, gantry tilt, orientation, label, patient information, study information and reconstruction center of the images.
Study In this area you can find information (number of images, type of compression, pixel size...) about the study to convert. You can also select which studies should be converted by changing the checkmark in the Convert column.
Skip Images You can choose to skip images during the import, by selecting one of the studies (the selected study will be colored blue) and then choose how many images to skip. In the screenshot above, the first sequence has a skip images setting of two. This means that only image0, image3, image6, image9, ... will be imported.
Compression There are different types of image compression to choose:
CT: this compression is typically used for the removal of background noise for CT-images. It is a lossy compression and changes the grayvalue of all the voxels with a grayvalue between 0 and 200 to 0 MR: this compression is typically used for the removal of noise for MR-images. It is a lossy compression and sets the grayvalue of all the voxels with a grayvalue between 0 and 10 to 0. Lossless: when choosing lossless compression, nothing is changed to the voxels of the images
Note: for technical CT images it is best to use the lossless compression.
Invert Table Position When this option is active, the table position will be inverted during import. This function allows you to set the Bottom and Top of a patient on the Bottom and Top of the screen.
Selecting s tudi es to open Select in this window the study you want to open in Mimics. If the data contained only one study, step 3 will be skipped and you will go automatically from step 2 to the next step.
File Menu
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Changing o rientation and gantry tilt sign If one of the orientation parameters is unknown, a window Change orientation is displayed on top of the images. You need to fill in the missing orientation strings, indicated by an X, before you can proceed. To do this, right-click on the X and choose one of the remaining orientation characters.
When the patient has been scanned at an angle (see picture) a Gantry tilt window will pop up after the import. The gantry tilt is the angle of the scanning plane relative to a vertical plane. The sign of the gantry tilt can be positive or negative, but there is no convention for this. This means that the absolute value of the gantry tilt is known, but the sign is not. A decision about the correct sign has to be made by visual inspection of the images in the YZ or sagittal view. You can change the sign by clicking the Switch button. If you're not sure about the correct sign, contact the radiologist. Click the Close button to save the correct sign.
File Menu
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Note: the orientation strings can still be changed after loading the project by selecting Change Orientation from the File menu. But this
change results in the loss of all your segmentation. The gantry tilt sign cannot be changed anymore after the project is loaded.
Reading Tiff and B itmap im ages When you select images in Bitmap or Tiff format an extra window will be displayed on the screen after clicking Next in the first Import images Wizard window. In this Bmp/Tiff Import window you need to fill in some image related coordinates before a conversion can be performed. The radiologist should provide this information.
Filenames The data you want to import can be seen here.
Files Sorting Sorts the images numerical or alphabetical.
The sort order can be changed interactively by selecting an image in the list and clicking the Up or Down arrow in the Move box. The image will be moved up or down one position in the list.
Image Information Image size
This value (0 - 65535) represents the horizontal and vertical size of the input image(s) in pixels. Common values are 256, 320, 512 and 1024. Note: If Mimics displays the error message that your images are not the same size when you want to
import them, you have to change the size of these images manually in an image-editor, like Photoshop.
File Menu
Import table position from
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This option allows you to convert Bitmap or Tiff images with a variable slice distance. After selecting this option, the first table position and a slice distance parameters will become disabled. You need to browse to a text file by clicking on the button with the yellow folder. The text file should contain 2 columns. The first column should list all the file names (with extension) and the second column all the corresponding table positions. In between these 2 columns there need to be a TAB. By selecting this text file, Mimics will put every image on the right table position, even if the distance is variable. If you selected more files than written in the text file, he will give you the message "Not all files could be assigned a table position". If you click OK, Mimics will proceed and makes a Mimics project with all images on the correct table positions. In order to make a text file very quickly, first make an Excel sheet and then export from within Excel to a text document with a tab in between the 2 columns.
First Table position
Slice distance Pixel size Gantry Tilt
This option defines the table position for the first image slice of the first input file. Always try the default value, i.e. a table position of 0, except for the case in which two conversion steps are necessary. In this case you have to ensure the correct distance between the images converted in the first step and the images converted in the second step. This can be arranged by filling in the correct value for this parameter. This option defines the distance in mm between all image slices converted at once, whether they are stored in one file or not. This option defines the actual size of one image pixel in mm. The software always assumes that the pixels are square! This option defines the angle of the scanning plane relative to a vertical plane. It is very important to know whether a patient has been scanned with a gantry tilt (angle different from 0) or not. Although the MIMICS software has been adapted to support data scanned with gantry tilt, interpolations and 3D representation will have an inferior quality due to the gantry tilt. It is advised not to use a gantry tilt.
Exam Information Patient Name Institute Name Orientation
Fill in the Name of the patient Fill in the Name of the Institute Fill in the Orientation string of the patient. If unknown, fill in the default XXX, the orientation can also be changed after the conversion. Note: A correctly filled in orientation is very important. If filled in incorrectly, a mirrored model might be
the result.
Show Preview The Show Preview button, allows you to check the used parameters before conversion. When changing a parameter, click the Update button to update the Preview.
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The slider at the right side of the image makes it possible to scroll through the different images. The Contrast toolbar on the bottom allows you to change the contrast. The contrast is immediately optimized to the values of the image(s). Values can be examined image by image or can be sampled through the complete data set. The user can define the sampling interval. By moving the contrast sliders, you will also see two vertical lines moving on the histogram. These lines indicate the interval of the values that will be taken in to account. Values below this user minimum will be converted to black, values above the user maximum will be converted to white. This will not only lead to an increased compression on the images but makes it also easier for the user to define proper values during the conversion operation.
Manual import When selecting the Manual impor t option in the Import Images wizard and clicking the Next button, the following window appears.
If you select only one file for doing a manual import, you will see another window. With this window you can import several images that are grouped in one file.
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As you can see, the only difference with the regular manual import window is that you can define how many images are grouped in the file and what the header size is between each image.
Multiple Files Sorting The multiple files sorting tab is only active when more than one file is selected and allows sorting the images numerical or alphabetical. Example numerical sorting CT0, CT1, CT2, CT3, CT4, CT5, ....CT9, CT10, CT11, CT12, ... alphabetical sorting CT0, CT1, CT10, CT100, CT101, ... The sort order can be changed interactively by selecting an image in the list (e.g. PUMP8.XP) and clicking the Up or Down arrow in the Move box. The image will be moved up or down one position in the list.
File Structure File Size
This field gives the file size.
File header Size
This value represents the position (number of bytes) of the first image pixel. This header size is calculated automatically by Mimics. If needed, you can adjust the value manually. A way to calculate this value : file size = header size + (number of images in one file * horizontal size * vertical size * number of bytes used by one pixel) + inter image header size * (number of images in one file - 1) therefore : header size = file size - (number of images in one file * horizontal size * vertical size * number of bytes used by one pixel) inter image header size * (number of images in one file - 1)
Only active when only one file is selected : Number of images per file
This value represents the number of image slices available within one file. The default value is 1.
Inter-image header Size
When a file contains more then one image, general structure is mostly a header with general information at the beginning of the file, followed with an image and then between every two images a short description of each slice. This option represents the number of bytes to be skipped between every two images read from the same file. Only active when one file is selected.
Exam Information Patient Name
Fill in the Name of the patient
Institute Name
Fill in the Name of the Institute
Slices
Indicate the type of slices: axial, sagittal or coronal.
Orientation
Fill in the Orientation string of the patient. If unknown, fill in the default XXX, the orientation can also be changed after the conversion. Note: A correctly filled in orientation is very important. If filled in incorrectly, a mirrored model might be
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the result.
Image Information Horizontal and Vertical image size
This value (0 - 65535) represents the horizontal and vertical size of the input image(s) in pixels. Common values are 256, 320, 512 and 1024.
Import table position from
This option allows you to convert Bitmap or Tiff images with a variable slice distance. After selecting this option, the first table position and a slice distance parameters will become disabled. You need to browse to a text file by clicking on the button with the yellow folder. The text file should contain 2 columns. The first column should list all the file names (with extension) and the second column all the corresponding table positions. In between these 2 columns there need to be a TAB. By selecting this text file, Mimics will put every image on the right table position, even if the distance is variable. If you selected more files than written in the text file, he will give you the message "Not all files could be assigned a table position". If you click OK, Mimics will proceed and makes a Mimics project with all images on the correct table positions. In order to make a text file very quickly, first make an Excel sheet and then export from within Excel to a text document with a tab in between the 2 columns.
First Table position
This option defines the table position for the first image slice of the first input file. Al ways tr y t he defau lt val ue , i.e. a table position of 0, except for the case in which two conversion
steps are necessary. In this case you have to ensure the correct distance between the images converted in the first step and the images converted in the second step. This can be arranged by filling in the correct value for this parameter. Slice distance
This option defines the distance in mm between all image slices converted at once, whether they are stored in one file or not.
Pixel size
This option defines the actual size of one image pixel in mm. The software always assumes that the pixels are square.
Gantry Tilt
This option defines the angle of the scanning plane relative to a vertical plane (see figure).
Pixel properties Pixel type
This option is a string representing the different formats available for storing pixel values. The next table shows all possible values : Name
byte unsigned byte short unsigned short long unsigned long float
NR. of bytes Range of values 1 -128 127 1 0 255 2 -32768 32767 2 0 65535 4 -2 milj. 2 milj. 4 0 4 milj 4 non integer values
The most common pixel formats are US and S. The default value therefore is US. Al ways tr y US first. If the result gives a recognizable image but with the lack of soft tissue and with low intensities, use the S parameter together with an add value of 1024. If it fails, try the other pixel formats, or ask your client which pixel format they are using. Byte swapping
This value represents to the storage format of values in the input files. There are two common ways of storing values on different computer systems (and therefore also in binary files)
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High byte first (SGI): storage order of multiple bytes to represent large values is from Most Significant Byte to Least Significant Byte. Low byte first (DOS): storage order of multiple bytes to represent large values is from Least Significant Byte to Most Significant Byte. E.g., to store an ushort value, 2 bytes are needed, one representing the least significant part of the value, one representing the most significant part. The ordering of these two bytes can be Most significant first as well as Least significant first. Most probably, your client will not be able to give you this information. As there are only two possible values, you can easily try out both . If with one value, the output images look very noisy and have no clear visual information, change the option to the other value. Minimum Image value Maximum Image value
These values represent the range of pixel values (intensity) to be projected in the range of 0 to 4095. All CT scanners will create images with a range of at most 4096 different values, but some use negative values as well as positive values. In these cases you have to specify the S pixel type instead of US and enter the correct Minimum Image value and Maximum Image value to ensure that all output pixels will have positive values. Always try the default value 0 to 4095 together with a US pixel type. If in this case a lot of information is missing in the images (e.g. all soft tissue) and the default threshold value in MIMICS has no sense, then use the S pixel type together with the correct min and max value. (This is most often a value of –1024 and 1024.) Another possibility is that the range of pixels will be scaled. This is necessary only for images with pixel types L, UL or F. (Which are not common.)-
Templates A template containing all parameters can be stored for future use. Please keep in mind that parameters such as Slice Distance, Pixel size and all other exam information are case dependent and not depending on the scanner. When the Templates Tab is pressed, the Templates window appears. New templates can be created, old ones can be copied (Save As ..), deleted or used.
Show Preview The Show Preview button, allows you to check the used parameters before conversion. When changing a parameter, click the Update button to update the Preview.
The slider at the right side of the image makes it possible to scroll through the different images. The Contrast toolbar on the bottom allows you to change the contrast. The contrast is immediately optimized to the values of the image(s). Values can be examined image by image or can be sampled through the complete data set. The user can define the sampling interval. By moving the contrast sliders, you will also see two vertical lines moving on the histogram. These lines indicate the interval of the values that will be taken in to account. Values below this user minimum will be
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converted to black, values above the user maximum will be converted to white. This will not only lead to an increased compression on the images but makes it also easier for the user to define proper values during the conversion operation.
Organize images In the organize images interface you can choose which images in your Mimics project should be visible and used while working with Mimics. Image List
List of images. Here you can select/unselect the images. The red marked images will be displayed in the project. You can easily select e.g. every 2 images with the skip images setting at the bottom of the window.
Preview
Shows a preview of the images if selected. You can set the size of the preview in the drop down list at the left bottom.
Contrast
Displays the current minimum and maximum contrast values for displaying the images. These minimum and maximum contrast values can be changed in the adjust grayscale toolbar. You can change the current contrast to the default for CT or MR images by clicking on the appropriate bullet.
Delete Unselected images
When marked all unselected images will be removed from the project. This action can not be undone.
Add/Remove
Adds or removes images from the project. This can also be done by checking or un-checking the project column (2nd column) in the Image List or the images in the grid on the right.
Note: Please be advised that you can lose existing segmentations, measurements etc., when you organize your images.
Change orientation If one of the orientation parameters is unknown a window "Change orientation" is displayed on top of the images. In this last step you need to verify the orientation before you can proceed.
The orientation parameters are necessary to display the images correctly in Mimics. The radiologist should provide these orientation parameters, but sometimes this information is incomplete (in this case there is a red X instead of a string in the orientation windows). The orientations that Mimics needs to know are the Left-Right, the Anterior-Posterior and the Top-Bottom orientation. You will see immediately the result in the images. The orientation strings within the images, "L", "R", "A", "P", "T" and "B", respectively stand for Left, Right, Anterior, Posterior, Top and Bottom. Move the mouse cursor to an X in the sagittal or coronal image. The cursor shape changes to a hand and if you right-click, a menu appears with all possible orientation strings. Note that all the other orientation strings are completed automatically. Note: Please be advised that you can loose existing segmentations, measurements, objects etc., when you change the orientation of your
project.
Online reslice Using this function you can reslice your project drawing a curve on the axial images. The curve consists of a series of points, connected by an interpolated line. The parallel and cross-sectional images are constructed, based on this curve. Select File > Online Reslice from the menu or go to Project Management, Curves tab and click on the button called New. The reslice
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curves toolbox will appear on the screen with the second button already selected. The cursor will change to a pencil.
Note: STLs are only visible in the parallel images when a straight online reslice curve is drawn.
The reslice curves toolbox
Select a reslice curve Select the cursor tool and click on a reslice curve to select it. The points of a selected reslice curve are in white. The points of a non-selected reslice curve have the same colour as the lines of the reslice curve. The action you do is always performed on the selected reslice curve.
Create a reslic e curve Creates a reslice curve. Click several times with the left mouse button on the axial image to create a reslice curve. Double click with the left mouse button or click with the right mouse button to finish the reslice curve.
Delete reslice curve Select the reslice curve you want to delete and click on the Delete reslice curve button.
Ad d a p oi nt to a res li ce c ur ve Click on the Add point to reslice curve button to add a point in the middle of the selected line. When you hover the mouse above the reslice curve, the cursor will change into a pencil. Click with the left mouse button to add a point.
Remove a point f rom a reslice curv e Click on the point of the reslice curve you want to delete. The selected point will be colored green. Click on the remove point from reslice curve button to delete the point.
Reslice Curve Dialog Click on this button to visualize the Curves tab in the Project Management
X-Ray image A yellow border surrounds the X-ray image or parallel view. Its thickness can be set in the Reformatting tab of the Preference Settings (choose Options > Preferences > Reformatting from the menu bar). To display the x-ray view, click on this button
, next to the parallel view. To return to the parallel view, click on this button:
.
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Zooming i n Resli ce Layout When you left-click once when zooming on a cross-sectional image, that image gets enlarged. By clicking with the unzoom tool on the enlarged cross-sectional image, you will see the original view again.
Original View
Zoomed cross-sectional image
Reslice Project You can reslice a project by going to the File menu and then choose the Reslice Project button. Following window will appear:
Projects can be resliced according to a straight line in any direction. This will create a new Mimics project on your hard drive. There is an easy to use interface available. The reslice line can easily be drawn in the 2D or 3D views by clicking on the Draw Line button. The mouse icon will change to a pen and you will be able to draw a straight line in any of the 2D views by clicking once with the left mouse button to indicate the starting point. To finish drawing the line, click again with your left mouse button on the ending point of the line. The bounding box of the new image volume will be shown on the 2D images and in the 3D view.
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The coordinates of the beginning and e nd point of the reslice line can be adjusted in the edit fields. You can also rotate the project that will be resliced around the reslice line by adjusting the rotation angle. Several predefined orientations can be chosen in the orientation dropdown. Image width, height and slice distance can be specified and you immediately get information about the number of slices that will be in the resliced project. After drawing, you can still adjust the end points of the reslice line. When reslicing a project, Mimics will also write out the transformation matrix that was applied during the reslicing. The file with the transformation matrix will be saved in the folder of the original project.
Crop Project You can crop a project by going to the File menu and then choose the Crop Project button. Following window will appear:
The outlines of a box will appear on your 2D views and 3D view. When you apply the cropping, a new Mimics project will be created for only that part of the dataset in the box. This way it is possible to create a small project for only the structure you are interested in. Since the cropped project will contain smaller slices, the speed of Mimics will be increased while working on the project. The box can be adjusted by dragging the borders of the box in the 2D views or by adjusting the box properties in the crop interface. In the following example, we create a new Mimics project for only the femur, starting from a dataset that contains the hip.
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When cropping a project, Mimics will write out the transformation matrix that was applied during the cropping. The file with the transformation matrix will be saved in the folder of the original project.
Export anonymou s project This function will save a copy of the project without any patient related information.
Project infor mation This window displays the most important project in formation. After clicking the edit button you can add or change the dentist name, the clinician name and some comments. With the copy button you can copy all the project information in order to paste it in a document.
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Save/print screenshot After selecting the image type on the left of the screen, you will immediately see a preview on the right. You can select 2 destinations: 1.
To a file: Select Filename in the Destination frame to save the image as a BMP or JPEG file. A default name will be proposed (patient name + view) and the default folder will be the folder where the project is stored. You can browse to a new folder by using the yellow button on the right.
2.
To the printer : select Printer to print the image
3.
To clipboard : copies the image to the clipboard allowi ng you to paste it into another ap plication
The image or the print will show you exactly the same information that is on the screen, so you will have to prepare your screen with rulers, measurements, . . . first before creating the image or print.
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Printing Allows you to print a standard report showing a General Information page, the axial, coronal, sagittal images and, after an Online Reslice, the cross-sections and parallel images.
Properties Resolution White background
Resolution of the images Option to print a white background
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Option to print the page dithered or not (halftone) - printer dependent
Navigatio n Display in the Print Preview a specific page of your standard report by clicking the arrow button and selecting one of the pages out of the list. You can display the next or previous page by clicking the buttons Next and Prev.
Print Pages All pages Current page Range
Print all pages Print only the page in the print preview Enter the page numbers and/or page ranges (separated by commas) for the pages that have to be printed. For example 1,3,5-12.
Functions Advanced Edit Info Print Setup Page Setup Print
To set some advanced print options. To add comments on the prints. To select the printer To define the page margins and the font. You can also choose the unit: mm or inch. To start printing
Edit Info In this dialog box you are allowed to type some information concerning the study. This information will be shown in the prints. Open this dialog by clicking the Edit Info button in the Print window.
Advan ced Pri nti ng In this Advanced Print dialog box you can temporarily overrule some print preferences before printing. If you prefer another setting permanently, go to Options > Preferences > Printing .
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Pages to print Objects to print Distances between images
Axial image
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Select the pages to print. Select the objects to print. Spacing between the cross-sectional images and the parallel images in the prints. If the crosssectional spacing in the prints is not the same as in the images a message will appear about measurements that may not be visible anymore. The box in the axial image indicates the region of interest. The important point is the center point of the box and not really the edges. To move the box, select one of the edges and drag it with your left mouse button. In this window you will find the info about the printer that you have installed. Use the force color option when you have a color-printer, but when you print a project, you only get black and white prints. This can happen with e.g. Codonics printers.
List of previously opened files A list of recently processed files is shown in the File menu or when you click on the arrow next to the folder icon in the toolbar. Click once on the file name to open the study.
Exit Will Close the Mimics application and will save if necessary.
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The edit menu contains the following items:
You will also find the corresponding buttons in the toolbar.
Undo Undo the last action performed. The type of action is mentioned after the word "Undo" in the Edit menu.
Redo Redo the last action you have "Undone". The type of action is mentioned after the word "Redo" in the Edit menu.
Show undo l ist A list is displayed with all actions that have been performed. Every action is added to the top of the list, so the first one on the list is the last action performed.
View Menu This menu contains the following items.
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You will also find the corresponding buttons in the toolbar.
Toolbars Mimics lets you choose which toolbars are visible and which are not.
The toolbars are shown as tabbed toolbars by default. They can be undocked from the main toolbar by selecting the tab with the left mouse button and dragging it outside the toolbar.
To dock a toolbar back into the main toolbar, select the toolbar bar and drag it over the main toolbar.
Main Ma in to olbar A Main toolbar is displayed underneath the menu. It holds the other toolbars as different tabs. If the Main toolbar is not displayed, select from the menu bar. You can remove the Main toolbar by selecting View > Main toolbar from the menu bar again. You View > Main Main t oolbar from can dock the Main toolbar along the top or allow it to float freely anywhere in the image area by dragging it into place.
Tools toolbar A Tools toolbar can be activated by on of the tabs next to the the main toolbar. If the Tools toolbar is not displayed, select View > Tools toolbar from the menu bar. You can remove the Tools toolbar by selecting View > Tools toolbar from the menu bar again. You can add the Tools toolbar as a tab to the main toolbar or allow it to float freely anywhere in the image area by dragging it into place. The Tools toolbar displays buttons that are shortcuts to the following menu commands: Measure a distance
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Measure an angle Measure a distance in the 3D view Measure an angle in the 3D view Measure the area and average density within a rectangular region Measure the area and average density within an elliptical region Add an annotation to a Mimics object Draw a profile line Show 3D histogram
Segmentation Se gmentation to olbar A Segmentation toolbar can be activated by on of the tabs next to the main main toolbar. If the Segmentation toolbar is not displayed, select View from the menu bar. You can remove the Segmentation toolbar by selecting View > Segmentation toolbar from the > Segmentation Segmentation toolbar from menu bar again. You can dock the Segmentation toolbar in the main toolbar or you can allow it to float freely anywhere in the image area by dragging it into place. The Segmentation toolbar displays buttons that are shortcuts to the following menu commands: Thresholding Region Growing Dynamic Region Growing Morphology Operations Boolean Operations Cavity Fill Edit Masks Multiple Slice Edit Crop Mask 3D Mask Editing Calculate Polylines Update Polylines Calculate 3D Label Cavity Fill from Polylines Calculate Polylines from 3D Calculate Mask from 3D
Navigation toolbar A Navigation toolbar can be activated by on of the tabs next to the main toolbar. If the Navigation toolbar is not displayed, select View > from the menu bar. You can remove the Navigation toolbar by selecting View > Navigation from the menu bar Navigation toolbar from Navigation toolbar from again. You can dock the Navigation toolbar as a tab onto the main toolbar or allow it to float freely anywhere in the image area by dragging it into place.
You can navigate to a certain position in the image dataset by filling in coordinates in the edit boxes for the Axial, Coronal and Sagittal slice position and by clicking on Apply.
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If you change the position of the images by scrolling through the images or by doing a one-click-navigation, the slice positions in the navigation toolbar will update automatically.
Status Sta tus bar A status bar is displayed along the bottom of the screen. If the the status bar is not displayed, select View > Status Bar from from the menu bar. You can remove the status bar by selecting View > Status Bar from the menu bar again. The status bar displays the following useful information:
tips that describe actions taken by tools and menu commands
current gray scale value or Hounsfield unit in the voxel currently pointed at by the cursor
current cursor position in 3D coordinate system
Project Ma Manageme nagement nt The project Management gives you an overview of the different objects. If the Project Management is not displayed, select view > Project Management from the menu bar. You can find more information about the separate tabs in the in the Project Management chapter in the General Information part.
Project Proj ect Management Management tabs You can Show/Hide each tab in the Project Management
Interpo Inte rpolate lated d images This function will allow you to toggle between an interpolated view of the reslices in XZ and YZ direction
Interpolated Images off
Interpolated Images on
Note: This function will only interpolate the grey value images, the mask will remain the same. Editing on the mask on interpolated images is
possible.
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Show/H Show /Hid ide e The following menu is shown:
Show Masks Hide Masks Show measurements Hide measurements Show CAD objects Hide CAD objects Show polylines Hide polylines Show annotations Hide annotations
make all masks visible when they are invisible make all masks invisible when they are visible make all measurements visible when they are invisible make all measurements invisible when they are visible make all CAD objects visible when they are invisible make all CAD objects invisible when they are visible make all polylines visible when they are invisible make all polylines invisible when they are visible Make all annotations visible when they are invisible make all annotations invisible when they are visible
Pan Pa n vi view ew Every image and 3D object can be panned or moved. When you select the pan function, the cursor will change to a cross-shaped double arrow. There are different ways to select the pan function:
hold down the SHIFT key, right-drag your mouse button
right-click in an image or in the 3D view and select Pan View from the context menu
click on the Pan View button in the toolbar
hold down the SHIFT key in combination with the arrows-keys for precise rotation
Hold down the SHIFT key in combination with Home / End for quick Left / Right panning
select View > Pan View from the menu bar
Rotate view The rotate function is only available on a 3D object. There are different ways to select the rotate function:
right-drag with your mouse button
use the arrows-keys for precise rotation
use Home / End to rotate 10 degrees Left / Right
use Page Up / Page Down to rotate 10 degrees Up / Down
right-click in the 3D view and select Rotate View from the context menu
click on the Rotate View button in the toolbar
select View > Rotate View from the menu bar
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Zoom Allows to Zoom in at a user defined rectangle. Click on the left mouse button to to indicate a corner of the zoom rectangle, drag and release to indicate the opposite corner. Can be used on every image. There are different ways to select the zoom function:
hold down the CTRL key, right-drag your mouse button
hold down the CTRL key in combination with the up / down arrow keys
hold down the CTRL key in combination with the Page Up / Page Down key
right-click in an image or in the 3D view and select Zoom from the context menu
click on the Zoom button in the toolbar
select View > Zoom from the menu bar
Note: The behaviour of zooming is different in Reslice Layout.
Unzoom Changes the display scale to show the whole image. You need to select the function first and then indicate the view on which you want to apply the function.
Zoom to f ull scree screen n Allows you to display a view on the whole screen. Click on the Zoom to full screen button and the cursor will change to a magnifying magnifying glass. Then click on an image. To return to a normal view, click again on the Zoom to full screen button. Zoom to full screen on axial view
When you hover with the mouse over a view and press the spacebar the view is also put to full screen. To unzoom press the spacebar again.
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3D Background color Click View | 3D Background Color from the menu bar to select another background color for the 3D image.
To set a default color, click Options > Preferences from the menu bar. Preferences > Color from
Toggle Toggl e gr gray ay sc scale ale You can quickly toggle between the last two gray scales you selected in one of several ways: select View > Toggle Gray Scale from the Menu bar or press the Toggle Gray Scale button on the Main toolbar. The current gray scale's description, level and width will be displayed on the status bar.
Pseudo Pse udo Colors Color s Mimics provides you with several color scales that can be helpful in viewing the image data. One gray scale and three pseudo-color scales are provided. The pseudo color scales vary the hue (color) and luminance (brightness) within the images. Use color scales to enhance small differences in the soft tissue or the bone. Unlike the gray scale, the pseudo-color scales are non-linear. The pseudo-color scales can be used for instance to examine the porosity in materials. You can change the scale to one of the pseudo-color scales by selecting View | Pseudo Color from the menu bar and selecting one of the three color scales from the cascading menu. To revert back to a gray scale, select Gray from the cascading menu.
Gray This is the default gray scale.
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Full Spectru Spectru m The Full Spectrum color scale varies within the standard, continuous range of hues from orange to yellow to green to blue to red. In order to make air black and bone white, it also varies in luminance from dark (black) to light (white).
Sawtooth The Sawtooth color scale places five discrete hues next to each other. In order to emphasize differences between tissues of very nearly the same tissue density, the hues are very different: orange, green, red, blue and yellow. Within each hue, the luminance varies from dark to light.
Triangle The Triangle color scale places the same five discrete hues next to each other. But, within each hue (except for yellow, which varies from dark to light), the luminance varies from dark to light back to dark again.
Masks Shades Mimics allows you to change the shades and transparency of the mask. The different settings are explained below: Semi
All visible masks will be displayed. Only the active mask
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will be transparent. All gray shades from the surrounding tissues remain visible.
Full
All visible masks will be displayed and all masks will be transparent. All gray shades from the surrounding tissues remain visible. Example:
Active
Only the visible masks are displayed. Only the active mask is transparent, the surroundings are displayed in black. Example:
Binary
All masks are displayed in binary, the surrounding background is displayed in black. Example:
Layouts The Layouts list let you easily switch between different layouts. Click on the image below to see more information about the different layouts.
Image layout The Image Layout is the default layout. It shows the axial, coronal and sagittal view in case of 3-panes setting and includes also the 3D view in case of 4 panes. In case of 3-panes setting, toggling the 3D view will replace the sagittal view. For more information on how to change between 3-panes and 4-panes setting please look at the Visualization Preferences page.
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3D layout The 3D layout shows an axial view and 2 3D views in the 3-panes setting and 3 3D views in the 4-panes setting. In each 3D view, there is a 3D toolbar and each 3D can be manipulated separately.
Reslic e layout This layout is only enabled after an online reslice. It shows the axial, cross-sectional and parallel view. In case of 3-panes setting, toggling the 3D view will replace your axial view.
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Toggle 3D Window To view the 3D pane in the Mimics work area in 3-panes setting, click on the 3D button on the Main Toolbar. The sagittal view will be replaced with the 3D view and a 3D toolbar. You can also work in 4-panes setting, in which case you see all image views and a 3D view. In that case, the Toggle 3D button is not present.
Toggle 3D
If you have not yet created a 3D, you can calculate a 3D by selecting this button in the Segmentation toolbar: . The 3D objects list dialog will be shown, listing all 3D objects. Click the Options button to adjust 3D generation parameters to your needs. Then click the Calculate button to start calculating the 3D. The 3D is automatically shown on your screen after calculation.
Alignment image You can view the alignment image by selecting View > Alignment Image from the menu bar or by clicking the Alignment Image button on the Main Toolbar. The alignment image (also called a Localizer, ScoutView, Pilot, Scanogram, Topogram, or Surview depending on the CT manufacturer) is a lateral X-ray-like view of the patient. Inspect the alignment image to check that your patient was positioned correctly for the CT scan. Left clicking in the alignment image allows you to navigate in all images. The alignment image is surrounded by a frame border. The H and F markers show you the direction toward the patient’s head and feet. Notice the red vertical line. It references the exact location of the axial image. The dashed red lines reference the first and last axial images and show the extent of the area that was scanned. You can move the alignment image anywhere on the screen by dragging its title bar. To remove the alignment image, select View > Alignment Image from the menu bar, click the Alignment Image button on the Main Toolbar, or click its Close icon. Note: Be aware that the Alignment Image will display incorrect information, when using a wrong orientation for a project. You can find more information about changing the orientation on the Change Orientation help page.
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Tools Menu The Tools menu contains the following items:
You will also find the corresponding buttons in the toolbar.
Measure distance This tool allows you to measure distances within the images. Select the measurement icon from the tools toolbar or select Tools > Measure distance from the menu. The cursor will change in a measuring rule. Click once the left mouse button to set the first point. A measurement will be shown together with its length (expressed in mm). Click again to fix the other end of the measurement. Fine adjustments can be made to the measurement by dragging either end to a new location.
To show its context menu, right-click on the measurement.
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Delete the measurement Hide the measurement
Measure angle This tool allows you to measure angles within the CT images and the alignment image. Select the angle icon from the tools toolbar or select Tools > Measure angle from the menu. The cursor will change to a measuring instrument. Click three points with the left mouse button to define the angle. The angle is expressed in degrees and shown on the screen. Fine adjustments can be made to the angle by dragging the center point or one of the ends to a new location.
To show its context menu, right-click on the angle.
Delete Hide
Delete the angle Hide the angle
Measure 3D distance This tool allows you to measure distances in the 3D view. Select the 3D measurement icon from the tools toolbar or select Tools > Measure 3D distance from the menu. The cursor will change in a measuring rule. While you move over the 3D you will notice that a star will follow the surface of the 3D object. Click once the left mouse button on a 3D object in the 3D view to set the first point. A measurement will be shown together with its length (expressed in mm). Click again to fix the other end of the measurement. You can measure distances on the same object or between different objects. Fine adjustments can be made to the measurement by dragging either end to a new location.
To show its context menu, right-click on the measurement.
Delete Hide
Delete the measurement Hide the measurement
Measure 3D angle This tool allows you to measure angles in the 3D window. Both angle measurements between different 3D objects or measurements on the same object are possible. Select the 3D angle icon from the tools toolbar or select Tools > Measure 3D angle from the menu. The cursor will change to a measuring instrument. Click three points with the left mouse button to define the angle. The angle is expressed in degrees and shown on the screen. Fine adjustments can be made to the angle by dragging the center point or one of the ends to a new location.
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To show its context menu, right-click on the angle.
Delete Hide
Delete the angle Hide the angle
Measure density in rectangle This tool allows you to measure the area and average density within a rectangular region. Select the rectangle icon from the tools toolbar or select Tools > Measure density in rectangle from the menu. Move the rectangle to the image you want to measure. Click to drop the rectangle on the image. Or, drag with the left mouse button to drop the box and change its size in one step. The rectangle expands and contracts as you move the mouse. Release the mouse button when you are satisfied with the size of the rectangle. Information appears about the area (mm²), the mean density (Hou nsfield Units or Gray Values) and the standard d eviation of the density (Hounsfield Units or Gray Values) within the rectangle. You can adjust the size of the rectangle by dragging a border or corner when the cursor changes to a white double arrow. To move the rectangle, place the cursor on a yellow border (the cursor changes to a hand) and drag it. The measurement data is recalculated when you release the mouse button. When you scroll through the images, the measurements are updated.
To show its context menu, right-click on the rectangle.
Delete Hide
Delete the rectangle Hide the rectangle
Measure density in ellipse This tool allows you to measure the area and average density, within an elliptical region. Select the ellipse icon from the tools toolbar or select Tools > Measure density in elli pse from the menu. Move the ellipse to the image you want to measure. Click to drop the ellipse on the image. Or, drag the left mouse button to drop the ellipse and change its size in one step. The ellipse expands and contracts as you move the mouse. When you release the mouse button, the area (mm²), the density (Hounsfield Units or Gray Values) and the standard d eviation of the density (Hounsfield Units or Gray Values) within the elliptical region is displayed. You can adjust the size and shape of the ellipse by dragging one of the four markers on the ellipse when the cursor changes to a double arrow. To move the ellipse, place the cursor on a non-marker portion of the yellow border (the cursor changes in a hand) and drag it. When you release the mouse button, the new measurement data i s displayed. When you scroll through the images, the measurements are updated.
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To show its context menu, right-click on the ellipse.
Delete Hide
Delete the ellipse Hide the ellipse
Add Text Annotations You can add text comments using the annotation tool . Select the annotation tool and indicate the structure on which you want to comment. You can indicate structures on the images or on the objects in both, 2D and 3D views. Selected the annotation tool and left click your mouse, the Annotation Properties dialog will pop up. You can now add your comments in the text field.
Arrow Style Text Rotation Text alignment Text
Style of the line ending Direction of the text Alignment of the test Comments that will be shown in the project
Note: When you add a long text as comment, it will be visualized as three little dots. The full text is shown when you hover over the annotation. When you double-click the text comment, you can edit it. To show the annotation context menu, right-click on the annotation.
Delete Hide Properties Annotation List
Deletes the text annotation Hides the text annotation Opens annotation properties dialog Brings the annotation tab in the project
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management to the front
Profile line Visualizes an intensity profile of the HU or Gray Values along a user defined line. To draw this line, click the left mouse button to indicate the starting point of the profile line, move the mouse to the end position of the line and click again. The Profile dialog graph will be displayed:
.
Figure In the figure you can see the intensities for each point along the created profile line. The minimum and maximum threshold you want to apply can be changed by moving the horizontal lines.
List of p rofile lines Profile Visible
Profile name of the profile line. Click on its name to change it (similar as in Windows Explorer). Shows by means of glasses if the profile line is visible or invisible in the images. Left-click on the glasses to toggle between visible/invisible.
Functions on pro file lines Color Delete End/ Start Thresholding
Allows you to change the color of the selected profile lines. Deletes the selected profile lines. By Clicking this button, this dialog box will be closed/ opened and the threshold will be applied in you r images.
Options Scale to fit Grid X-axis Grid Y-axis
Allows you to see the vertical axis with all Hounsfield values or only the values lower than the maximum value along the profile line. To show or hide the vertical grid lines. To show or hide the horizontal grid lines.
Measuring There are three measurement methods:
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4 point method (suggested for technical parts): The user will see four full lines numbered from 1 to 4, each with a different color. The full
lines represent the input. The software calculates the intersection point of the vertical lines with the profile line: four points are calculated. The corresponding HU values can be read by following the full horizontal lines. On each side of the peak, a point is calculated as follows: P1 is at the position of the profile line where the HU value equals “T(gvalue2-gvalue1)+gvalue1” and lies between line1 and line2 on the horizontal axis. The dashed white lines indicate this point. The “T” function in above expression is the percentage of threshold difference. Most of the time this is about 50%. P2 is calculated in a similar way but with lines 3 and 4 as parameters. This point is indicated by the dashed yellow lines. The distance between P1 and P2 is the requested dimension. 4 interval method (suggested for technical parts): Instead of indicating 4 points, the user will indicate 4 intervals. For each interval the
average value is calculated. These four average values will than take over the role of the 4 points as described in the 4 point method. Threshold method (suggested for medical images)
Start the thresholding and drag the threshold line to the right position. Click on the End Thresholding button. The yellow and white dotted lines will move to the intersection between the profile line and the threshold line. The distance between the lines is displayed in mm. The 4 point method and the 4 interval method are suggested for technical CT images, while the threshold method is suggested for medical applications. In case you choose the 4 point method or 4 interval method, you will also see two horizontal lines (yellow and white). They indicate the position of the threshold value following the percentage filled out in the dialog box. The measurements are shown in the images and are saved to the project. They are also listed in the Measure tab page of the project management. Like this you can always refer to the measurements made and pop-up exactly the same profile line as initially created.
3D Histogram The 3D Histogram is the histogram of the complete data set. The X-axis lists the HU or Grayvalues, along the Y-axis the number of pixels that have this value. The range of this axis can be user defined or automatic (all values). The Y-range can be logarithmic or decimal. To activate the changing of these settings, you need to click on the Update button. The histogram function can be saved as a text file which can be easily imported i n other programs. Note: The Grayvalue 0 (-1024 HU) is not included in the histogram, since for most data sets, the number of pixels for that value is much
higher than for other values, resulting in a non-optimal view of the rest of the histogram.
Segmentation Menu This menu contains the following items:
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You will also find the corresponding buttons in the toolbar.
Thresholding There are two ways of thresholding:
With the thresholding toolb ar Set the threshold of the active mask. You can set or change the active mask in the Masks tab of the project management.
Thresholding is used to create a first definition of the segmentation object. The object can be defined based on one lower threshold, or based on a lower and a higher threshold. In the former case, the segmentation object will contain all pixels in the images with a value higher than or equal to the threshold value. In the latter case, the pixel value must be in between both threshold values to be part of the segmentation object. The predefined threshold allows you to quickly select a threshold for a specific tissue type. The threshold can still be adapted to your needs. The threshold value can be changed by moving the sliders in the thresholding toolbar with real time visual feedback. The threshold value will be displayed in the threshold toolbar and the segmentation area is changed accordingly. With the two sliders a minimal and a maximal threshold can be set. (Mostly only the minimal value needs to be set) In the Min and Max box, a threshold value can be filled in or the value can be increased or decreased using the up-down controls (ideal for fine tuning the threshold).To accept these values, click Enter. Note: The upper and lower threshold limit is limited to the maximum and minimum intensity in the project.
To use the threshold, press the App ly button.
With a Profile Lin e To use a profile line for thresholding, first select Thresholding button
from the tools toolbar or select Thresholding from the
Segmentation Menu. Then select the profile line button from the tools toolbar. To draw the line, click the left mouse button to indicate the starting point of the profile line. Then, click the left mouse button again to determine the end point of this line. Now you can use the measurements made with the profile line to determine the lower and upper threshold values. When Start Thresholdin g is enabled on the Profile Line dialog box, you can easily change the lower and upper threshold values by grabbing and moving the green lines. These lines represent the lower and upper threshold values.
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You can find more information about profile lines on the Profile Line help page.
Region Growing
The region growing tool provides the capacity to split the segmentation into separate objects. The operation can be performed on one single slice (multiple layer is Off) or in 3D on all slices (Multiple layer is On): to do this, turn Multiple Layer On or Off in the Region Growing Properties toolbar. Source and target masks are set here. The target mask can be a New mask or an existing object, in which case the selected region will be added to this object. After entering the appropriate values, click the left mouse button (cross shaped) on one point of the object of interest (which has to be part of the current segmentation object.). All points in the current segmentation object that are connected to the marked point will be moved to the target mask. If two existing masks are chosen in the source and target box, the double arrow can be used to switch source and target. When the check "Leave Original mask" is marked, all selected information will be copied and pasted in the new mask. When it is turned off, all selected information will be removed from the target mask and placed in the source mask (compare it to cut and paste).
Dynamic Region Growing
The dynamic region growing tool a llows you to segment an object based on the connectivity of gray values in a certain gray value range. It allows an easy segmentation of blood vessels, nerves, ... in CT images. The Dynamic Region Growing function is the only operation where you don’t have to threshold. A threshold value will be set automatically, the minimum and maximum value of the created mask will serve as threshold values. The creation of this new mask starts when you select a pixel. Mimics starts comparing the gray values of the neighboring pixels. The pixels with gray values that obey the following rule will be added to the new mask. |î -i | < d with î the average gray value i the new gray value d the deviation. If you make a second mouse click, above rule will also be applied on the gray value of the selected pixel.
Target
The new mask that will be created or if you select an existing mask, Mimics will take into account the
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gray values of the pixels that are already in this mask. When auto-update is enabled, you can adjust the deviation after indicating the source of the Dynamic Region Grow, making it possible to instantly see what the result of a different Deviation would be. When this is marked, Mimics will look in the complete data set. When it is unmarked, the function will only be applied on the single slice.
Auto-Update Multiple Layer 4-connectivity 6-connectivity 8-connectivity 26-connectivity
4-connectivity
6-connectivity
8- connectivity
26-connectivity
4-connectivity will only look at the neighboring pixels in the plane. When "multiple layer" is marked, Mimics will look to the same XY coordinates of the selected point in the following slices. 6-connectivity will look at the neighboring pixels in 3D 8-connectivity will only look at the neighboring pixels in the plane. When "multiple layer" is marked, Mimics will look to the same XY coordinates of the selected point in the following slices. 26-connectivity will look at the neighboring pixels in 3D. Is the deviation parameter in above rule. The maximum distance allows to limit the region wherein Mimics will search for the pixels (the endresult can thus be spherical). A value of zero will look in the complete data set.
Deviation Distance
In-slice distance is be the distance in the plane of the original slices. Inter-slice distance is be the distance perpendicular to the original slices. Note: The deviation parameter in previous versions of Mimics was expressed with 1 byte (0-255), while from Mimics 8.0 the complete
grayvalue range of 12 bits (0-4095) is used so the deviation can be better fine-tuned. This means that you have to use a deviati on that is much higher than in Mimics 7.3 to get the same results. Example:
Selection of the alveolar nerve with one mouse click:
2D
3D
Morphology Operations
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Morphology Operations will perform actions on the 'form' of a mask. The different morphology operations are:
Erode
Dilate
Open
Close
All these functions will take or add pixels from the source mask, the result will be copied in the target mask. Source
The Source mask is the mask that will be altered.
Operation
Erode: erode will take pixels from the edges. Erode followed by a region grow can separate parts. Dilate: dilate will add pixels from the edges. This can be used to restore the effect of the erosion. You
can limit the effect of dilation to another mask. This is to prevent that you will have an end-result that is larger than wanted. Open : will perform first an erosion, immediately followed by a dilation. Small edges will be removed or
opened. Close: will perform first a dilation, immediately followed by an erosion. Small cavities will be closed. Target
The new mask that will be created.
Limited to :
You can limit the effect of an operation to another mask. This is to prevent that you will have an endresult that is larger/smaller than wanted.
Number of pixels
is the amount of pixels you will take/add in one operation
8-connectivity 26-connectivity
8- connectivity
26-connectivity
8-connectivity will only look at the neighboring pixels in the plane. (The operation is performed on the complete dataset) 26-connectivity will look at the neighboring pixels in 3D. However, to take effect, the slice distance must be equal or less than the size defined by the number of pixels (pixelsize * number of pixels). The lower and upper threshold boundaries of the target mask will be taken over from the source mask After entering the appropriate values, click the Apply button.
Boolean Operations The Boolean operations allow you to make all different kinds of combinations based on two masks. It is a very useful tool to reduce the work that needs to be done when separating two joints. After entering the appropriate masks and operation, click the App ly button. The threshold limits of the resulting mask will be updated according to the values of the masks A and B and the operation applied. :
Subtraction (Minus): Threshold value = Threshold value mask A Intersection : lower threshold = max (low mask A, low mask B)) higher threshold = min (high mask A, high mask B)) Union : lower threshold = min (low mask A, low mask B)) higher threshold = max (high mask A, high mask B))
Exampl e: Separation o f a knee joint
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The image with the green mask is the starting situation. As you see the tibia and femur are connected with each other. So some erasing is necessary. The result is shown in the cyan mask. You only have to edit one part. Then region grow it e.g. to the purple mask. Now you can subtract the purple mask with the first structure from the cyan mask that contains both structures and you immediately have the second structure (red mask).
Cavity Fill Fills internal gaps of the selected mask and places this in a new mask.
Source and target masks are set here. The multiple layer check box indicates if you will fill in 3D or just in 2D. Select the cavity to fill by a click of the left mouse button (bucket shaped). Please save your project first before performing the Cavity Fill. The Cavity Fill function might lead to surprising results when there is a "gap" to the surrounding area. Therefore, it is best to take a new mask to fill the cavity in. Below is a trick to fill a lot of internal holes at once:
Edit Masks All manual editing functions are performed on the active mask. You can draw, erase, or restore the image with a certain threshold value indicated below. The drawing cursor can be a rectangle or a circle (ellipse) and can have different sizes, or you can use the lasso tool to draw a shape. Below the following bar appears:
Type
Shape of the edit cursor: square (rectangle), circle (ellipse) or the Lasso tool. To use the Lasso tool: select Lasso as Type, then draw with your mouse on a slice while pressing the left mouse button. To end the drawing, release the left mouse button.
Width/Height
Size of the edit cursor (can be different if the Same Width and Height check box is switched off). The size can be adjusted interactively by keeping the CTRL button and the left mouse button down, when you move the mouse now, the size will change.
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Draw
Draws in the active mask
Erase
Erases in the active mask
Threshold
Changes the edited zone back to a local threshold value which is set on the right side. When the default values are used, areas where some drawing or erasing has been done can be restored to their original threshold. This local threshold tool can be used to remove artifacts in the images, to restore the original threshold after you draw or erased some pixels by mistake… There are 3 threshold ranges. The middle threshold range is the default threshold that is currently applied to the active mask. This default threshold cannot be changed. To use your own threshold range, click on the arrow keys (up or down), double click on a threshold value, change the value and press enter.
When you move the edit cursor (square/circle/outline) over an image while pressing the left mouse button, every pixel within the square/circle/outline and which has a threshold within the threshold range you set, will be added to the active mask. On the other hand, all the pixels that already belong to the active mask and which don’t have a gray value within the range, will be removed from the mask. Note: This threshold is a local threshold, meaning that you apply a threshold in a particular area of one
image and not on the other images in the project. You need to repeat the local threshold action on each image that is needed. The difference with the threshold function in the Segmentation menu is that the one from the segmentation menu is a global threshold that applies to every image in the data set. After editing, pressing this button will update the polyline in the current image.
Note: you can still access the 1-click navigation function by pressing the SHIFT button while you are editing. You can then click with your left
mouse button on the point you want to navigate to.
Multiple slice edit The multiple slice edit tool is great to remove scatter easily. It allows you to reuse the manual editing that you have done on one slice, on other slices. The multiple slice edit works by creating a temporary mask that can be edited. The active voxels of the temporary mask are then added or removed from the original mask or a local threshold is done on the original mask at the active voxels.
In the interface, first choose which slices you want to edit (Axial, Coronal or Sagittal). You will notice that all masks are hidden except the active mask. Then choose to draw on the selected view and you will notice that a new temporary mask is created automatically with a different color. You can draw or erase pixels from the temporary mask and copy the current slice of the temporary mask on the current slice to other slices. The intersecting parts of the temporary and active mask are colored in a third color. To copy the temporary mask of the current slice to other slices, adjust the number of slices the current slice will be copied to and click on one of the arrow buttons. If you choose to copy to 0 slices, the current slice will be copied to all slices above or below the current slice. You can still adjust the temporary mask on the other slices and then use this new result again for copying to other slices. Finally, the temporary mask is removed or added from or to the active mask or a local thresholding operation is done on the active mask at all the active voxels of the temporary mask. The original mask.
Remove the scatter by selecting the scatter on the temporary mask. In this example, the temporary mask has a purple color and the intersecting parts of the temporary and active mask, have a yellow color.
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Remove the pixels in the temporary mask from the original mask.
The mult iple sli ce edit interface
Type Width/Height Draw Erase Copy to slices Number of slices
Operation on the active mask
Shape of the edit cursor: square (rectangle), circle (ellipse) or the Lasso tool. To use the Lasso tool: select Lasso as Type, then draw with your mouse on a slice while pressing the left mouse button. To end the drawing, release the left mouse button. Size of the edit cursor (can be different if the Same Width and Height check box is switched off). The size can be adjusted interactively by keeping the CTRL button and the left mouse button down, when you move the mouse now, the size will change. Draws in the active mask Erases in the active mask Determines on which view you can edit the temporary mask and in which view the mask will be copied to the other slices. You can choose between Axial, Coronal and Sagittal. To which slices you want to copy the temporary mask of the current slice. If you set the number of slices to 0 you will copy the current slice to all slices before or after the current slice. If you set a value different from 0, you will immediately jump to the last slice where the temporary slice is copied to. Determines the operation that will be done on the active mask. You can choose to remove the voxels in the temporary mask from the active mask, add the voxels in the temporary mask to the active mask or do a local thresholding on the voxels of the active mask, where the voxels of the temporary mask are active.
Crop Mask The mask cropping tool allows you to easily select a region of interest and restrict your segmentation to that region of interest. When cropping a mask, everything outside region of interest will be removed from the mask. The difference with the Crop project tool is that even though you restrict your mask, the images in the project remain untouched.
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Edit Mask in 3D The 3D mask editing tool allows you to visualize and edit the mask in 3D. You can select or deselect the voxels and by clicking on apply or close, the selected voxels are removed form the mask. This tool is very helpful when removing scatter and for separating complex structures like vessels.
The tool works with a region of interest that can be moved and rescaled in the 2D views. The region of interest is needed to make sure rendering is fast enough. You can change the size of the ROI in the Mask tab of the preferences in case you pc is too slow for the default option.
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Calculate Polylines The calculated polylines are the high resolution segmentation contours for the current segmentation object identical to how they will be calculated by STL+. It can be used to determine the exact threshold value(s) for a correct segmentation. Pressing the Calculate polyl ines button results in the following window:
To start calculation, select the desired masks and click Calculate.
If your selection contains a polyline that has a deformed shape, update that polyline in the following way:
Select the Edit tool
.
Alter your segmentation mask with the draw or erase function. Click the Update button
or select Update polylines from the Segmentation menu.
Repeat this in every slice where the polylines need to be updated. If polylines need to be updated in a lot of slices you better alter first your segmentation mask in every slice and then recalculate the polylines for the whole mask.
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Update Polylines After changing the segmentation on one layer, the current polyline can be updated by clicking this button. Note: When the threshold value has changed, the complete set of polylines needs to be calculated again.
Calculate 3D Click on Calculate 3D from the Segmentation Menu , on the Calculate 3D button in the Masks tab, or on the Segmentation toolbar, to open the 3D generation dialog. The following dialog will pop up:
button in the
Listed masks Here the created masks (with the lower and higher threshold mentioned) are listed. Select the masks from which you want to create a 3D. Note: You can not calculate a 3D for an empty mask
Quality When you calculate a 3D object you can choose the quality. Take low or medium quality if you want a short calculation time, but the dimensions of the 3D will not be accurate because of the matrix reduction that is applied on the images! You will get the most accurate result when you select the optimal quality setting. The high quality setting will still do a matrix reduction in the XY plane but can give in some situations a smoother and better looking 3D. Only when you select custom quality you can choose the 3D calculation parameters yourself by selecting the Custom radiobutton. The recommended quality (according to your computer) will be highlighted with a *.
Calculate Click the Calculate button to start calculating the 3D. The 3D is automatically shown on your screen after calculation.
Options For more information about the 3D generation parameters, click the Options button. Here you can set the parameters for the Custom setting for generating a 3D model. 3D visualization is performed by means of triangulation of a segmented 3D area. The number of triangles determines the quality of the reconstruction: the more triangles, the higher the quality. The downside is that more triangles require more memory. This should be considered when calculating a 3D image. Two methods for reducing the number of triangles are available: Image matrix reduction and/or triangle reduction.
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A smoothing algorithm changes the overall appearance of the triangular mesh.
Quality All these quality aspects are grouped in the predefined Low, Medium and High settings. The Custom setting is user defined. Especially for technical CT applications (and all high resolution scans), it is recommended to study the 3D generation parameters and to define practical custom settings.
Interpolation methods Grey value Interpolation Grey value interpolation is a real 3D interpolation that takes into account the Partial Volume effect and therefore it’s more accurate. With the grey value interpolation method we assume that the bone densities give an indication on the amount of bone within one pixel. All edges of the surface are decided based on the grey values. Also the place in between these 2 pixels is based on the grey values of the 2 pixels. The advantage of grey value interpolation is that it gives lots of detail and that the dimensions are correct. The disadvantage is that you get unnecessary details due to the noise within the images. With a femur head for instance, you will get better results (meaning: a nicely rounded edge) when using this grey value interpolation. Of course, you will need to do a little smoothing as well in order to reduce the noise. However, it is important to realize that grey value interpolation does not always produce good results. When the slice distance of the scan deviates considerably from the slice thickness, the resulting mesh gives a noisy surface. Only if the slice thickness and slice distance are the same, grey value interpolation works fine. This condition should be fulfilled during the scanning (acquisition). Changes of the Z resolution (see the paragraph about Matrix Reduction) therefore should not be used in combination with grey value interpolation. A reduction of the XY resolution does not violate the condition. Grey value interpolation is recommended to use for technical CT applications.
Contour Interpolation Contour interpolation is a 2D interpolation in the plane of the images that is smoothly expanded in the third dimension. This interpolation algorithm uses the grey value interpolation within the slices, but in the Z direction a linear interpolation between the contours is used (as schematically represented below). This interpolation method gives the best results for medical purposes.
Example of contour interpolation
Conclusion:
Principle of contour interpolation
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A contour interpolation results in a 3D that looks smoother and better (less gaps). Contour interpolation is recommended to use for medical CT applications. A Grey value interpolation results always in correct dimensions and correct positioning of the 3D, but the 3D can be noisy. Grey value interpolation is recommended to use for technical CT applications.
Shell Reduction This feature is an extra filter which removes small inclusions by only keeping a number - defined by the user - of the largest shells.
Slices By default, the table positions of the first and the last image are shown in the dialog. A default calculation is a calculation of the whole segmentation. The calculation can be reduced to a part of the segmentation by adapting the tab le positions. The Reset button will restore the default values.
Smoothing This function is meant to make rough surfaces smoother. It works like a filter for noise reduction. 1.
The Iteration parameter expresses how many cycles of the smoothing are performed. Don’t exaggerate the number of cycles! All iterations change the triangulation. If too many cycles are passed, every 3D object will turn into a sphere-like object! The number of iterations defines the area of influence for smoothing.
2.
The Smooth factor indicates the importance of local geometry. If this factor is low (close to 0), the local geometry is considered as important and the smoothing is limited. With high values for the ratio (close to 1), the new position is mainly determined by the position of the other points of the triangles in the neighbourhood. In this last case it is obvious that we talk about smoothing.
STL generation without smoothing
STL generation with smoothing
Note: If you take a high smooth factor, the number of iterations should be kept low.
Matrix r eduction This option allows grouping of voxels to calculate the triangles. The reduction is given relative to the X-size (= Y-size) of a pixel in the image and relative to the height (Z-size) of a pixel in the 3D data set. XY resolution
Decides how many voxels are grouped in the XY plane
Decides how many voxels are grouped in the Z-direction Z resolution An XY- or Z-resolution of 1 means no matrix reduction in the plan or the Z-direction. Note: When using grey value interpolation, reducing too much will lead to a loss of information for thin or small objects. Artificial holes might
appear in the 3D image but the dimensions of the object will stay quite accurate. Note: When using contour interpolation, reducing too much will lead to incorrect dimensions of the object. The visual representation will be
quite good, but when measuring items they will typically appear too large. If a matrix reduction is set in the plane, you have to option to choose the matrix reduction algorithm, Continuity or Accuracy.
Continuity algorithm Using this algorithm for matrix reduction in the XY-plane, will give a very nice result, but the 3D dimensions will become larger when using a bigger matrix reduction.
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Accuracy algorithm Using this algorithm for matrix reduction in the XY-plane, results in a 3D that is less nice, because there will appear gaps in the surface on places where the wall thickness is smaller than the pixel size after matrix reduction. The positive effect is that the dimensions of the 3D model stay exact. For the predefined settings (low, medium and high), Mimics automatically selects accuracy for greyvalue interpolation and continuity for contour interpolation. Remark: these were also the settings of Mimics 7.3, where the option to choose between continuity and accuracy were hidden for the user.
Triangle Reductio n Triangle reduction allows you to reduce the number of triangles in the mesh. This makes it easier to manipulate the file. There are three Reducing modes of triangle reduction, the Point-type, the Edge-type and the Advanced Edge-type. They all have the same parameters. The advanced edge reduction algorithm generates less noise on the resulting surface and creates a smaller object. The point reduction and the edge reduction are better for technical objects since they create more uniform meshes. The Tolerance indicates the maximum deviation in mm that a related triangle may have, to be part of the same plane that contains the selected triangle. It makes sense to keep this value related to the pixel size (e.g. half the pixelsize or a quarter). The Number of Iterations is a user-set value that defines how many times the program should make the calculations. The algorithm needs several iterations to reduce the number of triangles in larger flat areas. This algorithm converges to a stable result after about 15 iterations. More iterations therefore do not make a lot of sense. The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed. Triangles deviating less than this angle will be grouped into the plane of the other triangles. The Working Buffer size relates directly to the amount of memory used to process the reduction. The higher the buffer size, the greater the part of the segmentation that can be calculated at once. It is advisable not to use the reducer on very noisy objects. In this case it is better to perform a smoothing first. If a plane, defined by the Tolerance and the Angle consists out of several triangles, the program will try to re-triangulate this area. The Pointtype reduction mode will try to reduce the amount of triangles by removing a point. The Edge-type will remove a triangles edge (two points + the connecting line between these two points). If the tolerance-value is too big, essential part information may get lost.
Labels
Label
Enter label text here
Mask
The mask that will contain this label
Font
Type of text font. To choose a font, use the Set Font button on the right of the Font field.
Size
Text size in mm
Depth
Depth of the text in mm. The label will start from the current position and will move upwards, unless the top image is reached, then the label will be copied downwards.
2D slice-able label
Determines if the label is 2D slice-able or not. 2D slice-able labels are restricted to horizontal or vertical direction.
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Orientation of label
Horizontal or Vertical
Orientation of label Note: Changing the font of labels is not possible with 2D slice-able labels. View from top or View from Bottom
Labels can be exported in STL format in any direction (don't check the 2d slice-able label button). If you want your labels to be visible in exported sliced files, check the 2D slice-able label button. When this option is enabled, the labels are restricted to horizontal and vertical direction. You can move the label on the images (the mouse cursor changes to a cross). Keep the left mouse button down and place the label in the desired position (this can be done in all views). To further edit or delete the created label, click the right mouse button on the label. A pane appears with the function Delete, which will delete this label, and the function Properties, which will display the Label Prope rties Dialog box. The labels might look incorrect in the 3D View of Mimics. The "View from Top/Bottom" is related to the Top/Bottom of the stack of images.
Cavity Fill from Polylines The cavity Fill from Polylines will create a mask by filling every polyline in a polyline set.
Source polyline set and target mask are set here. Note: Please be aware that because the cavity fill from polylines, fills polylines that are calculated from a mask and interpolated during this
calculation, your new mask can be a bit larger as the original mask.
Calculate polylines from 3D The calculate polylines from 3D will create a polylines set from a 3D object or an STL. The polylines are created by taking the contour of the 3D object or STL on each slice o f the project.
Calculate mask from 3D The calculate mask from 3D will create a mask from a 3D object or an STL. The mask is created by taking the contours of the 3D object or STL on each slice of the project and then by filling the contour with a mask.
The source 3D object or STL and the target mask can be indicated in the dialog.
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Registration Menu This menu contains the following items:
Point Registration The point registration allows you to easily move an STL to a certain location. This is done by placing one or more sets of landmark points on the STLs, 3D Objects and images. Mimics will then calculate the transformation matrix that should be applied to have the best fit between the start en end points and applies that transformation matrix on the selected STLs. To use this function, first load an STL (File Menu -> Load STL). Then go to the Registration menu and choose the Point Registration function. This will open following interface:
List of STLs Name
Name of the object. By clicking on the name of the object, it can be changed.
Visible
Lists if the object is visible or not by means of glasses.
Contour Visible
Lists if the contour of the object is visible on the 2D slices or not by means of glasses. You can change the visibility of the contours by clicking on the glasses.
Move
Lists if the STL will move when registering another STL. If you e.g. select to register STL1 on Mask1 and that STL2 should move, STL1 will be registered on Mask1 and the same transformation matrix will be applied on STL2.
List of Landmark points Name
Name of the object. By clicking on the name of the object, it can be changed.
Add Point
Allows you to add a set of landmark points. You can do this by left clicking on the images or on a 3D object or STL to indicate the point that has to be moved and then by doing the same operation to indicate the point where the first point has to move to. To register an implant with the point registration, place landmark points on both objects.
File Menu
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And apply to find the best fit between the landmark points and to move the STL to the new location.
STL Registration The STL Registration function allows you to register STLs on masks. To use this function, first load an STL (File Menu -> Load STL) and create a mask of the feature on which the STL should be registered. Then go to the Registration menu and choose the STL Registration function. This will open following interface:
List of STLs Name
Name of the object. By clicking on the name of the object, it can be changed.
Visible
Lists if the object is visible or not by means of glasses.
Contour Visible
Lists if the contour of the object is visible on the 2D slices or not by means of glasses. You can change the visibility of the contours by clicking on the glasses.
Move
Lists if the STL will move when registering another STL. If you e.g. select to register STL1 on Mask1
File Menu
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and that STL2 should move, STL1 will be registered on Mask1 and the same transformation matrix will be applied on STL2.
List of Masks Name
Name of the object. By clicking on the name of the object, it can be changed.
Visible
Lists if the object is visible or not by means of glasses.
Lower Threshold
Lower Threshold setting of the mask.
Higher Threshold setting of the mask. When registering an STL, Mimics will also write out the transformation matrix that was applied during the registration. The file with the transformation matrix will be saved in the folder of the Mimics project. Higher Threshold
Settings You can choose to do a Global Registration or a Local Registration. In general, you want to do a global registration first and if you would then like to do a feature-based registration, you can use the local registration.
Global Registration The global registration will work on your whole STL. By using the Mimimal point distance filter, you can choose not to use all points of your STL. If you e.g. enter a filter value of 1mm, only points that have a distance that is higher than 1mm from each other will be taken into account. Using a filter value will make sure that your result is independent of the density of the STL and will speed up calculations. If you don’t want to use the filter, you can just give it a value of 0mm.
Local Registration The local registration will only work on all points that are within a certain distance of the border of your mask. By specifying the Maximal distance to mask border filter, you can define this distance. The local registration will only work if your STL is already positioned correctly.
Residu al Error The residual error gives you an i ndication of how good the position of your STL is with relation to the mask, after doing a registration. The error is a qualitative error, so you can only use this value for comparing the result when changing the parameters of the registration. Note: Before doing an STL registration, make sure that your STL is already located in the neighbourhood of your mask by using the
Translate and Rotate button on the STLs tab in the Project Management.
Image Registration The Image Registration function allows you to fuse two datasets by doing a landmark point based registration. To use this function, you have to first open the base dataset that you want to use for the registration. Then go to the Registration menu and choose the Image Registration function. This will open following interface:
File Menu
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Load in t he second dataset Next you can load in the dataset that you want to fuse with the base dataset by clicking on the browse button. This will open the open project dialog. You can browse through your harddisks and choose a second dataset from this interface. When you have chosen the second dataset, Mimics will show this dataset in the views on the right:
You can use the keyboard and mouse shortcuts for panning, zooming, adjusting the contrast, scrolling through the images. You can also use the toolbar at the top for panning, zooming.
Landmark Points
File Menu
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You can add landmark points by clicking on the Add button, the right-click in one of the views of Dataset 1 and then right-click in one of the views of Dataset 2. You can delete and locate landmark points by selecting the point from the list and clicking on the appropriate button. The landmark points can be moved by left-clicking on one of the landmark points in the views and dragging the points. You need at least 3 landmark points to be able to do the registration. You can however choose to use more points.
Fusion Method You can select different Fusion Methods from the list: Add
GVr = GV1 + GV2
Subtract
If GVr is higher than 4095GV, it is set to 4095. GVr = GV1 - GV2
Multiply
If GVr is lower than 0GV, it is set to 0. GVr = GV1 x GV2
Divide
If GVr is higher than 4095GV, it is set to 4095. GVr = GV1 / GV2
Difference
GV1 is divided by GV2. GVr = Abs(GV1 - GV2)
Average
The absolute value is taken of the difference between GV1 and GV2. GVr = (GV1 + GV2) / 2
Min
The average is taken of GV1 and GV2. GVr = Minimum(GV1,GV2)
Max
The minimum is taken of GV1 and GV2. GVr = Maximum(GV1,GV2)
AND
The maximum is taken of GV1 and GV2. GVr = GV1 AND GV2
OR
A bit wise AND is done of GV1 and GV2. GVr = GV1 OR GV2
XOR
A bit wise OR is done of GV1 and GV2. GVr = GV1 XOR GV2
Transparent
A bit wise XOR is done of GV1 and GV2. GVr = GV1 x (GV2 / 4095)
Opaque
The grayvalue of Dataset 2 is determining the transparency of the voxels of Dataset 1. GVr = GV2 The grayvalues of Dataset 2 are used. The result is that Dataset 2 is transformed to the coordinate system of Dataset 1.
App lying th e reg ist ratio n When you have placed at least 3 landmark points and you have chosen your fusion method, you can apply the registration. Mimics will then create a new Mimics project that is as big as Dataset 1. Dataset 2 will be resliced and registered and the part intersecting with Dataset 1 will be fused with Dataset 1.
Export Menu This menu contains the following items:
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Dicom Allows converting the axial images into Dicom format. Browse to a directory where you want the Dicom files to be saved.
3dd Allows exporting a mask to a 3dd file.
You can choose a mask from the list. Then you can choose an output directory by clicking on the Browse button. You then have to fill in a file name in the File name input box.
BMP/JPEG Allows exporting to an image file.
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The export of the 2D image(s) is an image that contains the correct pixel size and can thus be printed in a 1:1 ratio. You can choose to export the Axial, Coronal, Sagittal image and if available, the Parallel or Cross-section image. You can also export a range of slices. You need to fill in the root name of the filename, e.g. "Axial", in the filename input box. You can also choose the type of image file you want to save, bmp or jpg. The image filename will be constructed with the root name and the slice number, e.g. "Axial-523.bmp", "Axial-521.bmp", ... You can easily choose the path where the image files will be saved with the Browse button.
Grayvalues Allows exporting a text file with the grayvalues of your images. By selecting Grayvalues in the Export menu , a dialog is displayed where you can choose to export masks as a textfile with all the grayvalues of the voxels.
Descri ptio n of t he main areas Select a mask to export in Grayvalues Output directory
This area displays the masks that are currently available in your project. Select here the desired mask to process.
File Menu
File name Save as type Expressed in
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When you click the button a window appears. It will act like the Windows Explorer. You can look at all the drives of your computer and their directory structure. Select the location where you want your Grayvalues file to be placed. You can change the file name of your Grayvalues file. At this time the only possible output format is txt (textfile). Choose between Hounsfield units and Grayvalues.
Movie The export movie option allows you to export a movie of your Mimics User Interface while you are working. When you go to the export menu and choose movie, following interface will appear:
Descri ptio n of t he main areas Function buttons Options
With these buttons, you can start the recording, pause and stop it. When you click on the stop button or on the close button, the current movie file is closed. In the options menu you can choose some general options and some options for the movie itself:
You can choose to minimize the application during recording, to capture the mouse cursor, play the movie after recording and to use the auto rotate function. If the auto rotate function is on, your 3D view will be rotated 360 degrees and this will be exported to a movie.
View to capture Output Directory File Name
In the movie options section, you can choose the framerate of the movie and the codec that is used to export the movie. You can choose to capture the whole application, or only one of the views. When you click the browse button you select the location where you want your movie file to be placed. The filename of the movie that will be exported.
Options Menu
File Menu
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The Options menu contains the following items:
Licenses In the Registration dialog you can display your current license situation, display contact information, request passwords and register new modules. To display the Registration dialog, go to the Options menu and choose Licenses .
More information on how to register can be found in the Register section of the Introduction chapter.
Preferences In the preference dialog box you can set your preferences that will be appli ed every time you start the software. Possible preference settings are: General Visualization 3D Masks Predefined Thresholds Annotation Printing Reslicing SCSI
General settings like undo settings, autosave settings,... Settings about visualization of the indicators, view,... Settings concerning the 3D: the type of rendering, the 3D reference planes, performance settings,... Settings about colors and names of masks Settings about the Predefined Thresholds of the threshold toolbar Settings about the font and background of the annotations Settings about the pages and objects to print. Settings about the on-line reslice. On-line reslicing is the calculation of the cross-sectional images and parallel images based on the axial images. Settings concerning the 3D: the type of rendering, the 3D reference planes, performance settings,...
General pr eferences
File Menu
Working Directories Default Working Directory
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This directory will act as a default for all actions concerning importing of images, loading and saving projects, etc... . When you click the button a window appears. It will act like the Windows explorer. You can look at all the drives of your computer and their directory structure. Select the desired directory.
STL Library Working Directory
This directory will act as the root directory for the STL Library. When you click the button a window appears. It will act like the Windows explorer. You can look at all the drives of your computer and their directory structure. Select the desired directory.
Pixel Unit
Allows you to choose between a GreyValues scale or a Hounsfield scale. HIPAA Hide Filename Hide Patient Name
Select this option to hide all file names, in the open project window, the project information window, ... Select this option (in combination with the "Hide file name" option) to work in compliance with HIPAA. The patient name will be replaced by a unique patient ID in the project information window, the open project window, the print preview, the printed documentation, ... When saving the study, the proposed file name will be the patient ID instead of the patient name. The patient ID contains the initials of the patient and a unique number. Because the initials are still in the patient ID you can easily differentiate between the different patients, without having to keep a list with patient ID and associated patient name. The patient ID cannot be changed. Note: this function only hides the patient name. When you export the images to Dicom files and open the
images with a Dicom Viewer, you will still see the patient name. Or, when you exchange the file with another Mimics user, the other user can turn off the “Hide patient name” option to see the patient name. Preformance Always ask to reduce images when loading Maximum Undo Disk Space Autosave Settings
Select this option to have the Reduce Images dialog always displayed when importing images or when opening a project. More information about the reduction of images can be found on the Reduce images page. Indicates the maximum disk space that will be used to store information for the undo and redo operations. Select a time frequency from the drop-down list. This gives the frequency that the project will automatically be saved. Included is also an autorecovery function when an unexpected event like PC failure would occur. When opening the software again, it will recover your project you were working on.
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Image
When selected Mimics will use less memory for the visualization of the images.
Visualization p references
Default Indicators
You can decide if you want to see the tick marks, the intersection lines, the slice position and/or the orientation strings on your screen. You can also choose if you want to see all cross-sections or only the active cross-section and if you want to see full lines or dashed lines. View
You can choose between 3 or 4 panes. In the first case the 3D will replace the sagittal image in the image layout and the axial image in the reslice layout. In the 4 panes view, you will see all image views and a 3D view. In that case, the Toggle 3D button is not present. User Interface To restore the interface items to their default settings click the appropriate restore button.
3D preferences
File Menu
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Rendering
Select OpenGL or Direct3D rendering and select Use Hardware if you have a graphical card with hardware acceleration. With this renderering you get an optimal graphical visualization, because the software will look for the card and use the memory on the card for visualization. If you don’t have a graphical card with hardware acceleration, select OpenGL or Direct3D (Use hardware not selected) or Software rendering. Visualization and navigation 3D background color Use Gouraud shading Specular reflectivity Use world axis rotation
Defines the background color of the 3D view. To change this color click on the colored square. Enhances the 3D visualization. This setting can not be selected if you chose Software rendering. You can set the specular reflectivity of the 3D objects. This setting chooses the rotation axis of your 3D object. When the setting is enabled, the rotation will always be done around an axis perpendicular to the axial images.
Performance Frees the memory when the 3D is not shown. Unload 3D from memory when invisible Hide all 3D when opening a project Use this option for faster loading of proje cts. All 3D objects will be set invisible whe n you open a project Faster 3D interaction Reference planes
when this option is enabled. Will switch the 3D to a simplified representation when the frame rate drops below the selected value. Select the reference planes to be shown in the 3D view. These planes indicate the current position of all the image views in 3D.
Masks preferences
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Here you can adjust the default colors of the masks. Default mask names and colors Color Name Edit Mask in 3D ROI size Hide 3D objects Region of interest
Allows you to change the color of the selected mask. Allows to change the name tag of the selected mask All 3D objects will be put on invisible when you select to edit the mask in 3D. Allows you to set the dimensions of the region of interest. The 3D mask visualization tool is a demanding feature, reducing the ROI will make the visualization faster.
Restore
Restores all mask preferences to its default settings.
Predefined Thresholds
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List of Predefined Thresholds Name
Name of the predefined threshold
Lower Threshold
Indicates the Lower Threshold in the pixel unit, selected in General preferences.
Higher Threshold
Indicates the Higher Threshold in the pixel unit, selected in General preferences.
Edit Predefined Threshold setti ng Edit
Allows you to change the name, the Higher and Lower Threshold value of the selected predefined threshold.
Add
Allows you to add a new predefined threshold.
Delete
Deletes the selected predefined threshold.
Reset
Resets the values of the predefined threshold to their original settings.
Move Up
Moves the predefined threshold up in the list.
Move Down
Moves the predefined threshold down in the list.
Anno tati on
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Visualization Font
Allows you to change the font of the annotation. Select Modify… to visualize the Font selector dialog.
Box Background color
Allows you to choose the background color of the annotation box.
Printin g preferences
File Menu
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Print Pages
Select the pages to print. Objects to print
Select the objects to print. Distance between images
Spacing between the cross-sectional images and the parallel images in the prints. If the cross-sectional spacing in the prints is not the same as in the images a message will appear about measurements that may not be visible anymore.
Reslic ing preferences
File Menu
Reformatting images Distance between cross-sections Distance between parallels Maximum movement range
X-ray depth Snap to fixed positions of crosssectionals
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Spacing between two cross-sections. Spacing between two parallel images The maximum range of movement for the parallel on both sides of the one that is originally drawn. This originally drawn curve is at position 0. The real range can be different on both sides: the real range is limited so that the parallel curve does not self-intersect. If you draw a curve with a sharp bend, the movement range inside this bend will be very limited, while it will be the maximum range at the outside of the bend. The thickness used to calculate the parallel X-ray. If you don't select this setting you are able to navigate to virtually every position you want. Take a look at the picture below. When you click on the position like indicated with the red bullet, the cross-sectional images will be shown at the exact position (see blue dotted line) and not to the fixed position nearby (cyan colored cross-sectional, number 5).
. Cross-sectional grid
Defines the cross-section grid.
Advan ced SCSI
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To enable Mimics to import Data from a SCSI MOD or Tape reader select enable SCSI. Mimics can auto determine which SCSI devices to access therefore select auto determine and click on start. Mimics will try to detect all the services running on your system. The software will then check which of these are linked to a SCSI device by sending them a command. When a service is linked to a SCSI device, it will respond with a certain message. If it is not linked to a SCSI device, it will ignore this command. A problem found is that some of these services just generate a system crash when replying to this command. The "SymEvent" driver of Symantec for example has this effect. Symantec has created a patch for this problem but some other services may also be buggy. This List box displays a list of all the services present on your Windows system. It gives you the possibility to enable or disable sending the command to some of the services. All the services with a check mark next to them will receive the command. When you click on the Start Au to Tes t button the available services will be automatically marked. If you want to test a particular service, select the service and click on the Test button. Note: when Mimics is installed, all SCSI communication is disabled by default. If you want to import from a SCSI device (e.g. a MOD or
Tape drive), you have to enable SCSI in the advanced SCSI dialog.
Help Menu The Help menu contains the following items:
You will also find the corresponding buttons in the toolbar.
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General Help Select Help | General Help from the menu to start the help pages at the home location.
Context Help
Click on the Context Help button or select Help > Context Help from the menu. The cursor will change to this:
Click on a button or a menu item to open the help page about that specific subject.
.
Example: Opens the help page about the Toggle 3D button.
Opens the help page about licenses.
will start the help pages at the tutorial location.
About Mimics The About dialog box displays some information about the system you're working on. If you encounter any problem with the software, please forward it to Materialise together with your system information.
Import
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Import The import modules allow you to convert images from a variety of scanners to the Mimics file format. The images can be read from hard disk, floppy, CD, optical disk or tape. When the data is stored on an optical disk or tape you also need an optical drive that can read the optical disk or tape. Importing images from hard disk, CD, MOD and tape is very easy using the Import images wizard. Importing Dicom, Tiff and Bitmap images from hard disk or CD doesn’t require a license, but license passwords are required for all other images that you want to import automatically. More details can be found on the import licenses page. More details about the scanners and the devices supported by the Import module can be found in Overview scanner formats. Links to the sites of the different drivers and some hardware specifications can be found in Hardware Specifications.
Import licenses To convert images you need one or more licenses, depending on
The type of images you want to import from hard disk or CD
The type of MOD or tape
No license is needed when you
Import images manually
Import Tiff or Bitmap images
Import Dicom images from hard disk or CD
For example, if you want to import Dicom images from an Elscint optical disk you need an Elscint import license. If you want to import native Siemens images from CD you need a Siemens import license. Each module can be registered separately or combined. If you don’t know what module you need, import some images and Mimics will display the required module. The provided modules are: Siemens import GE Advantage import GE DAT import Philips import GE YMS import Dicom import Toshiba import Picker import Elscint import
module for Siemens scanners module for General electric scanners module for General electric scanners, DAT medium module for Philips and Hitachi scanners module for Yokogawa Medical Systems scanners module for DICOM format module for the IS&C format of Toshiba scanners module for Picker format module for Elscint format
Reading from Optical Disk Reading from optical disk Connect the optical drive to your computer and start your computer. Start Mimics and open the Import images wizard by selecting Import im ages from the File menu. If your computer recognized the drive, the drive should
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already be listed in the favorites list. You can click immediately on the drive icon or you can browse for the drive in the Windows Explorer tree. Select in the tree the SCSI Adapter to access to SCSI devices. A list with the attached SCSI devices will be shown. When the Import module recognizes the disk or tape format, this will also be listed (see picture).
Select at the right side of the window the images on the optical disk to convert, click Next and continue the wizard like described in Step 2 of the Import images wizard page. Remarks:
If an optical disk is DOS formatted you can access the disk via My Computer > Removable drive.
When you work on Windows NT, you need to have Administrators rights in order to access the SCSI devices.
When you have Import problems, read the SCSI troubleshooting page or the Frequently Asked Questions page. When you need help configuring your SCSI device, read the Hardware configuration for SCSI devices page.
Hardware configur ation for SCSI drives Hardware configuration for Pioneer DE-7001 series At the back of your MO-Drive (Pioneer DE-7001 series) you will find a DIP-switch containing eight small switches as shown in the next figure. Keep all switches in the position as marked in this figure, except those to change the SCSI address or those to change the drive operating mode.
SCSI address
Operating mode (WORM - MO)
The first three switches are used for selecting the scsi address, the last two for selecting the operating mode of the drive (WORM mode or MO mode). Never change these switched without switching the drive to power-off. (It is not needed to switch off the computer, as long as the computer performs no operations while the drive is still switched off.) Setting u p the SCSI- addr ess.
Import
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The switches 1, 2 and 3 have the values 1, 2 and 4 res. when in the Off position (and a value of 0 when in the On position). So to calculate the SCSI-address you have to add the values of the switches in the Off position. e.g. the switch positions in the previous figure give an address of 2. To generate an address of 5, put the switches 1 (value 1) and 3 (value 4) to On, and put switch 2 (value 2) to Off, the address is then 1 + 4 = 5 ! Selecting the o perating mode.
The switches 7 and 8 are used to select the operating mode of the drive. Always keep switch 7 in the off position! When switch 8 is in On position, the drive is in WORM mode. When switch 8 is in Off position, the drive is in MO mode.
Hardware configuration for Pioneer DE-7101 series At the back of your MO-Drive (Pioneer DE-7101 series) you will find a DIP-switch containing five small switches. If the SCSI card has SCSI II mode, the driver automatically swaps between MO and WORM mode when necessary. At the left side of the power button, you will find a SCSI address selector switch. The drive has to be set as follows:
If there’s no SCSI II mode, keep all switches in the position as marked in this figure, except those to change the drive-operating mode. At the left side of the power button, you will find a SCSI address selector switch.
Never change any of these switched without switching the drive to power-off. (It is not needed to switch off the computer, as long as the computer performs no operations while the drive is still switched off.) Setting u p the SCSI- addr ess.
Pressing the + or - switches on the SCSI address selector will increase res. decrease the SCSI address. At any time, the selected address is displayed within the window between both buttons. Selecting t he operatin g mo de ( no SCSI II mode ).
The switches 4 and 5 are used to select the operating mode of the drive. Always keep switch 5 in the off position. When switch 4 is in On position, the drive is in WORM mode. When switch 4 is in Off position, the drive is in MO mode.
Hardware configuration for LMSI LD 520 series At the back of your MO-Drive you will find a DIP-switch containing eight small switches as shown in the next figure. An x in the figure means that that side of the button is pressed in. Keep all switches in the position as marked in this figure, except those to change the SCSI address or the one to change the drive operating mode.
Import
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The first three switches are used for selecting the scsi address, switch 7 for selecting the operating mode of the drive (WORM mode or MO mode). Never change these switched without switching the drive to power-off. (It is not needed to switch off the computer, as long as no operations are performed by the computer while the drive still is switched off.) Setting u p the SCSI- addr ess.
The switches 1, 2 and 3 have the values 1, 2 and 4 res. when in the Off position (and a value of 0 when in the On position). So to calculate the SCSI-address you have to add the values of the switches in the Off position. e.g. the switch positions in the previous figure give an address of 2. To generate an address of 5, put the switches 1 (value 1) and 3 (value 4) to On, and put switch 2 (value 2) to Off, the address is then 1 + 4 = 5. Selecting the o perating mode.
The switch 7 is used to select the operating mode of the drive. When switch 7 is in On position, the drive is in MO mode. When switch 7 is in Off position, the drive is in WORM mode.
Hardware configuration for Hitachi OU152S-1 series At the back of your MO-Drive (Hitachi OU152S-1 series) you will find a DIP-switch containing 4 small switches as shown in the next figure. Keep all switches in the position as marked in this figure, except if you need to change the termination settings. (Check with your drive manual for these settings. The settings as in the figure below should be correct.) Right below the DIP switch you will find a scsi address selector as shown in the figure below.
Never change any of these switched without switching the drive to power-off. (It is not needed to switch off the computer, as long as no operations are performed by the computer while the drive still is switched off.) Setting u p th e SCSI- address
Pressing the + or - switches on the SCSI address selector will increase res. decrease the SCSI address. At any time, the selected address is displayed within the window between both buttons.
SCSI Troubleshooting You don't see drives in the SCSI Adapter list It can be a hardware configu ration prob lem
Make sure when that when you boot your system, you see your device(s) in the list that will appear on your screen. This list typical displays the SCSI addresses that are in use and will also display the brand name of the attached devices. If you don't see your device here, check: if you made a correct termination of your devices If you made a correct daisy chain when working with several devices. if your cables are still OK the dip switch settings of your device You're working on NT
When you work on Windows NT, you need to have Administrators rights in order to access the SCSI devices. You h ave SCSI Wide
You will need to change some settings in the BIOS of your machine. Typically for the HP kayak, the settings are
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set to SCSI wide (32 bits), you need to change that (for the SCSI address that you will use) to SCSI narrow (16 bits): Example for an Adaptec AHA 2940 SCSI card in an Alpha PC: When you boot the PC, press
for the SCSI Select Utility - (This message is displayed when booting, look for something similar) Select from the menu : "Configure/ View Host Adapter Settngs" Select from the menu : "SCSI Device Configuration" Now you see a list of all the available SCSI addresses, for the ones you will use for the device drivers, set "Initiate Wide Negotation" to NO. Save the new settings.
This will probably solve your problem. When you boot your PC, check if you see the devices listed together with their SCSI address. If they still don’t appear in the list, check if you have the correct drivers for your SCSI card.
You get the message that you have no license to run this converter In order to access data via SCSI interface, extra passwords are required. Each module can be registered separately or combined.
Blue Screen on pressing import button When you have a blue screen from the moment you click on the Import button, check the Advanced SCSI Options (for Windows NT)
Unknown medium This might sound stupid, but also try reading the other side of the disk.
Reading from tape Dumping data from tapes must not be confused with the automatic conversion of GE HiLight Advantage tapes. When the files from a tape are dumped, the conversion still needs to be performed. The conversion is then similar as Importing images from hard disk. Picker tapes are tapes that can be dumped using the Eliant 820 from Exabyte. Typically all images are stored in
one file that is the fourth one on the tape. Sometimes there is also a fifth file containing some images. The third 'file' on a Picker tape is some blank data that needs to be skipped. Picker tapes can be read as follows: Click on SCSI Adapter, this line is shown: " EXABYTE: Picker tape ".
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. The following parameter window is displayed:
Since typically all images are stored in the fourth file (or partition), you need to dump this file. It is this "Dumpfile" (with *.dmp extension) that needs to be converted afterwards. The dump file is stored in the Target directory you’ve set in the Tape Dump Parameters window. To import this dump file, follow the instructions as described in the Import section of Mimics (see picture below).
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Other tapes than Picker tapes can be dumped as well in a similar way. Then you need to try out yourself on what partitions the data is stored. Several messages can appear while dumping the tape. If Mimics is reading an empty partition you get the following message:
Answer Yes if you want to skip the empty partition and continue reading the next partitions. Answer No to stop reading. If there are no other readable partitions on the tape, you get the message:
When the end of the tape is reached, the following message is displayed. It means that 6 dump files have been made.
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Dicom Input Application The Dicom Input Application allows you to receive Dicom images that are sent via a Dicom network. The Dicom images are stored on your computer in a local folder (DIA folder), which can be chosen during installation. When the Dicom input application is installed and licensed, you will notice a yellow folder icon on the bottom right corner of your desktop. When Dicom images are received, a message will be displayed to inform you. The received images can be viewed via Windows Explorer or via the Import Images Wizard. Start the wizard by selecting Import Images in the File menu or by clicking on the Import button in the toolbar.
In the Import Images Wizard, click the DIA button to visualize the images stored in the DIA folder. Then select the files to import and click on the Next button. When new images are received, you need to update the DIA database by clicking on the Rebuild DIA Database button steps described in the help pages about the Import Module.
. Continue the import operation following the
Installing the DIA The DICOM Input Application or DIA is a licensed feature that allows you to receive images via a DICOM network. We recommend that you close all other applications before installing the DICOM Input Application. If you are running Windows NT or Windows 2000, you must have administrative privileges to install the software. During the installation of the DICOM Input Application, following dialogs will be shown:
STEP 1:
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Wait until the progress bar is finished and then click Next to proceed.
STEP 2:
After reading the license agreement, click the Yes button.
STEP 3:
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The DICOM Input Application will be installed in the directory: C:\Program Files\Materialise\DICOM Input Application. If you prefer another directory, select an existing directory by clicking on Browse. Click Next to proceed.
STEP 4:
Program icons will be added to the Program Folder > Materialise Software. If you want another folder name, then type a new name or select one from the existing folder list.
STEP 5:
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Enter the workstation’s AE Title, IP address and port number assigned by your network administrator. Click Next to proceed.
STEP 6:
The installation program suggests a folder on you computer to store all images that will be received via a DICOM network. Click Next to proceed if you agree with the chosen folder. If you want DIA to use another folder, click Browse and choose a new destination folder.
STEP 7:
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When everything is filled in like you want, click Next to proceed. If you want to change or review something, click Back.
STEP 8: The DICOM Input Application gets installed. This can take a few moments. This window will close automatically when the progress bar is finished.
STEP 9:
The software is successfully installed. Click Finish to close the installation dialog. It’s recommended to reboot your computer to finalize the installation.
STEP 10:
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When you reboot the system, the DICOM Input Application will start automatically and will ask you if you want to register it. For more information about the registration process, please look at the Registration help page. To uninstall the DICOM Input Application, go to Start > Settings > Control panel > Add/Remove programs . Select DICOM Input Application and click the Remove button. All DIA folders will be removed.
Overview of supported images DICOM Mimics supports the latest DICOM 3.0 standard but also previous ACR-NEMA formats (1.0 and 2.0). The DICOM format is a standard in the Medical Imaging world and most recent scanners areDICOM compliant. Mimics can import DICOM images that are compressed with the JPEG algorithm. Both lossy and lossless JPEG compression is supported. Even DICOM images made with cone beam scanners from Morita and NewTom scanners and proprietary images made with cone beam scanners from Aracor are supported.
BMP, TIFF Mimics supports BMP and TIFF images. The properties of these images are recognized automatically and you only have to fill in the information about the data set (e.g. patient name).
User-defined Import If the image format is not supported but you know all the properties of the images (pixel size, image size, slice distance…), you can also do a manual import of the images. The only restriction when importing images manually is that the images have to be uncompressed.
Proprietary Formats Beside these image formats that are supported by the Mimics base module, we also offer different Import
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Modules. With every Import Module, you can import several proprietary formats from scanner manufacturers. Different types of media and devices are supported. Below you can find a list of some of the scanners, devices and media we support. If your scanner is not on the list, please contact us. It could be that we already support your scanner or that we can provide you with a solution for your type of scanner.
Supported Scanners Asahi Roentgen PSR9000N Elscint CT twin Elscint Elite Elscint Exel 2400 Elscint Omnipro Elscint Twin GE 9800 GE Advantage GE CT/e, Dual GE GEMS Jupiter, Zeus, ZeusRP GE Hilight Advantage GE HiSpeed, QX/i, RP GE Lightspeed, 16, Plus, QX/i, Ultra GE Prospeed GE Sytec GE CT Pace GE Sigma (MR) Hitachi MRP 7000 Hitachi W2000 Hitachi W950 Philips Aura Philips Brilliance Philips Easyvision * Philips Mx 8000, Dual, IDT Philips Secura Philips Tomoscan 60/TX, TX, CX, CX/S, CX/Q, LX, LX/C, SR Picker MxTwin Picker PQ, 2000, PQ 5000, PQ 6000 Shimadzu SCT Siemens Balance Siemens Emotionm Duo Siemens Esprit Plus Siemens Magnetom (MR scanner)*
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Siemens Sensation 4, 6, 10, 16 Siemens Somatom 4 AR *, 4 Plus, AR*, AR/SP, DRH*, HiQ*, Plus* Siemens Volume Zoom * Toshiba Toshiba Aquilon Toshiba Asteion Toshiba IS&C Format Toshiba Xpress Toshiba Xvision Yokogawa ProSpeed
Supported Devices 4 mm tape drive Exabyte Eliant 820 (8200 format) Hitachi 5” Optical disk drive type OU152S-1 LMSI LD 520 MOD-WORM devices Max Optix drive type T4-2600 Max Optix drive type T5-2600 Pioneer DE-7001 series Pioneer DE-7101 series Pioneer DE-H9101 series Sony RMO-S551
Supported Media 5.25 inch MOD like MaxOptix, Verbatim, Sony... 4mm DAT tape 8mm DAT tape Maxell LM510 Maxell OC-112P-2 Maxell OC-112P-2 MaxOptix Pioneer DC-17GWO Pioneer DC-502 Pioneer DEC-17GMO Pioneer DEC-702 Verbatim
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* Uncompressed image files are required General Remark : Every disk drive has a limited capacity that it can handle, always check on the physical compatibility between the disk and the drive. More information about the devices can be found on following web-pages : MaxOptix drives: http://www.maxoptix.com/ Pioneer drives: http://www.pioneer-eur.com/pioneer/deskpage.jsp?taxonomy_id=43 Exabyte, Eliant 820 tape drive: http://www.exabyte.com/products/products/eliant.cfm Sony drives: http://www.sel.sony.com/SEL/rmeg/data/ General Remark : Every disk drive has a limited capacity that it can handle, always check on the physical
compatibility between the disk and the drive. If your scanner is not on this list, contact us, maybe we can help you. More information about the devices can be found on following web-pages : MaxOptix drives: http://www.maxoptix.com/ Pioneer drives: http://www.pioneer-eur.com/pioneer/deskpage.jsp?taxonomy_id=43 Exabyte, Eliant 820 tape drive: http://www.exabyte.com/products/products/eliant.cfm Sony drives: http://www.sel.sony.com/SEL/rmeg/data/
RP Slice RP Slice interfaces from Mimics to Rapid Prototyping systems via sliced files to build models. Optimal accuracy is achieved in a very short time by the direct conversion of the images to several sliced machine file formats: SLI and SLC for 3D Systems, CLI for Eos). High order interpolation (bilinear and inter plane) algorithms result in excellent surface reproduction from scan to model. RP Slice supports color stereolithography: tumors, teeth and teeth roots, nerve channels can be highlighted in the RP model, giving an e xtra dimension. Patient information can be displayed by a punched or colored label. One of the major difficulties in Stereolithography and most other Layer Manufacturing techniques is the need for support structures. Both the generation (automatic or manual) and the removal of these support structures are complex problems: not enough or not strong enough supports are causing inaccuracies; too much or too strong supports are resulting in bad surface quality and/or a lot of cleaning work. The basic function of the support structure is to support the part during the building process. The whole part is connected with a platform, and 'islands' which are isolated at a certain moment during the process need to be attached with the rest of the part. Another function of the supports is to reduce curling effects. Stereolithography resins have a tendency to deform during the building process because of internal stresses generated by the shrinkage. By building a strong support structure under a part, this deformation can be minimized. When Stereolithography is used starting from a CAD representation, the support structures can be designed in the CAD system. This is a large work, sometimes exceeding the drawing work of the part itself. For that reason, software was developed in the past to generate automatically support structures starting from an STL description of the part, e.g. Magics RP. In some instances however, one is not able to generate a support starting from an STL description. This is the case in medical applications where the layer information of the CT scanner is interfaced directly to the layer information of the Stereolithography machine. This means that there is no surface information available and the standard techniques for automatic support generation cannot be used. In addition the manual generation of the supports is impossible because the information is not present in a CAD system.
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The solution developed at Materialise has been called "RP Slice". This module allows you to calculate contour files and support structures starting from these contour files.
Starting RP Slice All RP Slice functions are loaded immediately in Mimics after registration of the RP Slice module. The RP Slice dialog can be started in one of the following ways: Via the main toolbar:
Select the RP Slice button
Via the menus:
Select RP Slice from the File menu . Select a contour format (CLI, SLI or SLC) from the Export menu . This opens the RP Slice dialog with the chosen contour format already selected.
Via the Project Management:
You can open the RP Slice dialog by selection the RP slice icon in the Action list of the Mask tab.
Note: If you're not able to start RP Slice, you probably haven't entered the passwords yet. Go to Options >
Licenses and fill in the correct passwords.
Exporting contour files RP Slice Mask or File selection In the RP slice dialog you start with the selection of one or more masks, 3dd files or contour files. When no project is opened in Mimics or when only the STL+ module is licensed (and not the Mimics basic module) you can only select 3dd or contour files. By clicking the Ad d button you add your selection to a queue. Remark that you are not allowed adding a combination of masks, 3dd files and contour files. All files in this queue will be exported in the selected output format and will be saved in the selected output directory.
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To generate a contour file, start with selecting a mask or 3dd file. To generate a support file, start with selecting a contour file. Depending on the selection, different dialogs will be shown after clicking the Next button.
Descrip tion of th e main areas Start from Mask Start from 3DD file Start from contour file
This area displays the masks that are currently available in your project. Select here the desired mask(s) to process. If you have a .3dd file you wish to process, press this button in order to go to the RP Slice file selection window. If you have a contour file for which you want to generate the support structure, press this button in order to go to the RP Slice file selection window.
Output directory
When you click the button a window appears. It will act like the Windows explorer. You can look at all the drives of your computer and their directory structure. Select the location where you want your support files to be placed. Masks/3dd/contour files to After selecting a mask, 3dd file or contour file and clicking the Add button, it will be convert placed here in a queue. The files will be processed according to the list. Selecting the files and pressing the Remove button removes the files from the queue. Clicking on the files in the Output Filename column allows changing the file name. Output Format The possible output formats are CLI, SLI and SLC.
RP Slice/STL+ to CLI, SLI, SLC, IGES
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This function will generate files for different Rapid Prototyping Systems. The files are very close to machine files and contain all the vectors which will be used on the RP machine. For the stereolithography machine, both the contours and the internal hatchings will be generated. Note: It is advised to use these functions for interfacing to the RP machine whenever possible. The functions
provide higher order interpolation algorithms and give the most accurate and highest resolution models possible. Only when no direct interface is provided, and in some other restricted cases, it might be better to use the STL interface.
Slice Positions Position First Slice Position Last Slice
The table position of the image data set has to be entered. Standard the lowest position will be displayed. This table position indicates up to where the part should be made. Standard the highest position will be displayed.
If you want to bui ld the entire mask or file, you don't have to change anything here.
If the model is too high to fit in the RP machine, or the user wants to build it in two pieces, one can process the same file twice: one time from the start to the middle, another time from the middle to the end. It is also possible to build a part in two pieces with one part from top to middle and the other from end to middle. In this way the pieces will fit better. This can be interesting when building a complete skull or if one wants to avoid supports inside the skull.
Build Direction Here you can toggle between ascending or descending: Ascending: the lowest table position will be built first. The highest table position will be built last. Descending: the highest table position will be built first. The lowest table position will be built first.
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The program will take care of mirroring. Sometimes building the model upside down is preferred because less support is needed in this direction.
Cubic Interpolation Two inter-slice interpolation schemes are implemented: Cubic and linear interpolation. Linear is the default as it is faster and gives good results in cases with small slice distances. Cubic interpolation will give smoother surfaces as show in the next figure. In the figure, the dashed lines show linear interpolation between 4 points of a contour, the full lines show the cubic interpolation. If the original images are only 1 mm separated, a linear interpolation is in most cases good enough. When the slices are 2 or more millimeters separated it is advised to use the cubic interpolation.
In the image you see a comparison between linear interpolation and cubic interpolation. The black dots are the original contour points, the small vertical lines mark the interpolation distances. The solid line is the cubic interpolation and the dashed line shows the linear interpolation.
Labels This radio button determines whether the label will be in color (color stereolithography only) or punched. Choose the option "none" when there is no label.
Color Stereolithography only If a part needs to be built in color, the checkbox should be marked.
Clicking the Next button will link you to the RP Slice calculation parameters page.
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RP Slice Calculation Parameters
Hatchin g parameters X hatching space
For interfacing to a 3D systems SLA 250 (SLI files), it is possible to create directly the vector files for the machine. This will speed up the procedure even more. This parameter defines the distance between the hatchings on the Stereolithography machine.
Y hatching distance X color hatching space Y color hatching space
For other output formats this parameter has no influence. Same as in X but in the Y direction. For creation of a model with colored regions, one can define the hatching space for the coloration. Mostly this value is the half of the X hatching space. Same as in X, but in the Y direction.
Build parameters Layer thickness
This parameter defines the output layer thickness in mm. It must be chosen in function of the Rapid Prototyping machine and its material. For having an acceptable surface quality a layer thickness of maximum 0.25 mm is advised. It is a good compromise between model quality and build time. For epoxy resins (Stereolithography) with a low penetration depth, a layer thickness of 0.15 mm is faster than 0.25 mm.
Slice Resolution
This value determines the internal representation of the output file: the units are one over the slice resolution. If the slice resolution is 100, the values in the output file are
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1/100 mm. The higher the slice resolution, the more accurate one can work. On the other hand, a higher slice resolution gives a smaller working space. If you encounter contours which are cut of at a certain maximum x and y value, it is possible that the slice resolution is too high. Some examples :
First layer height
Scale factor
Slice Resolution Units Maximum dimensions 200 0.005 mm 327 mm 100 0.01 mm 535 mm 80 0.0125 mm 819 mm Note: on the 3D systems SLA only resolution 40, 80 and 200 are supported. The first layer height gives the value of the translation according to the direction of building in mm. In this way support height can be chosen afterwards by choosing the start of the support (e.g. support starts at 0 mm, the part at 10 mm, or support starts at 6 mm, the part at 10 mm). This parameter allows you to rescale the original object with a factor larger than 0.1 and smaller than 100.
Filters These parameters filter out data points of the contours in order to reduce the file size and thus the calculation time. Minimal Segment Length
When the distance between two points is smaller than the minimal segment length, one of the points will be removed.
This
becomes
Out of Line Distance
This
When the distance between a point and a line – constructed by two other points – is smaller than the out of line distance, this point will be removed.
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becomes
Minimal Contour length
These parameters will remove contours whose length is longer than the parameters set.
Restori ng Defaults Pressing the Restore Defaults button restores the parameter values to their original values. These are stored in a file called material.ini which you can find in the installation directory. Pressing the Finish button starts the RP Slice calculation which runs in a separate program so you can continue to work in Mimics.
Support Generation After the creation of a sliced file, you can also generate a support file. To do this go again to RP Slice and choose to generate a file from a Contour file:
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Select the type of the Input and Output file, add the desired file and click on Next. You will then go to step two of the RP Slice wizard where you can choose different parameters for your support file.
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Hatching Parameters X Hatching Space
The distance between two support walls in the x-direction.
Y Hatching Space
The same in the y-direction.
Perforation Perforation Length
Distance (1) in the drawing below. (must be smaller than half the hatching distance) If this value is 0, the perforation option is off
Perforation Angle
Angle (2) in the drawing below.
Nr. of straight layers
The length of the straight part: distance (3) expressed in numbers of layers.
Perforated Borders
When this is checked, the perforation will also continue on the borders of the support.
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Support Angle
The maximum angle which can be built without support. All surfaces which are flatter than that angle will become supported. (angle in function of the horizontal plane, in degrees)
Starting Height
Starting height of the support structure (see picture). Be aware that the support will not go below 0 (in the z-direction).
Ending Height
All features higher than the Ending Height will not be supported (see picture). This is useful if you know that no supports are needed higher than a certain height. For instance, if you build a complete skull, in a lot of cases, no support is needed inside the skull. By putting this parameter above the orbits, no supports will be created for the cranium. You can calculate the Support Ending Height by calculating the height of support via table positions in Mimics and adding the First Layer height (parameter from STL+).
Instead of specifying an ending height one can also select the Full Height option. This will force the support to be build up to the top of the part, where needed (see picture).
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If you don't want the support to damage vertical walls, it might be interesting to use an xy-offset for the support generation. This value will determine how far the support must be separated from the part. Depending on which file format you have chosen, some of these parameters will be of no interest. In that case they will be disabled so that the box to fill in the parameters is not accessible. XY Offset
Restori ng Defaults Pressing the Restore Defaults button, restores the parameter values to their original values. These are stored in a file called material.ini which you can find in the installation directory. 'Pressing the Finish button starts the RP Slice calculation which runs in a separate program so you can continue your work in Mimics.
How to work with sli files on the 3D systems SLA 250 ? The sli files are the most direct way to make models on the SLA 250. STL however it is an internal 3D systems file format which is not directly supported by Partman. But, there is an easy workaround to bring these files on your machine. Generate the sli file with RP Slice (e.g. name.sli). Make sure that the x and y hatching spacing are filled in correctly. Together with the sli file, the program will also generate a dummy stl file with the same name as the sli file, but with extension stl (name.stl): this stl file is just a box with the same dimensions as the slice (sli) file. Generate support for the sli file with the RP Slice program (generate also an sli file) : s_name.sli On the Unix prompt type : cp name.stl s_name.stl (depending upon your file name) In Partman you can translate the file s_name.stl downwards in the z-direction with the same amount as the height of the support (save it again). In this way we have a stl file with the same position as our support sli slice file.
Do the normal preparation in Partman with the "s_name.stl" and "name.stl" as you do for normal stl files (including support settings, ranges etc.…)? When you are finished, save the spreadsheet. (File / Save) and clear (File / Clear)
In Partman do: File / UNIX. And type: "touch *.sli" [enter] exit [enter]. In Partman do : File / Load (your spreadsheet file) Then prepare your parts with "Prepare" (choose "prepare" and not "prepare all") The program should tell you that the files are already sliced, and it will directly generate the machine files. Copy the machine files to your SLA computer, and build your parts.
RP Slice and Lightyear
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This section will give an explanation about how to make models in Mimics that can be built on 3D Systems SLA machines. We will use Mimics, RP Slice and Lightyear to make the link between Mimics and the SLA machine. Most of the time exporting the models to STL and then importing them in Lightyear is very difficult because of the size of the files. It is far better to use the RP Slice module to make a sliced file of the model. The three main advantages of this approach are: 1.
No Problems with big files, because it is already sliced
2.
Cubical interpolation can be applied. The model will look less stair-stepped.
3.
High resolution can be maintained.
4.
Support Generation: the perforated supports save material, are easier to clean and can be build faster (up to 4 times as fast)
Note: This procedure was tested on Lightyear 1.3.
Create a sliced file The first step in the process is making a sliced file from your model. RP Slice can export to three different sliced formats: 1.
CLI: Common Layer Interface
2.
SLI: 3D Systems Layer Interface file
3.
SLC: 3D Systems Layer Contour file
The latest version of Lightyear is only compatible with the SLC format, so we will use this format. To export the model to an SLC file, click on File -> RP Slice or click on the RP Slice button on the main toolbar: . This will bring up following interface:
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You can export sliced files from Masks, 3dd-files or Contour Files. To export from a mask, select a mask and click on the Add-button. This will list the mask in the list of the files that will be converted. Now select the SLC format as the Output format. You can also change the name of the sliced file by clicking on the output file name. When you click on the Next-button, you can adjust the slice positions, the build direction and choose if you want to use cubic interpolation:
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When you click again on the Next-button, Several other calculation parameters can be adjusted. For more information about these parameters, please refer to the calculation parameters page.
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Note: To make the import process in Lightyear faster, please make sure the Layer Thickness of the sliced file is
the same as the layer thickness that you will use in Lightyear. When you then click on the Finish-button, the conversion process is started and the sliced file is saved. Saving sliced files from a 3dd file is done in the same way. Just select the 3dd tab on the first screen.
Generate the support file To generate a support file for a sliced file, click on File -> RP Slice or click on the RP Slice button on the main toolbar:
.
This will bring up following interface:
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Select the tab Contour Files. Now select the SLC format as the Input and the Output format and then browse to the directory where you have saved your sliced file. You can then add the file with the Add-button.
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When you click on the Next-button, you can adjust several support generation parameters. For more information about these parameters, please refer to the support generation page.
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When you then click on the Finish-button, the support generation process is started and the support file is generated.
Open the files in Lightyear In Lightyear, go to File and then Open File. You can then browse to the directory where you have saved the sliced file and the support file. Select both files and click on Open. Both the model and the supports will then be loaded in Lightyear and can then be prepared for building on the SLA machine.
STL+ The STL+ module provides interface options via triangulated formats: Binary STL, ASCII STL, DXF, VRML 2.0 and PLY. Using the STL+ module, a triangle mesh will be generated around the selected volume. The number of triangles determines the quality of the reconstruction: the more triangles, the higher the quality. The disadvantage is that more triangles require more memory. The STL+ module provides powerful tools to perform a significant reduction of the file size. Read more about this on the STL+ calculation parameters page.
Starting STL+
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All STL+ functions are loaded immediately in Mimics after registration of the STL+ module. The STL+ dialog can be started in one of the following ways: Via the main toolbar:
Select the STL+ button
Via the menus:
Select STL+ from the File menu Select an STL+ output format (Binary STL, ASCII STL, DXF, VRML or PLY) in the Export menu . This opens the STL+ dialog with the chosen output format already selected.
Via Project Management:
Select the action button
in the mask or 3D tab and select the STL+ icon.
Note: If you're not able to start STL+, you probably haven't entered the passwords yet. Go to Options > Licenses
and fill in the correct password.
Exporting triangulated files STL+ mask, 3D or fi le selection In the STL+ dialog you start with the selection of one or more masks, 3D objects, 3dd files, CAD objects or FEA meshes. When no project is opened in Mimics or when only the STL+ module is licensed (and not the Mimics basic module) you can only select a 3dd file. By clicking the Ad d button you add your selection to a queue. Remark that you are not allowed adding a combination of masks, 3D objects, 3dd files, CAD objects and FEA meshes. All files in this queue will be exported in the selected output format and will be saved in the selected output directory. When masks or 3dd files are added to the queue, the 3D calculation parameters dialog will appear after clicking the Next button. After completing these parameter values the files will be exported. When 3D objects, CAD objects or FEA meshes are added to the queue, all objects will be exported immediately after clicking the Finish button.
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Descrip tion of th e main areas Start from Mask Start from 3D Start from 3dd File Start from CAD Start from FEA Output directory
This area displays the masks which are currently available in your project. Select here the desired mask(s) to process. This area displays the 3D objects that are currently available in your project. Select here the desired 3D object(s) to process. If you have a .3dd file you wish to process, press this button in order to go to the STL+ file selection window. This area displays the CAD objects that are currently available in your project. Select here the desired CAD object(s) to process. This area displays the FEA meshes that are currently available in your project. Select here the desired FEA mesh(es) to process.
When you click the button a window appears. It will act like the Windows Explorer. You can look at all the drives of your computer and their directory structure. Select the location where you want your triangulated files to be placed. Masks/3Ds/3dd files to convert After selecting a mask, 3D object or 3dd file and clicking the Ad d button it will be placed here in a queue. The files will be processed according to the list. Selecting the files and pressing the Remove button removes the files from the queue. Clicking on the files in the Output Filename column allows changing the file name. Output Format The possible output formats are Binary STL, ASCII STL, DXF, VRML 2.0, PLY and single PLY file. VRML files can be used as input to Virtual Reality. When exporting multiple objects to a single PLY file, Mimics will create one PLY file that contains all objects. The color of the objects will also be saved, enabling you to create
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multi-color objects suitable for color 3D printing.
STL+ - STL / VRML Parameters The STL/VRML interface will generate a triangle mesh around the selected volume. The number of triangles determines the quality of the reconstruction: the more triangles, the higher the quality. The downside is that more triangles require more memory. This should be considered when calculating an STL file. Two methods for reducing the number of triangles are available: Image matrix reduction and/or triangle reduction. The Triangle reduction algorithm reduces the file size (the amount of triangles) keeping the STL surface as close as possible to the original one (e.g. without decreasing the resolution). It will search for (approximately) flat surfaces in the STL file and reduce the amount of triangles to fill in these surfaces. The method used to interpolate the images and generate the 3D triangular mesh can be chosen out of two options: grey value interpolation and contour interpolation. For medical applications the contour interpolation gives nicer results, for technical applications grey value interpolation is preferred A smoothing algorithm changes the overall appearance of the triangular mesh.
Quality All these quality aspects are grouped in the predefined Low, Medium, High and Maximum settings. The Custom setting is user defined. Especially for technical CT applications (and all high resolution scan’s), it is recommended to study the 3D generation parameters and to define practical custom settings.
Method Basically, contour interpolation is a 2D interpolation in the plane of the images that is smoothly expanded in the
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third dimension. Grey value interpolation is a real 3D interpolation and therefore more accurate. However, it is important to realize that grey value interpolation does not always produce good results. Only if slice thickness and slice distance are the same, grey value interpolation works fine. First of all, this condition should be fulfilled during the scanning (acquisition). Secondly, changing the Z resolution (see below) will most likely result in a violation of this condition because the slice distance for the calculation will increase. Changes of the Z resolution therefore should not be used in combination with grey value interpolation. A reduction of the XY resolution does not violate the condition. Contour interpolation is recommended to use for medical CT applications. Grey value interpolation is recommended to use for technical CT applications.
Slices Default, the table positions of the first and the last image are shown in the table. A default calculation is a calculation of the whole segmentation. The calculation can be reduced to a part of the segmentation by adapting the table positions. The Reset button will restore the default values.
Scaling The scaling option allows you to scale the part during export. This way you can e.g. easily build demo parts on a scale of 50% (value 0.5).
Matrix reduction This option allows the grouping of voxels to calculate the triangles. The reduction is given relative to the X-size (=Y-size) of a pixel in the image and relative to the height (Z-size) of a pixel in the 3D data set. XY resolution Decides how many voxels are grouped in the XY plane Z resolution Decides how many voxels are grouped in the Z-direction Note: When using grey value interpolation, reducing too much will lead to a loss of information for thin or small
objects. Artificial holes might appear in the 3D image but the dimensions of the object will stay quite accurate. When using contour interpolation, reducing too much will lead to incorrect dimensions of the object. The visual representation will be quite good, but when measuring items they will typically appear too large.
Smoothing This function is meant to make rough surfaces smoother. It works like a filter for noise reduction. The iteration parameters express how many cycles of the smoothing are performed. Don’t exaggerate the number of cycles! Every iteration changes the triangulation. If too many cycles are passed, every 3D object will turn into a sphere-like object! The number of iterations defines the area of influence for smoothing. The smooth factor indicates the importance of local geometry. If this factor is low (close to 0), the local geometry is considered as important and the smoothing is limited. With high values for the ratio (close to 1), the new position is mainly determined by the position of the other points of the triangles in the neighborhood. In this last case it is obvious that we talk about smoothing. You can also choose to use a shrinkage compensation. This shrinkage compensation will make sure that the volume of the part before smoothing and after smoothing is similar. Using the shrinkage compensation will have a negative effect on the speed of the calculation. Note: if you take a high smooth factor, the number of iterations should be kept low.
Triangle Reducti on Triangle reduction allows you to reduce the number of triangles in the mesh. This makes it easier to manipulate the file. There are three Reducing modes of triangle reduction, the Point-type, the Edge-type and the Advanced Edge-
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type. They all have the same parameters. The advanced edge reduction algorithm generates less noise on the resulting surface and creates a smaller object. The point reduction and the edge reduction are better for technical objects since they create more uniform meshes. The Tolerance indicates the maximum deviation in mm that a related triangle may have, to be part of the same plane that contains the selected triangle. It makes sense to keep this value related to the pixel size (e.g. half the pixelsize or a quarter). The Number of Iterations is a user-set value that defines how many times the program should make the calculations. The algorithm needs several iterations to reduce the number of triangles in larger flat areas. This algorithm converges to a stable result after about 15 iterations. More iterations therefore do not make a lot of sense. The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed. Triangles deviating less than this angle will be grouped into the plane of the other triangles. The Working Buffer size relates directly to the amount of memory used to process the reduction. The higher the buffer size, the greater the part of the segmentation that can be calculated at once. It is advisable not to use the reducer on very noisy objects. In this case it is better to perform a smoothing first. If a plane, defined by the Tolerance and the Angle consists out of several triangles, the program will try to retriangulate this area. The Point-type reduction mode will try to reduce the amount of triangles by removing a point. The Edge-type will remove a triangles edge (two points + the connecting line between these two points). If the tolerance-value is too big, essential part information may get lost.
MedCAD MedCAD is designed to make a bridge between medical imaging (CT and MR) and CAD design. This means that it can export data from the imaging system to the CAD system and vice versa. Use the right tools in the right software.
MedCAD is not a design software. Many software packages are available to make designs and most designers are already familiar with a certain CAD package. Learning yet another CAD system would be a waste of time. A CAD software is not an imaging software. If you try to convert all the medical data to your CAD system, your system will slow down drastically. Not all the data from the images can be converted to the CAD system: only a surface representation of the images is visible in the CAD system. Therefore it is better to make the interpretations on the images in MedCAD, taking into account all the gray value information (soft tissue, different types of bone, tendons, etc.…). On the images, basic features can be recognized and converted to geometrical entities (basic axes, reference curves, anatomical landmarks). Only the surfaces which are needed to make a fit are really converted to B-spline surfaces. On the other hand, CAD design can be imported in the Mimics via the STL interface. The designs are visualized in 2D sections together with the actual images, or in 3D shaded representations, with the anatomical data in a transparent mode. With this method, it is possible to bridge between the images and the CAD system in a few minutes time.
Starting MedCAD All MedCAD functions are loaded immediately in Mimics after registration of the MedCAD module. There is no specific way to start MedCAD. When the module is registered the extra feature appear in the interface. On the menu bar:
The MedCAD menu lists geometrical objects that can be drawn freely or fitted onto polylines. It also allows you to
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fit freeform curves and surfaces on polylines. In the Export menu:
Two new export file formats are added: Point Cloud and Iges.
In the Project Management:
Extra CAD Objects tab page. Extra options are added to the action list of the Polylines tab : select a polyline-set and click on the action button to fit a MedCAD object on the polylines or to export the polylines as Iges.
Note: If you're not able to start MedCAD, you probably haven't entered the passwords yet. Go to Options >
Licenses and fill in the correct passwords.
CAD Objects tab
List of created Objects Name
Name of the object. By clicking on the name of the object, it can be renamed.
Visible
Lists if the object is visible or not by means of glasses.
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Functions on Objects New
Creates a new Object. The object menu appears :
Click on the desired object to go to the correct help page. Delete
Deletes the selected objects.
Properties
Displays the properties of the selected object.
Locate
Locates the selected MedCAD object
Action
The action button lists all the available action on MedCAD objects. You can generate a mask from a MedCAD object or export them as IGES (International Graphics Exchange Standard) or as STL.
Exporting Iges files Different Iges export possibilities are available in MedCAD:
Starting fro m the Export menu: By selecting Iges in the Export menu, a dialog is displayed where you can choose to export the contours of a mask or a 3dd file as an Iges file. The entities used are of type 106 and form 12 (linear path entity). The advantage of starting the Iges export from a mask is that you can create extra contours (inter-layer) due to interpolation (see the “layer thickness” parameter on the RP Slice calculation parameters page). The disadvantage is that all contours of your mask will be exported. Although, there are filters available to filter out small contours and data points of contours in order to reduce the file size. Note: If you only want the contours of the mask, make sure the “layer thickness” parameter is set to the slice
distance of the image set. If you want to maintain the original position in space, make sure the First Layer height parameter is set to the first table position. (Otherwise the contours will be translated to this value)
Starting fr om the Polylines tab page:
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By selecting a polylines set in the Polylines tab page of the Project management and by clicking the Iges Export button, the selected polyline set is exported as an Iges file. The entities used are of type 106 and form 12 (linear path entity). The advantage of starting the Iges export from a polyline set is that only the contours of interest are exported. The disadvantage is that interpolation between the contours (interlayer) is not possible. The same filters are available as in the RP Slice module.
Starting from the CAD Objects t ab page: By selecting one or more CAD objects in the CAD Objects tab page of the Project management and by clicking the Iges Export button, the selected CAD Objects are exported as one Iges file. The entities used are:
Analytical Geometrical objects (sphere, line, plane, …): according the standard IGES representation. For example, a sphere is exported as a circular arc revolved around an axis.
Free form objects (Curves, Surfaces): NURBS representation.
Starting from MedCAD menu: By selecting Export all Objects to Iges in the MedCAD menu, all available CAD objects in the project are exported as one Iges file. If you want separate Iges files for each CAD object, use the Iges Export button in the CAD Objects tab page of the Project Management.
Exporting point cloud files By selecting Point Cloud in the Export menu , a dialog is displayed where you can choose to export a 3D object as a Point Cloud file.
Description of the main areas Select a 3D to export in
This area displays the 3D objects that are currently available in your project.
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Point Cloud format Output directory
File name Save as type
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Select here the desired object to process. When you click the button a window appears. It will act like the Windows Explorer. You can look at all the drives of your computer and their directory structure. Select the location where you want your Point Cloud file to be placed. You can change the file name of your Point Cloud file. At this time the only possible output format is Ascii.
MedCAD Menu MedCAD Menu This menu contains the following items:
Polyline Growing Starts the Polyline Growing mode. The Polyline Selector Toolbar appears:
The Polyline Growing tool provides the capacity to create several sets of polylines. The operation can be performed on one single polyline or in 3D. The parameters needed are: The set from where the polylines are grown The set to where the polylines are grown to. This can be an existing selection or a new created one. Correlation A measure for the strength of matching (%). This is done with a geometrical comparison. Auto multi-select This parameter can be turned on/off. If it is turned off only the current polyline will be grown. If this parameter is turned on, all polylines according the Matching parameter will be grown. Keep Originals By default the polyline that is grown into a new set is removed from the source set. You can choose to keep this polyline in the source set by enabling the Keep Originals checkbox. Selection is done on the images in 2D by drawing a rectangle (Press the left mouse button to indicate a corner of From To
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the zoom rectangle, drag and release to indicate the opposite corner) around the d esired polyline.
If there is a polyline where the shape is a bit deformed, you can alter it by editing on your segmentation mask. In the edit mode you will be able to update the polylines.
Point Creating Point s There are two ways to create a point:
Draw The cursor will change to
. Simply click on the 2D images to create a point.
The point can be moved in the 2D images and 3D view by dragging it with the left mouse button.
Keyboard The following window appears:
Type in the X, Y, and Z coordinates of the point.
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Click on the colored button in order to change the color of the MedCAD object.
Context menu
Delete Hide CAD Objects List
Deletes the selected point. Hides the selected point. Opens the CAD Objects tab page in the Project Management.
Line There are three ways to create a Line:
Fit on Polylines When creating an object based on a polyline set, the following window appears:
Select the desired polyline set to fit the object on and press OK .
Draw The cursor will change to . Simply click a start and end point on the 2D images to create a line (Start and end point can lie in different images) The line can be moved in the 2D images by dragging the end points with the left mouse button.
Keyboard
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The following window appears:
Type in the X, Y, and Z coordinates of the start and end point of the line. Click on the colored button in order to change the color of the MedCAD object.
Context menu
Delete Hide CAD Objects List
Deletes the selected line. Hides the selected line. Opens the Objects tab page in the Project Management.
Circle There are three ways to create a circle:
Fit on Polylines When creating an object based on a polyline set, the following window appears:
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Select the desired polyline set to fit the object on and press OK .
Draw The cursor will change to . Simply click three points on the 2D images to create a circle. Changing to another slice or to another 2D window is possible. The circle can be moved in the 2D images by dragging its center point with the left mouse button.
Keyboard The following window appears:
Type in the X, Y, and Z coordinates of the center point, followed by the direction: the coordinates of the direction of the normal vector of the plane in which the circle is located. Entering the radius fully determines the circle (see figure). Click on the colored button in order to change the color of the MedCAD object.
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Context menu
Delete Hide
Deletes the selected circle. Hides the selected circle.
Sphere There are three ways to create a Sphere:
Fit on Polylines When creating an object based on a polyline set, the following window appears:
Select the desired polyline set to fit the object on and press OK .
Draw
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The cursor will change to . Simply click four points on the 2D images to create a sphere. Changing to another slice or to another 2D window is possible. The sphere can be moved in the 2D images by dragging the control points with the left mouse button.
Keyboard The following window appears:
Type in the X, Y, and Z coordinates of the center point and the radius. Click on the colored button in order to change the color of the MedCAD object.
Context menu
Delete Hide CAD Objects List
Deletes the selected sphere. Hides the selected sphere. Opens the Objects tab page in the Project Management.
Plane There are three ways to create a Plane:
Fit on Polylines When creating an object based on a polyline set, the following window appears:
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Select the desired polyline set to fit the object on and press OK .
Draw The cursor will change to
. Simply click three points on the 2D images to create a plane.
The plane can be moved in the 2D images by dragging the control points with the left mouse button.
Keyboard The following window appears:
Type in the X, Y, and Z coordinates of a point which is part of the plane followed by the coordinates of the normal vector of the plane. Click on the colored button in order to change the color of the MedCAD object. Change the width and height of the plane to change the visualization in the 3D view of the plane.
Context menu
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Deletes the selected plane. Hides the selected plane. Opens the Objects tab page in the Project Management.
Cylinder There are three ways to create a cylinder:
Fit on Polylines When creating an object based on a polyline set, the following window appears:
Select the desired polyline set to fit the object on and press OK .
Draw The cursor will change to . Simply click a start and end point of the cylinder axis, followed by a point which indicates the radius on the 2D images to create a cylinder (see figure). The cylinder can be moved and in the 2D images by dragging the control points with the left mouse button.
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Keyboard The following window appears:
Type in the X, Y, and Z coordinates of the start and end point of the cylinder axis, followed by the radius of the cylinder. Click on the colored button in order to change the color of the MedCAD object.
Context menu
Delete Hide
Deletes the selected cylinder. Hides the selected cylinder.
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Freeform Curves There are two ways to create a Freeform Curve:
Fit On Polylines
Polyline Set Set Check Order Number of control points
Closed
Select the desired polyline set. This area (under the Polyline Set selection) indicates if the polyline set is valid for freeform curve generation. The order of the polynomials used. Best values are either 3 or 4, e.g. an order of 3 means that cubical polynomials are used. Control points can be seen like little magnets which attract the curve. The more control points used, the better the fit will be. Some caution in increasing the number of control points is advised. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. So, if the number of points is too high, the fit of the polyline will become worse. The curve can be closed or not.
Draw When Draw Curve is selected the cursor changes to
.
Left click on the images where the curve has to pass through, double click to end the curve. The curve can be moved in the 2D images by dragging the control points with the left mouse button.
Properties
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You can view the properties of a Freeform Curve by clicking on the Properties button in the Project Management, CAD Objects tab. Here you can change the color and the name of the curve. You can also find some information about the order and the control points of the curve.
Freeform Surfaces The only way to create a freeform surface is to fit it on a polyline set. The following window appears:
Polyline Set Set Check
Select the desired polyline set. This area (under the Polyline Set selection) indicates if the polyline set is valid for
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Closed U en V parameters
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surface generation. The order of the polynomials used. Best values are either 3 or 4, e.g. an order of 3 means that cubical polynomials are used. Control points can be seen like little magnets which attract the surface. The more control points used, the better the fit will be. Some caution in increasing the number of control points is advised. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. So, if the number of points is too high, the fit of the polyline will become worse.. The surface can be closed or not. A parametric surface typically has 2 parameters: a u-parameter and a v-parameter. These are the running coordinates in two in-plane orthogonal directions. In MedCAD those two plane-directions are fixed. The u-parameter runs perpendicular to the image plane. The v-parameter runs in the image plane. For each parameter Order , Number of control points and Closed have to be set. Caution: a surface closed in two directions is NOT a cylinder closed on top and
bottom, but a torus.
Freeform Surface Info
You can view the properties of a Freeform Surface by clicking on the Properties button in the Project Management, CAD Objects tab. Here you can change the color and the name of the surface. You can also find some information about the order and the control points of the surface.
Freeform Tree This tool allows you to calculate the centerline of a 3D object. These centerlines can be exported together with a range of measurements.
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Resolving resolution Select the minimum detail you want to resolve. Number of iterations Set the amount of iterations you want the algorithm to perform. Distance between control points Set the distance between two successive control points
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Label Name Visualisation Color
Branches Name Length(mm) Visibility
Delete
Export
Name of the centerline Sets the color of the centerline The name of the branch Length of the branch The visibility of a branch can be toggled by clicking on the sunglasses. Select a branch and click on delete to remove the branch from the list. You can export the centerlines as Iges files or export the coordinates of the centerlines and the measurements
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on the centerlines as Text file.
Export of centerline Properties
Export Output Directory File Name Save as type
Select the destination folder. Select the file name The centerlines can be exported as Text or as Iges file. The text file will list the position and measurement information of the control points. The information is grouped per branch and is listed in columns, the coordinates of the control points are indicated by Px, Py and Pz., the normal are represented as Nx, Ny and Nz. The Iges file exports the control points and the connection between them. Besides the control points also the best fitted, minimal and maximal diameter can be exported as an Iges file.
Measurment Best fitted diameter Minimal diameter
Maximal diameter
Diameter of the best fit circle in a control point. The measurement is exported as Dfit. Diameter of the inscribing circle in a control point. The measurement is exported as Dmin. Diameter of the subscribing circle in a control point. The measurement is exported as
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Curvature
Tortuosity Hydraulic Diameter Hydraulic Ratio
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Dmax. The coordinate and normal of the curvature point. This is the point of the circle that determines the curvature for the segment that has a length as indicated in the measurement interface and has the control point as a mid-point. The coordinates of the curvature point are exported as Pcx, Pcy, Pcz, the normals are indicated by Ncx, Ncy, Ncz and the radius that defines the curvature is represented by Rc. Tortuosity of the segment that has a length as indicated in the measurement interface and the control point as a mid-point.The Tortuosity is exported as T. Hydraulic diameter in each control point. The Hydraulic diameter is exported as Dh. Hydraulic ratio in a control point. The Hydraulic ratio is exported as Xh.
Export all object to IGES When "Export all objects to IGES ..." is selected, all created objects (spheres, freeform surfaces, ...) will be exported to one iges file. The name of this file can be given in the dialog box that will be displayed. If however you want to created separate IGES files for every object, use the IGES button in Project Management, CAD Objects Tab.
FEA The Mimics FEA Module enables you to link from scanned images to Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD) by exporting the files in the appropriate file format. You can calculate 3D objects based on the scanned images and prepare these surface meshes for Finite Element Analysis purposes. The Remesher in the FEA Module assures that you'll end up with the most optimal input for the pre-processor of your FEA software. After converting the surface mesh to a volume mesh in the pre-processor, the volume mesh can be imported in Mimics again. Materials can then be assigned to the volume mesh, based on the Hounsfield Units in the scanned images or on the segmentation of the project.
Starting the FEA module All FEA functions are loaded immediately in Mimics after registration of the FEA module. When the module is registered, a few extra items are visible in the interface: On the menu bar:
An extra FEA menu, listing the different FEA functions. In the Export menu , new export file formats are added: Abaqus, Ansys, Patran neutral, Fluent and Nastran.
In the Project Management:
Extra FEA Mesh tab.
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Extra buttons on the 3D Objects tab and the STLs tab: select a 3D Object or STL and click on the Remesh button to open the remesher with the part already opened.
Note: If you're not able to start the FEA module, you probably haven't entered the passwords yet. Go to Options >
Licenses and fill in the correct passwords.
FEA Mesh tab
List of created Objects Name
Name of the object. By clicking on the name of the object, it can be renamed.
Visible
Lists if the object is visible or not by means of glasses. You can change the visibility by clicking on the glasses.
Material
Lists if the material assignment is visible or not by means of glasses. You can display or hide the material assignment by clicking on the glasses. Note: If you haven't assigned any materials to a FEA mesh, you will not be able to
make the material assignment visible. Contour Visible
Lists if the contours of the volume mesh are visible in the 2D images or not by means of glasses. You can display or hide the contours by clicking on the glasses.
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Functions on Objects Import
Imports a volumetric mesh. For more information about the import process, please refer to the Import help page.
Delete
Deletes the selected objects.
Properties
Displays the properties of the selected object:
Material
Calls the window to do a material assignment for the selected object.
Export
Exports the selected object to a Patran neutral, Ansys, Abaqus or Fluent file.
FEA Menu FEA menu When the FEA module is licensed, the FEA menu appears in the menubar. This menu lists the different features of the FEA module:
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Remesh Allows you to select a 3D object or an STL that will be remeshed. You can select exactly one 3D object or STL out of the list. When you click on the Ok button, the remesher will automatically be started with the selected object already loaded.
When you close the remesher, you will be asked if you want to save the changes or not. If you choose yes, the selected 3D or STL will be replaced in Mimics by the remeshed part.
Import Allows you to browse for a volumetric mesh. When you have selected the right file and click on the Open button, the volumetric mesh will be loaded and listed in the FEA mesh tab. You can import Patran neutral, Ansys and Abaqus volumetric meshes. For more information about which elements are supported please read the Supported Files page.
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Material Allows you to select a FEA mesh out of the list for which you want to assign materials. When you have selected the correct mesh and click on the Ok button, the material assignment window will be opened for the selected mesh.
Export Allows you to export a 3D object, a STL or a FEA mesh to a Patran Neutral, Abaqus, Ansys, Fluent or Nastran file. In the case of a FEA mesh, both the mesh and the material assignment (if available) will be exported.
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Note: FEA meshes can also be exported to a colored STL file. These colored STL files are invalid STL files and
should only be used for visualization purposes! The colored STL file could for instance be used to view the material assignment inside the volumetric mesh.
Remeshing A STL or 3D object can be remeshed using the remesh module. This is needed in order to raise the quality of the triangles so that the preprocessor of an FEA package can build a tetrahedron mesh from them. There are some steps you can do to make sure that your 3D object that is calculated in Mimics to make sure that the remeshing will go smoothly:
When calculating a 3D in Mimics, you can do a shell reduction so that small shells are removed. If you go to the Segmentation Menu and choose Calculate 3D and then Options. In that dialog you can choose to do a Shell reduction with value 1.
It is also interesting to fill as much holes as possible. You can use the Fill Cavity from Polyline tool to remove holes from your 3D object.
Most FEA packages don't like small details. Thanks to the morphology operation in Mimics, you can already smooth out small details on the surface.
Note: When you are remeshing an object, you cannot switch to Mimics. To return to Mimics, close the remesher.
If you have altered the object, the remesher will ask you if you want to save your changes. If you choose yes, you will return to Mimics and your object will be replaced with the remeshed object. Note: If you remesh a STL and choose to save the temporary file when returning to Mimics, the original STL file
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that you have loaded will NOT be changed. Only the STL file that is saved in your Mimics project is altered.
Remeshing Protocol Below you can find a basic remeshing protocol. These are the steps that are normally taken to make sure the mesh is optimal for FEA purposes. The different parameters for each step are dependant on each dataset and won't be given in this basic protocol, but an example of the application of this protocol can be found in Tutorial Case 8. STEP A: Check if the 3D object doesn’t have thin walls or structures that will be hard to model but are of no
importance for your FE Analysis. Removing these structures in the remesher is possible but can be time consuming. Therefore it can be easier to return to Mimics and make the changes in the mask. STEP B: Depending on the parameters you’ve selected for 3D calculation, the resulting 3D object may include too
much detail. As a first step you can do a defeaturing on the 3D object therefore select the smoothing
button.
STEP B: Start with normal triangle reduction with a large angle value. Sometimes iterating between point- and
edge-based reduction decreases the number of triangles even further. STEP C: Check the size of the triangles. Therefore select from the inspection dropdown box smallest edge
length. In the quality histogram, activate the inspection parameter and check the mean value of the smallest edge length! Do exactly the same for the largest edge length. Remember or write down these values. STEP D: When you notice in the inspection diagram that there are still too much small triangles. You can filter
them out with the small triangles filter
.
STEP E: After you’ve reduced the amount of triangles you can optimize your mesh with the Split-based automatic
remeshing . First select the desired quality parameter from the quality metric dropdown box. Typically for FE analysis the Height/Based (N) parameter is used, for CFD the Skewness (N) parameter is used. With the SplitBased automatic remeshing a quality threshold of 0.3 to 0.4 can be achieved. To make sure to attain this result, select a min and max edge length that do not differ more then a factor 5. The min edge length should be around the mean value of the smallest edge length inspection parameter STEP F: You can now reduce the amount of triangles preserving the achieved quality with the Quality preserving
triangle reduction
.
STEP G: In some cases there are still some low-quality triangles left at this point (you should not have started any
local operations already). They are usually removed by another call to the split-based algorithm (with larger geometric error as before). STEP H: If low-quality triangles still persist, use local operations to fix them. STEP I: Make the mesh more uniform by doing several calls to the quality-preserving triangle reduction with
increasing geometric error. Stop when both the mesh looks uniform enough and the total number of triangles is small enough. STEP J: Call the self-intersection test and fix them by deleting the appropriate triangles and filling the resulting
hole. STEP K: If small triangles persist and you do not want to increase the geometric error any further, use the
grouping around 'smallest edge length' to collapse them manually. STEP L: Check and remove sharp geometry using the sharp geometry measures (sharp geometry, peaks,
shafts). You can do this step based on intuition or on the feedback from the created volume mesh quality from your FEA-preprocessor. STEP M: If needed you can control the growth of your triangles with the Smooth Size Transition tool. STEP N: If steps G, H and/or I introduced low-quality triangles call the split-based algorithm again. STEP O: Go on to your preprocessor to generate the volume mesh and to the real FEA-analysis. If the volume
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mesh is inadequate return to step I.
Quality Quality of th e mesh There are different ways to express the quality of a mesh. They all relate to the form of the triangles that constitute the mesh. The quality measurements are based on the properties that describe a triangle: base, length, height, ascribed circle, inscribed circle, angle magnitude. A perfect mesh would consist of triangles that are all equilateral (each side has the same length and the 3 angles are 60 degrees).
Quality parameters You select the quality measure you would like to use to evaluate the mesh quality of the part in the drop down menu in the iconbar, which is positioned under the main menubar. All parameters can be used to be optimized in the automatic remesh operations R-in/R-out (Normalized)
This parameter is the ratio of twice the radius of the inscribed circle to the radius of the ascribed circle of the triangle. The value is normalized with the factor 2 so that for an equilateral triangle it is equal to 1. This is also a dimensionless unit that lies between 0 and 1. Height/Base (Normalized)
This parameter is the ratio of the height of the triangle and the length of its base multiplied with sin 60 . The value is normalized with the factor sin 60 so that for an equilateral triangle it is equal to 1. As base the largest edge is taken. It is a dimensionless unit that lies between 0 and 1. Height/Base (Absolute)
This parameter is the ratio of the height of the triangle and the length of its base. It is not normalized, so the minimum value is 0, and the maximum value (for an equilateral triangle) is sin 60 . Skewness (Normalized)
The skewness of a triangle is defined as the ratio of its area and the area of an equilateral triangle with the same ascribed circle. For an equilateral triangle this value is equal to 1. It is a dimensionless unit that lies between 0 and 1. Smallest angle (Normalized)
The normalized smallest angle parameter equals the smallest angle of a triangle, divided by 60, so that its value lies between 0 and 1. Largest angle (Normalized)
The normalized largest angle parameter is a scaled value of the largest angle, so that its value lies between 0 and 1, with 1 representing an equilateral triangle. Largest angle (Normalized) = (180 - Largest Angle)/120. Smallest angle (Absolute)
This parameter classifies the triangles based on their smallest angle. The magnitude of the smallest angle of a triangle lies between 0 and 60. An gl e rat io (Normal ized )
The angle ratio is defined as the ratio of the smallest angle to the largest angle. The value lies between 0 and 1. Edge ratio (Normalized)
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The edge ratio is defined as the ratio of the length of the smallest edge to the length of the largest edge. The value lies between o and 1. Equi-angle skewness (Normalized)
The equi-angle skewness of a triangle is defined as the minimum of the values (smallest angle/60) and (180-the largest angle)/(180-60) Stretch (normalized)
The stretch is defined as (radius of the inscribed circle/longest edge length) * square root (12).
Inspection parameters The inspection parameters are also related to the quality of the mesh, but slightly different than the quality parameters above. It is not possible to do autormeshing with one of the following parameters as optimization criterion. The parameters below are used to inspect the mesh. This inspection can be very diverse. It can be useful to get an idea of the size of the triangles in the mesh (largest edge length), or you want to look for the bad edges in the mesh, or you probably want to check your mesh for sharp geometry (sharp, peak, shaft). For different applications, the following parameters are useful. Largest angle (Absolute)
This parameter classifies the triangles based on their largest angle. The largest angle of a triangle is always bigger than or equal to 60 and smaller than 180. Height (Absolute)
This parameter classifies the triangles based on their height, computed perpendicular on the longest edge. The height of a triangle can be 0 till any number. Smallest edge length (Absolute)
This parameter classifies the triangles based on their smallest edge length. The length of smallest edge can be 0 till any number. Largest edge length (Absolute)
This parameter classifies the triangles based on their largest edge length. The length of the largest edge can be 0 till any number. Bad Edge (Normalized)
A bad edge of a triangle is an edge of the triangle that has no triangle neighbor on this edge. It is used to group bad edges and easily identify problem areas. If there are no bad edges, all triangles will have quality measure 1. In order to be able to group bad edges, you need to set the maximum quality measure to less than 1. In fact, the quality measure a triangle for Bad edge can only have three discrete values: Bad edge = 1 (triangle has no bad edges) Bad edge = 0.67 (triangle has one bad edge) Bad edge = 0.33 (triangle has 2 bad edges) Surface smooth ness (Normalized)
This measure expresses the smoothness of the geometry. For each triangle, the normal is compared with the normals of the neighboring triangles. When the normals are similar, the result is close to 1, for triangles on edges or where the angle with neighboring triangles is large, the result is closer to 0. Non-manifold edge (Normalized)
This measure will detect when triangles have more than one neighbor over one edge. Peak (Norm alized)
A peak is in fact a special case of a sharp geometry. With Peaks, only sharp geometry of which the normals of the
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triangles are pointing away from each other, are considered. In other words, the geometry is concave. The definition is identical to sharp geometry, but when the normals are pointing towards each other, the peak is defined to be 1. In this case, the triangle is a shaft. Shaft (Normalized)
A shaft is also a special case of a sharp geometry. A shaft is a sharp geometry of which the normals of the triangles are pointing towards each other. In other words, the geometry is convex. The definition is identical to sharp geometry, but when the normals are pointing away from each other, the shaft is defined to be 1. In this case, the triangle is actually a peak. We can resume the definitions of sharp geometry, peaks and shaft in the following table. Sharp geometry (Normalized)
This measure is intended to detect sharp edges in the geometry. These sharp rims can be pointing inwards (shaft, see below) the material or pointing outwards (peak, see below) the material. The sharp geometry will detect both types of sharp edges. The definition is as follows: Sharp geometry = 1 – angle/180 degrees, where angle can range between 0 and 180 degrees. A sketch is given below.
Type Sharp
Definition =1-angle/180
Image
Always, comprises peaks and shafts
AND
Peak
= 1-angle/180
ONLY
= 1, when normals point towards each other
Shaft
=1-angle/180
ONLY
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=1 when normals point away from each other
Why can it be useful to split sharp geometry up in peaks and shafts? It can have importance when a volume mesh is generated from the surface mesh. When tetra elements are to be constructed from the triangle data, peaks can cause a problem. If the peak is too sharp, the tetra element will be “squeezed” into the peak geometry. This will create tetra elements with very poor quality. This problem is less severe for shafts. In any case, the sharp geometry inspection measures allow a fast check of the geometry. It is up to the user to determine if the geometry is good enough or whether it needs to be altered. Marked (Normalized)
The mark measure will indicate marked triangles. The value for a triangle is either 1 (unmarked) or zero (marked). The marked measure can be used to easily find small groups of marked triangles (i.e. after a self intersection test)
Growth Parameters The growth parameters focus on yet another property of the mesh: its growth. With growth we mean the transition from small to larger triangles. This can be sudden or very smooth. Mainly for creating 3D meshes, the surface mesh shouldn’t have sudden transitions from small to larger triangles. To express this growth, each triangle is compared in size with its neighbors. We use two kinds of size definitions:
Surface area
Largest edge length
The comparison happens in two steps. First of all, the smallest neighbor is selected from all the neighbors of the actual triangle. Next, the size of this triangle is compared with the actual triangle. If the smallest neighbor is still larger than the actual triangle, the growth value is 1. This means that the actual triangle is smaller than all of its neighbors. In the other case, the growth factor is the fraction of the small neighbor and the actual triangle. We could also express this mathematically:
Which triangles are considered to be neighbors? To determine the neighbors, we created the ring definition. Ring-1 means that all triangles, which are immediately connected through either a point or an edge, are considered neighbors. Ring-2 means that we look one level further. So, Ring-2 means that all immediate neighbors and their neighbors
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are considered to be neighbors of the original triangle. Ring-3 is the same as ring 2, but includes the point and edge neighbors of ring-2. The following figures illustrate the definitions.
In the section on automatic remeshing, you can find more information about how we can create meshes respecting certain growth parameters.
Part Quality Sheet (Quality histogram)
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Area-growth- 1-ring 0 1 Area-growth-2-ring 0 1 Area-growth-3-ring 0 1 Edge-growth-1-ring 0 1 Edge-growth-2-ring 0 1 Edge-growth-3-ring 0 1 Values at the left of the horizontal axis reflect a low quality (red color), values at the right reflect a high quality (green). Automatic remesh operations are only possible on the parameters in the dropdown list next ot the Q and G letter. The I parameters are used for mesh inspection purposes. Minimum and Maximum Threshold Minimum threshold: The triangles that have a quality parameter measure value below this threshold are
considered as having a low quality. The corresponding color is red. Their amount is shown in the left field below the histogram, together with the percentage they constitute of the total amount of triangles of the part. Maximum threshold : The triangles that have a quality measure value above this threshold are considered to be
of high quality. The corresponding color is green. Their amount is shown in the right field below the histogram, together with the percentage they constitute of the total amount of triangles of the part. Between minimu m and maximum: The triangles with a quality measurement parameter value that lies between
the minimum and the maximum threshold are considered to be of medium quality. Their corresponding color goes from red (low value of the quality parameter) to green (high value of the quality parameter). Their amount is shown in the field in the middle below the histogram, together with the percentage they constitute of the total amount of triangles. You can fill in a value in the fields for these two parameters or you can slide the red bar (at the left of the histogram) and the green bar (at the right of the histogram). The corresponding values will then be filled in the fields.
Visualization
Color Triangles with Low Quality
Also Menubar: Tools/Quality visualization/Color bad triangles You can color the triangles that have a quality measure value below the maximum threshold. The colors of the triangles correspond to the colors of the bars in the histogram. The triangles with the lowest quality are colored red, the ones with the highest quality green. The triangles that have a quality measure value above the maximum threshold will keep the part color. Group
Also: Menubar: Quality visualization/Group bad triangles When there are only a few low quality triangles left (e.g. after you have done an automatic remeshing,), you can search afterwards for the triangles that still have a low quality, and for example fix them manually. You can ease the search by doing a grouping operation. The part will be divided in groups that will consist out of a number of triangles. A group will contain at least one triangle that has a low quality. You determine yourself what you consider as low: when the value of the selected quality parameter of the triangle is below the maximum threshold,
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the triangle is viewed has having a bad quality, and will be accounted for in the grouping. So before you do the grouping: 1.
Determine a quality measure parameter (in the scroll down menu)
2.
Determine a maximum threshold
3.
Determine a boundary level: The grouping algorithm searches for a low quality triangle. This is the smallest group. Depending on the boundary level, triangles adjacent to the bad quality triangle are added to the group. When the boundary level is one, the triangles that have a common edge or common corner point with the low quality triangle are added to the group. When the boundary level is two, a new layer of triangles is added to the group of the low quality triangle. When the groups of two low quality triangles have a common triangle or common edges, they will be merged to one group. The amount of groups created depends thus on the amount of low quality triangles (determined by the Maximum threshold) and the boundary level.
4.
When there is more than one group, you can scroll through the groups with the help of the scroll bar. You can see how many groups there are at the right of the scroll bar. You can also show all groups by marking the checkbox.
When you change the quality parameter, the maximum threshold or the boundary level, and you would like to do a regrouping, click on the button calculate. Remark: When the renderer (Menubar/ Settings/ Preferences/ Visualization/ Colors/ Renderer) you work in is
‘software’, the program shows the wireframe of the whole part when you visualize one group. It is advised to switch to the other renderer modes when you group. Tip: Grouping works on all the parameters, not only the quality parameters. As such, grouping is a very powerful
tool to find bad edges, sharp geometry, marked triangles, etc. Mark Bad/ Mark Group / Unmark Grou p
Tools- > Mark Triangles -> Mark bad triangles. There are two marking options: marking the bad triangles, or marking the entire group. These buttons will always mark whatever is visible. For instance, if grouping is not enabled, the entire part is visible. If you click on Mark Bad, all poor quality triangles will be marked. In case you only want to mark triangles of a certain group, turn on grouping and browse to the interesting groups and mark the bad triangles. The rest of the triangles are hidden and will not be marked. For Mark group, the functionality is completely similar. Obviously, grouping needs to be enabled before mark group is possible. To unmark all triangles (visible and invisible) click on Unmark in the marking toolbar.
Automatic remeshing The automatic remesh module will remesh the part. It tries to reshape the triangles with a quality parameter value below the indicated maximal threshold, so that the resulting triangles all have a quality parameter value above the Maximum threshold. Remark: There is a limit on the quality the meshing can get:
Inspection method R-in/R-out (Normalized) Height/Base (Normalized) Height/Base (Absolute) Skewness (Normalized) Smallest angle (Normalized) Largest Angle (Normalized) Smallest angle (Absolute) Angle Ratio (Normalized) Edge Ratio (Normalized)
Maximum reachable Maximum threshold value 0.55 0.4 0.3 0.4 0.45 0.55 0.25 0.25 0.5
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Equi-angle skewness (Normalized) Stretch
0.5 0.1
Remark: Automatic remesh operations are only possible on the parameters in the dropdown list next ot the Q and
G letter. The I parameters are used for mesh inspection purposes. So before you do an automatic remeshing: 1.
Select the quality parameter you like to measure the quality of the triangles with.
2.
Determine the Maximal threshold.
3.
Choose the remesh algorithm and fill in the parameters.
Automatic remeshin g: Split -Based Menubar : Tools:/Auto Remesh/ Split Based method Icon:
The program will ask you to determine some parameters before remeshing the part.
Parameters Maximum quality threshold : You can define a maximum quality threshold value here, or in the part quality sheet
by filling in the field or sliding the green bar. During the remeshing, the algorithm tries to make triangles that all have a quality above the maximum threshold value Maximum geometry error: This is the maximum allowable deviation between the part’s surface before and after
the automatic remeshing. Remark: In the settings (Menubar/ Settings/ Preferences/ General/ Remeshing) you can define the following parameter: Geometry-quality weight ratio: During remeshing a geometric error may be introduced (the difference between the surface before and after the remeshing). It may be that high quality triangles can be made, at the expense of the geometry. Here you determine how much attention the algorithm should spend on the two of them relatively. Minimal edge length: This parameter sets a limit on the length of the edges of the triangles that will be created
during remeshing Number of iteration: The amount of times the program will try to make the triangles of better quality. Number of move iterations: This is a post-processing step in addition to the split-based algorithm, which further
optimizes the mesh quality. If you fill in a value bigger than zero, the post-processing will be activated. Typically, we recommend using values in between 2 and 5. Higher values tend to make the calculations longer and lower values have little effect. If you fill in 0, the post-processing step is deactivated. Max edge length: The maximum edge length will limit the longest edge of the generated triangles. Preserve initial mesh qu ality: The refiner algorithm starts with a reduce triangle operation. This operation often
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introduces long thing triangles and in general triangles that are far from equilateral. When you start the remesh operation on a file that already has a fairly well mesh, it is advised to skip the reduce step of this algorithm. Local: It is possible to mesh in local areas. When checked, the remesh algorithm is applied to the marked
triangles
Automatic remeshin g: Growth f actor Once the split based remesh is done, it can happen that the growth of the triangles is too big. This can cause problems when generating a 3D mesh from the surface mesh. To smooth the transitions from small to large triangles, the remesh based on growth factor can be used. The best results can be expected from the 2-, or 3-ring algorithms, as they look further for neighbors compared to the 1-ring algorithms. This has the effect that the growth is smoother over a longer distance. The program will ask you to determine some parameters before remeshing the part
Maximum quality threshold : You can define a maximum quality threshold value here, or in the part quality sheet
by filling in the field or sliding the green bar. During the remeshing, the algorithm tries to make triangles that all have a quality above the maximum threshold value Growth threshold: This threshold value determines which triangles need to be improved and until where the
algorithm will control the growth. Number of iterations: The amount of times the program will try to make the triangles of better quality. Maximum geometry error: This is the maximum allowable deviation between the part’s surface before and after
the automatic remeshing. Minimal edge length: This parameter sets a limit on the length of the edges of the triangles that will be created
during remeshing Max edge length: The maximum edge length will limit the longest edge of the generated triangles. Local: It is possible to mesh in local areas. When checked, the remesh algorithm is applied to the marked
triangles The effect of the growth algorithm is shown in the figures below.
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Automatic rem eshin g: Optim ize-Based Menubar : Tools:/Auto Remesh/ Optimise- Based method
The program will ask you to determine some parameters before remeshing the part.
Parameters Maximum quality threshold : You can define a maximum quality threshold value here, or in the part quality sheet
by filling in the field or sliding the green bar. During the remeshing, the algorithm tries to make triangles that all have a quality above the maximum threshold value. Maximum geometrical error: This is the maximum allowable deviation between the part’s surface before and
after the automatic remeshing. Remark: In the settings (Menubar/Settings/Preferences) you can define the following parameter: Geometry-
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quality weight ratio: During remeshing a geometric error may be introduced (the difference between the surface
before and after the remeshing). It may be that high quality triangles can be made, at the expense of the geometry. Here you determine how much attention the algorithm should spend on the two of them relatively. Subdivision strength : This parameter limits the quantity of triangles that will be subdivided during remeshing.
The closer the value is to 1, the more triangles will be considered. Number of optimizations : The number of iterations after each subdivision during which produced triangles will
be optimized. Max edge length: The maximum edge length will limit the longest edge of the generated triangles. Skip bad edges: When you mark this box, the algorithm will not take into account the bad edges. This will speed
up the process. Use post proc essing: After the optimization scheme, the algorithm will attempt to improve the remaining low
quality triangles using a post-processing subdivision scheme. This results in less low quality triangles especially for moderate to medium maximum quality thresholds.
Triangle reduction Normal Triangle reduction Menubar: Tools/Automatic Remeshing/ Triangle reduction/Normal Icon: Description: You can reduce the number of triangles in an STL file.
You can reduce the triangles of the whole part, or only a selected portion.
The reduce mode The Point-type reductio n: This mode will try to reduce the amount of triangles by removing a point. The Edge-type: This mode will remove a triangles edge (two points + the connecting line between these two
points). Local: When Local is set, only the marked triangles will be reduced. Some neighboring triangles can be changed. Parameters Tolerance: If 2 triangles are replaced by one triangle, it may be that there is a little deviation in position. The
tolerance indicates the maximum deviation allowed between the original surface and the new one. Number of iterations: This defines how many times the program should make the calculations. Doing a triangle reduction twice with the same Number of Iterations value gives the same result as doing it once with the Number of Iterations value doubled. The angle: The Angle-value defines two limits:
1.
When two triangles have an angle value bigger than Angle, they may not be reduced, the edge between
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them may not be eliminated. Otherwise too much geometrical information would be lost. When the program meets such an edge, the reduction will keep the edge but reduce the number of points on the edge. 2.
When there is no critical edge, this Angle-value determines the maximum angle that can be created during the reduction. This means: where there is an edge there will remain one. Where there is no edge, no edge will be added.
Remark: Because of the previous remark it is advisable not to use the reducer on very noisy objects. In this case
it is better to perform a smoothing first. Remark: If the tolerance and angle values are too big, essential part information may get lost.
Quality Preserving tri angle reducti on Menubar: Tools/Automatic Remeshing/ Triangle reduction/Quality Preserving Icon: Description: This reducing algorithm will reduce the amount of triangles, but will not create triangles that will have
a value of the selected quality measurement below the indicated maximum threshold.
Quality threshold: This value indicates the level below which no new triangles will be created. Number of iterations: This defines how many times the program should make the calculations. Doing a triangle reduction twice with the same Number of Iterations value gives the same result as doing it once with the Number of Iterations value doubled. Maximum g eometric error: This is the same as Tolerance: If 2 triangles are replaced by one triangle; it may be
that there is a little deviation in position. The tolerance indicates the maximum deviation allowed between the original surface and the new one. Max edge length: The maximum edge length will limit the longest edge of the generated triangles. Skip Bad edges: The remesher will not take into account the bad edges. This will speed up the process.
Filter Sharp tr iangles Icon:
When the part has long thin triangles, this filter will remove the sharp triangles.
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Filter : Triangles thinner as this distance will be marked or deleted, depending on your choice. An gl e: The thin triangle will only be selected when the angle it makes with its neighbors is bigger as the given
angle. This is easy to filter only thin triangles of folds and leave thin triangles of curves untouched. Collapse: The selected triangles will be collapsed, which re-arranges slightly the surrounding triangles to close
the gaps. Delete triangles: The selected triangles are deleted. The surrounding triangles are not modified. Mark: The selected triangles are only marked.
Detect self-intersectio ns When pressing the button , the model will be checked for self-intersecting triangles. The intersecting triangles will be marked and can then be removed manually. Note: Sometimes sharp edges can also cause problems when generating a 3D mesh. These areas are not real
intersections and are not detected with this function. To detect sharp areas in a part, use the sharp geometry inspection measure.
Smoothing Menu: Tools – Smoothing Description:
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General Options Global/Local: Global will smooth the whole part. Local will smooth only the selected triangles. Smooth Factor: We will explain this factor with the figure below. The figure shows eight triangles with one
common point in the center.
The algorithm changes the position of this center point according to the positions of the eight other points. The importance of the other points can be raised or lowered by adjusting the Ratio-parameter. If this Ratio is low (0.01) the new position is mainly dependent on the old position of the point. If this ratio is 1, the dependency is spread over the points. The new position is still 50% dependent on the old position. With high values for the ratio, the new position is mainly determined by the position of the other points of the triangles. In this last case it is obvious that we talk about smoothing. This algorithm is exercised on every point of the part. Shrinkage compensation factor: The smoothing algorithm has the side effect that the part is shrinking. This
factor will compensate this. This compensation step is similar to the first one except that the parameter has a negative sign - this means that point is actually moved in opposite direction (out of "smooth" position), so points "oscillate " forwards and backwards. Iterations: The remesher will perform the smoothing multiple times Ad van ced Opt io ns Av oi d i nv ert ed t ri ang les : To avoid the creation of flipped triangles, the movement of the points will be aborted
when the angle between the normals of the neighboring triangles is bigger as the given angle. Skip Bad Edges: When the point is at a bad edge, the point won't be moved. Use Curvature Smoothing: Curvature smoothing tries to choose the new position for points based solely on
geometry Remark: Be careful. When using too high values for these parameters, the shape of your part could disappear.
Manual Remeshing
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You can remesh manually which allows you to perform a number of local remesh operations on a selected number of triangles of the part. Depending on the operation, one, two or more triangles are involved. The process can be followed with the triangles quality toolsheet.
The triangles quality sh eet Menu: View/ Triangles Quality sheet Icon:
Geometrical error
Due to the remeshing operation a geometrical error may be introduced. Before you do the operation, the remesher will show you the error that will be introduced. Based on this value you can decide whether or not to perform the operation. In the Settings (see Menubar/Settings/Preferences/ General/ Remeshing), you can enter a threshold value. A geometric error above this threshold will be displayed in red and so attract your attention, and a warning will be given. Triangle Quality Quality before: Depending on the manual operation, a number of triangles will be selected that will undergo the
remeshing operation. This column shows you the value of the selected quality measure of these selected triangles before the operation is performed. Quality after: Depending on the manual operation, a number of triangles will be selected that will undergo the
remeshing operation. This column shows you the value of the selected quality measure of these selected triangles before the operation is performed. Delta: This column shows the difference of the values displayed in the quality after and the quality before
columns. If the qualities measure value of a triangle after the remeshing operation is less than before, the delta value will have a negative sign. The quality thus diminished. Av erag e (bef or e/aft er/d elt a): This row shows the average value of the quality measure of the selected triangles
(before the operation) and the resulting triangles (after the remeshing operation is performed). The delta value expresses the difference (after-before). Minimum (before/after/delta): The lowest quality measure value of all the selected triangles (before the
operation) and resulting triangles (after the operation) is shown. The delta value expresses the difference (afterbefore). Af fec ted Triang le L is t
When you want to perform a manual operation, the remesher will always show you when you point your mouse to
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the triangle or edge you want to adapt, the triangles that will be involved in the operation, and will outline in green the edges of the triangles that will result. In the Triangles quality sheet you can see the value of the selected quality parameter of the present triangles that will be involved in the operation, and the value of the triangles that will be formed when the operation should be done. When there are many triangles involved, you will not see all the values of the quality measurements in the list, because it is too short and you need to scroll. Press and hold down the control button, and you can move the mouse pointer to the scroll bar of the list and scroll.
The manual remeshing tools Menu: Tools/Manual remeshing Menu: View/Remesh Toolbar/Icons or
. The toolbar is positioned at the left of the screen at start up.
Measure single triangle quality If you click on this icon and point to a triangle the value of the selected quality measure will be shown in the Triangle Quality Sheet. Flip edge
When you point your mouse to an edge, the remesher will color the two adjacent triangles and show the flipped edge in green. The edges of the triangles that will be there after the operation are shown in green. When you click, the edge will be flipped. Collapse edge
When a triangle has one very short edge and a long height it is a very long thin triangle (we call it a needle). These kinds of triangles can be removed with the collapse edge tool. The triangles, which have the short edge as border will disappear because the remesher brings the two end points of the edge together in a new point which is positioned on the edge. The corner points of the triangles, that had these end points as corner, will move to the new point. When you point to a short edge, the remesher shows the present triangles in a white dotted line and colors them, and the edges of the ones that will be there after the operation in green. The point where the edge end points collapse is shown in red. When you click, the edge will collapse. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled. Collapse triangle
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Very small triangles can be removed with the collapse triangle tool. The corner points of the triangle will be collapsed to a point inside the triangle. The edges of the triangles adjacent to the triangle that is removed, and that had the corner points of the removed triangle as one of the end points, will be moved a bit, and all have the new point as an end point. If you point to a triangle, The remesher will show the new point in red, and the edges of the triangles that are influenced under the operation in green. When you click, the triangle will collapse. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled. Cap collapse
Triangles that have a very long base and small height (we call it a cap) are far from being equilateral. These triangles can be removed with the collapse cap tool. In the cap corner point (see figure above) ends an edge of a triangle adjacent to the cap. The other corner point of the edge will be projected perpendicular on the edge opposite of the cap corner point. This point will be a new corner point. When you point the mouse to a cap, the remesher will show the new corner point in red, and the edges of the triangles that result after the operation in green. When you click, the cap will be collapsed. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled.
Cap split (propagating)
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Triangles that have a very long base and small height (we call it a cap) are far from being equilateral. These triangles can be split in two with the cap split propagating tool. When you point your mouse to a cap, the remesher will split it in two. The new edge will end on the edge opposite the cap corner point (see figure). The triangle that has this edge as border, will also be split. This way, a cap is converted into two needles. When the new created triangle is also a cap (decided if the angle of the cap corner point is very big), the operation will proceed. When you point the mouse to a cap, the edges of the triangles that will be formed after the operation are shown in green. When you click, the cap(s) will be split. This operation introduces no geometrical error. Subdivide one triangle
It is possible to subdivide one triangle in more triangles. The remesher will create two or three new corner points on two or three – respectively- edges of the selected triangle. The remesher will color all the triangles involved and will show the edges of the triangles that will be formed after the operation in green. When you click, the triangle will be subdivided. This operation introduces no geometrical error. Add new point in triangle
You can add a point, and thus so subdivide a triangle in 3 triangles.
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When you point the mouse to a triangle, the remesher will show the edges of the triangles that will be formed after the operation in green. The cross point of these edges is shown in red. When you click, the triangle will be subdivided. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled. This operation introduces no geometrical error. Add point on edge
You can select an edge. The remesher will then create a new corner point on that edge. The triangles adjacent to that will both be divided in two. When you point the mouse to an edge the remesher shows the new edges in green lines, and the new corner point in red. When you click the mouse button, the operation will be done. It is possible to move the red point (before you do the operation) by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled. This operation does not introduce a geometrical error. Move point
You can point the mouse to a corner point and drag the point to a new place. The adjacent triangles will deform. When you point to a point, the program will show it in red. It is possible to move the red point by keeping the control button pushed together with the left mouse button. If you then release the mouse button, the operation will be done. If you release the ctrl button first, the operation is canceled. Create straight edge
You can click on two corner points of two different triangles one after another. The remesher will draw a line between those two points, and divide all the triangles this lines runs through, so that the line can be formed by edges of newly created triangles. This operation does not introduce a geometrical error.
Material Assignment
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You can assign materials to FEA meshes via the FEA menu or the FEA mesh tab. Before you can assign materials to the elements of the volumetric mesh, Mimics will first calculate a gray value for each element. This gray value will then be used in further calculations. Mimics uses an accurate method to assign gray values to elements by calculating exact intersections between voxels. While being accurate, care has been taken that the calculations can be performed efficiently. The gray value assignment is stored in the Mimics project file, so the gray value calculation only needs to take place once for each volume mesh in a Mimics project, no matter how many different material assignments are exported. After the calculation of the gray values of the elements of the volumetric mesh, the material assignment window will appear:
In the Elements Histogram, Mimics will show for each grayvalue the amount of elements that were assigned that particular value. After the grey value calculation, each element has its own gray value based on the image data set. Two methods can be used to convert this gray value into material properties: Uniform Method and Look-up File Method. A first step that is taken for both methods is discretization: the range of all gray values is subdivided into intervals. How this discretization is done depends on the chosen method. The third option to create materials is the Mask method. During the calculation of the grayvalue of each element, also the volume of intersection with the different masks in the project is calculated. Each element is assigned to one mask based on this volume of intersection. For each material the properties can then be defined in the material editor.
Material assignment method Uniform method In the uniform method, the discretization of the gray values is done by dividing the range of gray values that occur in the volume mesh into a specified number of equal sized intervals that each represent a material. The center
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gray value of each interval is chosen as a representative for that interval. After you have entered the amount of materials in the edit box, you can preview the material assignment by clicking on the Preview button. The color of the elements will be determined according to following color scale:
Look-up File Method Method For this method a look-up file is specified that indicates which intervals are used to divide the range of gray values (look-up files can also be expressed in Hounsfield units). Each interval can be assigned a specific density value. A lookup file can be chosen by clicking on the Load button. It is possible to call the default viewer or editor for the specified look-up file by clicking on the Open with button. After you selected the correct look-up file, you can preview the material assignment by clicking on the Preview button. The color of the elements will be determined according to following color scale:
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The format of the lookup table is very simple. The first line specifies the xml format of the file. In the header of the xml file, the version of the file can be specified (1.0 for the moment). Ranges of grayvalues are specified by their first boundary in the Start tag. The Density tag specifies the density that should be associated with the material. Example:
0.0e0 < Density> 0.0e0 < /Interval> 3.0e2 < Density> 3.0e2 < /Interval> 6.0e2 < Density> 6.0e2 < /Interval>
This Lookup file specifies 3 materials: 1.
Material 1 contains all elements with HU (Hounsfield Unit) between 0 and 300. That material is assigned a density of 0
2.
Material 2 contains all elements with HU between 300 and 600. That material is assigned a density of 300
3.
Material 3 contains all elements with HU between 600 and 3071. (HU is maximal 3071). That material is assigned a density of 600
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Note: You can choose between "Hounsfield" or "Grayvalue" as the Unit type.
Mask Method By using the material assignment from mask, you can use the segmentation in your project to assign materials to your elements. For each used mask, one material will be created. For each element one of the materials is assigned based on the volume of intersection of that element with each mask. If there are elements in the volume mesh that fall completely outside the selected masks, one extra material is created for those elements. If an element has the same intersection volume with several masks, the first mask in the list is used for assigning a material to that element. When choosing the mask method, click on the Select button to select which masks you want to use:
After this you can see the assignment of the materials in the histogram:
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Note: if you change one of the masks after doing the grayvalue calculation and choose to do a material
assignment from masks, Mimics will have to calculate the grayvalues again.
Material Ma terial Expressio ns Density De nsity Expression The density expression can be used for translating the grayvalue of an element to a density when using the uniform method. To do this, an empirical expression of the form A+B*X^C+D*X^E A+B*X^C+D*X^E can be entered to convert the gray value into a density value. This method can also be used to export gray values: if 0+1*X^1 + 0*X^1 is used as a density expression, the representatives of each interval are written out as densities. Note: For the look-up method, the density for each material is taken from the look-up file. For the mask method
you have to enter the density for each material yourself in the material editor.
E-Modulus EModulus expression Based on the density value, an expression can be entered to define the e-modulus for each material. The entered expression will only be used if the checkmark is enabled. If there is no density value available for a certain element, the e-modulus value will also remain empty.
Poisson expression Based on the density value, an expression can be entered to define the poisson coefficient for each material. The entered expression will only be used if the checkmark is enabled. If there is no density value available for a
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certain element, the poisson coefficient value will also remain empty.
Material Editor The assigned materials and their properties can be displayed and adjusted in the material editor. You can change the value of one of the fields by right-clicking twice on the value. You can also adjust multiple values at the same time by selecting them and filling in a new value. Fields that are empty in the material editor will either not be exported or will receive a value of 0 depending on the export format.
The color of each material can be changed by double-clicking on the color box:
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Note: about units (Hounsfield units/Gray values): Hounsfield units are the unit image data that comes from
medical scanning devices. Gray values is the unit that is used internally in Mimics. Both units relate as value in GV = value in HU + 1024. Mimics has a preference setting to select which unit is used in the user interface (Options -> Preferences -> General -> Pixel Unit). Warning: the current unit is also used for the density expression. Note: most FEA softwares do not allow you to enter a density with a negative value, so make sure you choose
your expression accordingly or adjust a djust the values manually in the material editor.
Usin sing g Mim Mimics ics wit with h Pa Patr tra an Export a surface file to Patran Patran After you have calculated a surface mesh and remeshed it to make it suitable for FEA purposes, you can export this surface mesh to an Patran neutral file. To do this, go to the Export menu and choose Patran. This will open following interface:
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You can export a 3D Object or an STL file to an Patran neutral file, by adding the object to the list, choosing the Neutral File format and clicking on the OK button.
Convert a sur surface face mesh to a volumetri c mesh This surface mesh can be imported in Patran by going to the File menu and choosing “Import”. This will open following dialog:
Make sure you use the same settings as above. After the import of the mesh, choose the Elements button in the toolbar and choose to create a solid mesh. Choose to create a Tetmesh with Tet4 or Tet10 elements. Have a look at the settings below how to do this:
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Next, choose to select triangles and select all triangles in the mesh. After clicking on the Ap pl y button, a volume mesh will be generated.
You can export this volume mesh by going to the File menu and choosing Export.
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Import the Patran volume mesh You can import a Patran neutral file by clicking on the Import button
in the FEA project management tab:
This will open a file chooser:
Change the type of the listed files to Patran Neutral if needed and all Patran files will be shown. Then browse to the directory where the files are located, select the correct file and click on the Open button, the files will be imported.
Support ed element types The Mimics FEA module supports four types of Patran elements:
5 (4-node tetrahedron)
7 (6-node wedge)
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8 (8-node hexahedron)
5 (10-node quadratic tetrahedron)
If you require other elements types, please let us know and we will try implement those elements in our future releases.
Supported Patran packets The Mimics FEA module supports 6 Patran packets:
25 (File title)
26 (Summary data)
1 (Node data)
2 (Element data)
3 (Material properties, export only)
4 (Element properties, export only)
Material properties: Patran writes out 96 material properties. Mimics assigns only 7 of them, the others are set to 0. Exported material properties: 2 (density), 27-29 (E-modulus), 30-32 (Poisson coefficient). For E-modulus and Poisson coefficient all three properties contain the same value.
Using Mimics with ABAQUS Export an ABAQUS surface mesh You can import an ABAQUS surface mesh by going to the Export menu and choosing the ABAQUS format. In the following interface you can then add 3D Objects or STLs and export them to ABAQUS surface meshes.
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Convert the surface mesh to a volu me mesh Import th e surface mesh In ABAQUS/CAE, go to File->Import->Model. Browse to the directory where you have saved the model and select to import it.
Depending on the version of ABAQUS you have choose one of the following workflows:
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Conversion in ABAQUS 6.4: Switch to the Part Module and choose to Edit the Mesh.
This will open following dialog:
After choosing the Conversion of Tri to tet, click on OK and the surface mesh will be converted to a volume mesh.
Conversi on in ABAQUS 6.5 In ABAQUS 6.5 you should go to the Mesh module, choose the Mesh menu and the Edit ... option. Then again choose to convert your mesh from tri to tet.
Export a volum e mesh After the conversion of the mesh you can export your volume mesh by going to the Job Module and choose to Create a Job.
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After choosing a name for your Job and choosing the correct model, click on Continue.
This will open following dialog:
Choose to use the default settings and click on OK. After this a Job is created for your model. Then you can go to the Job menu and choose the Write Input option to export an .inp file. This .inp file should be imported again into Mimics.
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Import the ABAQUS volume mesh in Mimics You can import an ABAQUS volume mesh by clicking on the Import button tab:
in the FEA project management
This will open a file chooser:
Change the type of the listed files from Patran Neutral to ABAQUS File and all ABAQUS files will be shown. Then browse to the directory where the files are located, select the correct file and click on the Open button, the files will be imported.
The ABAQUS file There are some limitations for the format of the ABAQUS file. The structure of the file should be:
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* HEADI NG
*NODE 1, 432.3656005859375, -245.597900390625, 54.94200134277344 2, 347.5975952148438, -158.1038970947266, 4.51170015335083 …
*ELEMENT, elset=region0, type=C3D4 474604, 14874, 14869, 14873, 14872 474605, 14874, 14868, 14870, 14869 …
Three important rules to follow are:
The commands *HEADING, *NODE and *ELEMENT should be written in capitals.
The commands *HEADING and *NODE should not have any text or spaces behind them.
There should be an empty line between the *HEADING section and the *NODE command and between the *NODE section and the *ELEMENT command and after the *ELEMENT section.
Supported element types The Mimics FEA module supports four types of ABAQUS elements:
C3D4 (4-node linear tetrahedron)
C3D6 (6-node linear triangular prism)
C3D8 (8-node linear brick)
C3D10 (10-node quadratic tetrahedron)
If you require other elements types, please let us know and we will try implement those elements in our future releases.
Supported ABAQUS commands The Mimics FEA module supports 5 ABAQUS commands:
*HEADING
*NODE
*ELEMENT
*SOLID SECTION
*MATERIAL
The *SOLID SECTION and the *MATERIAL command are only used during export and are ignored during import. The *ELEMENT command: *ELEMENT, TYPE=, ELSET= The *SOLID SECTION command: *SOLID SECTION, ELSET=, MATERIAL= The *MATERIAL command:
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*MATERIAL, NAME= *DENSITY *ELASTIC ,
Using Mimics with Ansys Export a surface file to An sys After you have calculated a surface mesh and remeshed it to make it suitable for FEA purposes, you can export this surface mesh to an Ansys file. To do this, go to the Export menu and choose Ansys. This will open following interface:
Mimics can export your remeshed 3D object to Ansys as an Area-based or an Element-based file Area-based: Each triangle is exported as a separate face into the ansys-file. Importing this file in Ansys will result in a remeshing of the file, and will loose the original triangulation. Element-based: The part is exported as a mesh, having triangles as elements. To generate the volume mesh in Ansys, the FVMESH command should be used. We advice you to use the Element-based export as this will preserve the obtained quality of the mesh. To export add the object to the list, choose the appropriate Ansys File format and click on the OK button.
Convert a surface mesh to a volumetric mesh in An sys This surface mesh can be imported in Ansys by going to the File menu in Ansys and choosing “Read Input From”.
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Convert an Area Based sur face mesh to a volumetric mesh First select an element type to which you want to assign the surface mesh. You can do this with the ET command e.g. ET,1,SHELL93. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a surface element type. To mesh the areas to elements, go to Main Menu > Preprocessor > Meshing > MeshTool. In the MeshTool check smart size and put it to coarse. Select as mesh Areas and as Shape Tri and free.
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To release all associations between the current solid model and finite element model, execute the command, MODMSH,detach. Add a solid element type to generate your volumetric mesh, you can do this with the ET command e.g. ET,2,SOLID92. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a solid element type. If you want to load your volume mesh back into Mimics for material assignment you should use one of the following element types: SOLID72 (linear tetrahedron) SOLID92 (quadratic tetrahedron) If you require other elements types, please let us know and we will try to implement those elements in our future releases. To generate the volume mesh you should use the command FVMesh or you can execute this command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area Elements.
Convert an Element Based sur face mesh to a volum etric mesh In Ansys select File | Read input from and load the file
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The surface element type is Shell93 by default. Note: If desired you can change the surface element type with the command ET, ITYPE, Ename, KOP1, KOP2, KOP3, KOP4, KOP5, KOP6, INOPR (e.g. et,1,Mesh200) Add a solid element type to generate your volumetric mesh, you can a gain do this with the ET command e.g. ET,2,SOLID92. Or in the main menu select Preprocessor | Element type | Add/Edit/delete and add a solid element type. If you want to load your volume mesh back into Mimics for material assignment you should use one of the following element types: SOLID72 (linear tetrahedron) SOLID92 (quadratic tetrahedron) If you require other elements types, please let us know and we will try implement those elements in our future releases. To generate the volume mesh you should use the command FVMesh or you can execute this command from the main menu Preprocessor | Meshing | Mesh | Tet Mesh From | Area Elements.
Import Ansys fi les in Mimics As stated in the Mimics help file, the Mimics Ansys importer needs three different ASCII files as input. These three files are the PREP7 file, a file with a list of the elements and a file with a list of the nodes. More information about these three files can be found further in this document. Mimics requires the user to import only the PREP7 file: Mimics will use the references to the two other files in the PREP7 file. To import the PREP7 file, click on the Import button in the FEA project management tab:
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This will open a file chooser:
Change the type of the listed files from Patran Neutral to Ansys File and all files will be shown (Ansys files do not have a general extension). Then browse to the directory where the files are located, select the PREP7 file and click on the Open button, the files will be imported.
The PREP7 fil e The Ansys PREP7 file contains references to the nodes and elements files and material property definitions. An example of such a file (without material properties) can be found below: /PREP7 ET,2,SOLID92 NRRANG,1,26407,1 NREAD,'AnsysTest_nodes_file',' ',' ' ERRANG,1,17317,1 EREAD,'AnsysTest_elements_file',' ',' '
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This PREP7 file should be created manually. The easiest way is to copy the text to a new file and adapt it to your needs. /PREP7
This command indicates to Mimics that the file is a PREP7 file ET,2,SOLID92
The first parameter (2) is the local element type and depends on your Ansys project. The second parameter (SOLID92) is the type of the elements that is used in the mesh NRRANG,1,26407,1
The first parameter (1) is the index of the first node and will be 1 in most cases. The second parameter (26407) should be equal to the maximum node number. The third parameter (1) is the increment of the indices of the nodes and will be 1 in most cases. These parameters can be derived from the Node status. The node status dialog is evoked by executing the following commands: NODES STAT
The nodes status lists the maximum node number and the number of nodes defined. The index of the first node is equal to the maximum node number minus the number of nodes defined plus 1. (index of first node =maximum node number - number of nodes defined + 1) NREAD,'Ansys Test_nodes_file',' ',' '
The first parameter (AnsysTest_nodes_file) is the filename of the nodes file. The second parameter ( ) is the extension of the file (we suggest not to use an extension). The third parameter ( ) is the directory the file was written out to (we suggest to not use a directory) ERRANG,1, 17317,1
The first parameter (1) is the index of the first node and will be 1 in most cases. The second parameter (17317) should be equal to the maximum element number. The third parameter (1) is the increment of the indices of the elements and will be 1 in most cases. These parameters can be derived from the element status. The element status dialog is evoked by executing the following commands: ELEM STAT
The element status lists the maximum element number and the number of elements defined. The index of the first node is equal to the maximum element number minus the number of elements defined plus 1. (index of first element =maximum element number - number of elements defined + 1) EREAD,'Ansys Test_elements_fi le',' ',' '
The first parameter (AnsysTest_elements_file) is the filename of the elements file. The second parameter ( ) is the extension of the file (we suggest not to use an extension). The third parameter ( ) is the directory the file was written out to (we suggest to not use a directory)
The nodes file The nodes file contains the coordinates for all nodes. The file can be written out in Ansys by going to: Main Menu > Preprocessor > Modeling > Create > Nodes > Write Node File. You can also write out the nodes file with following command: NWRITE, Fname, Ext, Dir, KAPPND With parameters:
Fname: File name (32 characters maximum)
Ext: File name extension (8 characters maximum)
Dir: Directory name (64 characters maximum)
KAPPND: Append key:
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o
0 - Rewind file before the write operation
o
1 - Append data to the end of the existing file
Note: We suggest to write out the nodes file without an extension.
The elements file The elements file contains the definitions for all elements. It’s strongly advised to write out the elements file in the LONG format. The file should be written out with following command: EWRITE, Fname, Ext, Dir, KAPPND, Format With parameters:
Fname: File name (32 characters maximum)
Ext: File name extension (8 characters maximum)
Dir: Directory name (64 characters maximum)
KAPPND: Append key:
o
0 - Rewind file before the write operation
o
1 - Append data to the end of the existing file
Format: Format key: o
SHORT - I6 format (the default)
o
LONG1 - I8 format
Note: We suggest to write out the elements file without an extension. Note: We suggest to write out the elements file in the LONG format. If you have more than 99.999 nodes, you have to write out in the LONG format or Mimics will refuse to import the files.
Support ed element types The Mimics FEA module supports two types of elements:
SOLID72 (linear tetrahedron)
SOLID92 (quadratic tetrahedron)
If you require other elements types, please let us know and we will try implement those elements in our future releases.
Supported material properties The Mimics FEA module supports three types of material properties:
DENS (Density)
EX (E-Modulus)
PRXY (Poisson coefficient)
Supported PREP7 commands
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The Mimics FEA module supports 6 PREP7 commands:
ET
MP
NRRANG
NREAD
ERRANG
EREAD
The ET command: ET,, The NRRANG/ERRANG commands: NRRANG,,, The NREAD/EREAD commands: NREAD,,, The MP command: MP,,,
Using Mimics with Simmetrix Export surface meshes from Mimics We advice to use the Abaqus file format when linking between Mimics and Simmetrix. You can export your 3D object to an Abaqus file by going to the Export menu and choosing Abaqus. This will show following dialog:
You can export a 3D object from the list by selecting it, clicking on the Add button and then clicking on the OK button.
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Change the Abaqus pattern in Simmetrix To make sure that you write out an Abaqus file in Simmetrix that can be imported in Mimics you will have to change the default Abaqus pattern file in the Simmetrix software. This pattern file will determine how an Abaqus file is written out exactly. To do this, first go to the export/case/abaqus folder in the root directory of the SimAppS folder and make a backup of the abaqus.sxp file in this folder. After this open the abaqus.sxp file in a text editor (e.g. notepad) and change the contents of the file to: sxp 0
# abaqus.sxp created 28-Jan-2004 jat # Write abaqus input file from input mesh # Use mesh node ids r equi r ed
= "mesh"
precision
= 16
showpoint
=1
mfaceNormals = "off"
# (runs faster when "off")
mregionIdOffset = 1 # Create mesh nodes mesh { nodeMessage = function:makeNodes() log:header = "$nodeMessage" } # Write first header header = "*HEADING\n" # Write mesh nodes mesh/mnodes { header = "*NODE\n" item = "$id, $x, $y, $z" } # Set element-code based on mesh degree map = "<1 'C3D4'> <2 'C3D10'>" element-code = function:mapI2S($meshDegree,$map,"C3D???") # Write element sets, 1 for each model region # For now, only support linear tetrahedra
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gmodel/gregions/* { header = "*ELEMENT, elset=region$tag, type=$element-code\n" mregions { item = "$id, $(mnodes[*]/id)" } # end context (mregions/*) } # end context (gmodel/gregions/*) # Remove mesh nodes mesh { nodeMessage = function:removeNodes() log:header = "$nodeMessage" }
Import Simmetrix fi les in Mimics Now you can start Simmetrix, import the Abaqus surface mesh from Mimics and make a volumetric mesh in Simmetrix. If you export this volumetric mesh to an Abaqus file you will be able to import this file in Mimics to assign materials to it by going to the FEA menu and choosing Import. This will open following dialog:
Browse to the directory where you have saved the Abaqus volumetric mesh, select it and click on the Open button. You can then start assigning materials to the volumetric mesh.
Using Mimics and Fluent
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To facilitate data exchange with Fluent, it is best to use the fluent mesh format. The msh file contains the triangle data from the STL file along with surface definitions. The notion of surface definitions is important and therefore the msh file contains more information than the STL file. Especially for fluid flow simulation applications, surfaces are necessary to define inlet and outlet of the flow. If only an STL is available, Gambit (Fluent’s preprocessor) will read in the STL and split the STL in surfaces according to a feature angle (comparable to our wireframe angle). As the wireframe of STLs can be noisy, especially for scanned parts, we would end up with many noise surfaces and unclosed wireframe and Gambit will not be able to recognize a volume inside the surfaces. This is where the Fluent mesh file proves its usefulness. In the fluent mesh file, we can write correct surface definitions to make sure Gambit will recognize the volume. In Mimics, we don’t have surface definitions, so we need a way to define surfaces on the STL. We use the wireframe in to do this. All triangles within a closed wireframe contour will belong to a separate surface. In the remesher, we can modify the wireframe angle in the view toolsheet to a value, which fits our needs. Typically, a fluent project contains inlet, outlet and boundary surfaces. So, we need to identify the wireframe angle, which will close the inlet and outlet surfaces. If there is some noisy wireframe on the boundary surface, we need to make sure this wireframe disappears by choosing a higher wireframe value or by altering the surface of the mesh. Note that increasing the wireframe angle will open the inlet and outlet contours at some point. If it is not possible to find the wireframe angle which still closes inlet and outlet surfaces and removes all noise wireframe, you need to inspect the noise wireframe. As long as the noise wireframe is not closed, there is no problem. If it is closed, you need to smooth the area to make sure the wireframe is either open or disappears.
Export t he object to a Fluent fil e When you have determined a good wireframe angle, you can go back to Mimics and export the file by going to the Export menu and choose Fluent. This will open following dialog:
When you click on OK, you can choose the wireframe that will be used for splitting up the surfaces in this file:
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Import t he surface mesh in Fluent You can then import this fluent file in fluent by using following parameters:
Empirical Expressions The tables below show some relationships between different density-, strength- and stiffness- related parameters.
Expressions for Trabecular/Cancellous Bone Expressions f or th e Femur - Distal Ap par ent d ensi ty
R²
Axi s
Young's mod ulus E (MPa)
R²
Sca Ref Tec
= 1.205 * HU + 139
0,77
A-P
E = 0.01 * ^ 1.79
0,93
S1
R1
T1
= 1.205 * HU + 139
0,77
A-P
E = 2.99 * - 423
0,84
S1
R1
T1
= 1.205 * HU + 139
0,77
M-L
E = 0.01 * ^ 1.82
0,91
S1
R1
T1
= 1.205 * HU + 139
0,77
M-L
E = 2.84 * - 416
0,85
S1
R1
T1
= 1.205 * HU + 139
0,77
S-I
E = 0.82 * ^ 1.27
0,95
S1
R1
T1
= 1.205 * HU + 139
0,77
S-I
E = 5.27 * - 384
0,91
S1
R1
T1
S-I
E = 0.65 * ^ 1.31 - 48
0,92
S2
R2
Young's mod ulus E (MPa)
R²
Sca Ref Tec
Expressions fo r the Femur - Proximal Ap par ent d ensi ty
R²
Axi s
= 1.067 * HU + 131
0,84
A-P
E = 0.004 * ^ 2.01
0,91
S1
R1
T1
= 1.067 * HU + 131
0,84
A-P
E = 3.91* - 657
0,90
S1
R1
T1
= 1.067 * HU + 131
0,84
M-L
E = 0.01 * ^ 1.86
0,89
S1
R1
T1
= 1.067 * HU + 131
0,84
M-L
E = 3.64 * - 506
0,89
S1
R1
T1
= 1.067 * HU + 131
0,84
S-I
E = 0.58 * ^ 1.30
0,94
S1
R1
T1
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= 1.067 * HU + 131
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S-I
E = 4.56 * - 331
0,90
S1
R1
S-I
E = 1.02 * ^ 1.22 - 56
0,95
S2
R2
P
E = 1.310 * ^ 1.4
0,91
S3
R3
S4
R4
= 1 * HU
P
E = 0.0041 * ² + 2.1142 * + 54.75
0,57
S5
R5
T3
= 1 * HU
P
E = 0.0057 * ² + 3.0586 * + 178.42
0,47
S5
R5
T3
Young's mod ulus E (MPa)
R²
Sca Ref Tec
= 0.0019 * HU + 0.105
0,84
0,60
T1 T2
Expressions f or the Humerus - Proxim al Ap par ent d ensi ty
R²
Axi s
= 0.624 * HU + 173
0,83
A-P
E = 2.22 * - 169
0,88
S1
R1
T1
= 0.624 * HU + 173
0,83
A-P
E = 0.06 * ^ 1.57
0,86
S1
R1
T1
= 0.624 * HU + 173
0,83
M-L
E = 2.50 * - 201
0,86
S1
R1
T1
= 0.624 * HU + 173
0,83
M-L
E = 0.07 * ^ 1.55
0,86
S1
R1
T1
= 0.624 * HU + 173
0,83
S-I
E = 0.32 * ^ 1.41
0,92
S1
R1
T1
= 0.624 * HU + 173
0,83
S-I
E = 4.25 * - 270
0,92
S1
R1
T1
S-I
E = 5.11 * ^ 0.97 - 301
0,92
S2
R2
Young's mod ulus E (MPa)
R²
Sca Ref Tec
Expressions f or t he Major Metaphyseal Regions Ap par ent d ensi ty
R²
Axi s
= 1 * HU
A
E = 1.3665 * - 38.644
0,79
S6
R6
T4
= 1 * HU
A-P
E = 1.6201 * - 97.448
0,68
S6
R6
T4
= 1 * HU
M-L
E = 1.0976 * - 60.822
0,43
S6
R6
T4
S-I
E = 1.3988 * + 39.069
0,58
S6
R6
T4
S6
R6
T4
= 1 * HU = 0.001141 * HU + 0.11837
0,82
Expressions f or t he Patella Ap par ent d ensi ty
R²
Axi s
Young's mod ulus E (MPa)
R²
Sca Ref Tec
Could not be measured
A-P
E = 0.005 * ^ 1.91
0,86
S1
R1
T1
Could not be measured
A-P
E = 3.37 * - 976
0,88
S1
R1
T1
Could not be measured
M-L
E = 0.0005 * ^ 2.21
0,91
S1
R1
T1
Could not be measured
M-L
E = 3.49 * - 1352
0,86
S1
R1
T1
Could not be measured
S-I
E = 0.04 * ^ 1.68
0,87
S1
R1
T1
Could not be measured
S-I
E = 5.65 * - 1327
0,85
S1
R1
T1
S-I
E = 3.64 * ^ 0.99 -1002
0,88
S2
R2
Young's mod ulus E (MPa)
R²
Sca Ref Tec
Expressions fo r the Spine - Lumbar Ap par ent d ensi ty
R²
Axi s
= 1.122 * HU + 47
0,69
A-P
E = 1.92 * - 170
0,92
S1
R1
T1
= 1.122 * HU + 47
0,69
A-P
E = 0.02 * ^ 1.69
0,86
S1
R1
T1
= 1.122 * HU + 47
0,69
M-L
E = 2.20 * - 209
0,94
S1
R1
T1
= 1.122 * HU + 47
0,69
M-L
E = 0.02 * ^ 1.75
0,89
S1
R1
T1
S-I
E = 7.136 * - 172.3
0,73
S7
R7
T1
= 1 * HU = 1.122 * HU + 47
0,69
S-I
E = 5.82 * - 349
0,96
S1
R1
T1
= 1.122 * HU + 47
0,69
S-I
E = 0.63 * ^ 1.35
0,94
S1
R1
T1
S-I
E = 8.24 * ^ 0.95 - 489
0,96
S2
R2
Young's mod ulus E (MPa)
R²
Sca Ref Tec
E = 0.06 * ^ 1.51
0,89
S1
Expressions fo r the Tibia - Proxim al Ap par ent d ensi ty = 0.916 * HU + 114
R²
0,80
Axi s
A-P
R1
T1
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= 0.916 * HU + 114
0,80
A-P
E = 1.52 * - 98
0,86
S1
R1
T1
= 0.916 * HU + 114
0,80
M-L
E = 0.06 * ^ 1.55
0,90
S1
R1
T1
= 0.916 * HU + 114
0,80
M-L
E = 1.81 * - 124
0,88
S1
R1
T1
= 1 * HU
S-I
E = 82.3 * ^ 8.29
0,63
S8
R8
T5
= 1 * HU
S-I
E = 1.91 * + 33.2
0,61
S8
R9
T5
= 0.00130 * HU + 0.103
0,87
S-I
E = 1371 * ^ 1.33
0,63
S8
R10 T5
= 0.00130 * HU + 0.103
0,87
S-I
E = 1173 * - 44.38
0,55
S8
R11 T5
= 1 * HU
S-I
E = 2.11 * + 76.5
0,55
S8
R12 T6
= 1 * HU
S-I
E = 117 * ^ 7.36
0,54
S8
R13 T6
= 0.00130 * HU + 0.103
0,87
S-I
E = 2132 * ^ 1.46
0,61
S8
R14 T6
= 0.00130 * HU + 0.103
0,87
S-I
E = 1689 * - 99.4
0,57
S8
R15 T6
= 1 + 0.001 HU
S-I
E = 35.48134 * r ^ 11.7
0,61
S9
R9
= 1 * HU
S-I
E = 80.6 * ^ 7.74
0,63
S10 R10 T5
= 1 * HU
S-I
E = 1.76 * + 30.4
0,61
S10 R10 T5
T7
= 0.00120 * HU + 0.101
0,88
S-I
E = 1371 * ^ 1.33
0,63
S10 R10 T5
= 0.00120 * HU + 0.101
0,88
S-I
E = 1173 * - 44.38
0,55
S10 R10 T5
= 1 * HU
S-I
E = 1.94 * + 75.1
0,55
S10 R10 T6
= 1 * HU
S-I
E = 116 * ^ 6.85
0,54
S10 R10 T6
= 0.00120 * HU + 0.101
0,88
S-I
E = 1689 * - 99.4
0,57
S10 R10 T6
= 0.00120 * HU + 0.101
0,88
S-I
E = 2132 * ^ 1.46
0,61
S10 R10 T6
= 1 * HU
S-I
E = 78.3 * ^ 6.96
0,64
S11 R10 T5
= 1 * HU
S-I
E = 1.54 * + 25.0
0,61
S11 R10 T5
= 0.00106 * HU + 0.0949
0,89
S-I
E = 1371 * ^ 1.33
0,63
S11 R10 T5
= 0.00106 * HU + 0.0949
0,89
S-I
E = 1173 * - 44.38
0,55
S11 R10 T5
S-I
E = 1.74 * + 59.6
0,57
S11 R10 T6
= 1 * HU = 1 * HU
S-I
E = 109 * ^ 6.33
0,56
S11 R10 T6
= 0.00106 * HU + 0.0949
0,89
S-I
E = 1689 * - 99.4
0,57
S11 R10 T6
= 0.00106 * HU + 0.0949
0,89
S-I
E = 2132 * ^ 1.46
0,61
S11 R10 T6
= 0.916 * HU + 114
0,80
S-I
E = 5.54 * - 326
0,95
S1
R1
T1
= 0.916 * HU + 114
0,80
S-I
E = 0.51 * ^ 1.37
0,96
S1
R1
T1
S-I
E = 0.50 * ^ 1.38 - 20
0,96
S2
R2
Expressions for Cortical Bone Expressions fo r the Mandibl e Ap par ent d ensi ty
R²
Ax is
Young's mo dulus E (MPa)
R²
Sca Ref Tec
S-I
E = 0.024 * - 23.93
0,37
S14 R1
T8
R
E = 0.013 * - 13.05
0,54
S14 R1
T8
Expressions for the Tibia Ap par ent d ensi ty
R²
Ax is
Young's mo dulus E (MPa)
R²
Sca Ref Tec
S-I
E = 0.013 * - 3.842
0,53
S14 R1
= 1 * HU
B
E = 0.00704 *
0,30
S15 R11 T9
= 1 * HU
B
E = 0.06456 * ^ 0.74
0,30
S15 R11 T9
T8
Expressions for the Humerus Ap par ent d ensi ty
R²
Axi s
Young's mod ulus E (MPa)
R²
Sca Ref Tec
S-I
E = 0.015 * - 6.326
0,72
S14 R1
T8
C
E = 0.011 * - 8.540
0,66
S14 R1
T8
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R
E = 0.011 * - 9.212
0,69
S14 R1
T8
Expressions for the Femur Ap par ent d ensi ty
R²
Ax is
Young's mo dulus E (MPa)
R²
Sca Ref Tec
S-I
E = 0.014 * - 6.142
0,77
S14 R1
T8
C
E = 0.009 * - 4.007
0,47
S14 R1
T8
R
E = 0.010 * - 6.087
0,61
S14 R1
T8
Legend Definitions Apparant density = hydrated tissue weight / bulk volume Effective density = (hydrated tissue + marrow weight) / bulk volume
Anatomi cal Axis (Axis ) A-P M-L S-I P A R B C
Anterior-Posterior Medial-Lateral Superior-Inferior parallel to neck axis Average Radial Bending Circumferential
Scanner Typ es (Sca) S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15
Phillips Tomoscan AV (120 kVp, 150 mAs) Ultrasonic Testing GE 8800 (120 kVp, 240mAs) GE 8800 (120 kVp) Philips Tomoscan AVE1 (120 kV, 100 mA, 1s) Technicare HPS 1440 (130 kVp, 100mA, 4s) / GE 9800 Philips EMI 7070 (140 kVp & 40mA) EMI 7070 (140 kV, 70mA, 3s) EMI 7070 (120 kVp & 50 mA) EMI 7070 (100 kVp & 60 mA) Phillips Tomoscan AV (120 kVp) Siemens Somatom DR3 Phillips Tomoscan AV (120 kVp, 150 mAs) GE 9800 CT (120 kVp, 140 mA, 3s)
Lit erature Reference (Ref) R1 R2 R3 R4 R5 R6 R7 R8
Rho, Hobatho, Ashman, 1995 Rho, Hobatho, Ashman, 1997 Lotz, Gerhart, Hayes, 1990 Esses, Lotz, Hayes, 1989 Pattijn, 2004 Ciarelli, Goldstein, Kuhn, Cody, Brown, 1991 Rho, Zerwekh, Ashman, 1991 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989
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R9 R10 R11
Bentzen, Hvid, Jørgensen, 1987 Hvid, Bentzen, Linde, Mosekilde, Pongsoipetch, 1989 Snyder, Schneider, 1991
Techniq ue used to determine Young’s modul us (Tec) T1 T2 T3 T4 T5 T6 T7 T8 T9
Ultrasound velocity measurement at 50kHz Destructive compression test (15% strain) Destructive compression test at high strain rate Non-destructive/destructive compression test Destructive compression test Non-destructive compression test Compression test Ultrasound velocity measurement at 2.25 MHz Three point bending
References Ciarelli, M.J., Goldstein, S.A., Kuhn, J.L., Cody, D.D., Brown, M.B. “Evaluation of Orthogonal Mechanical Properties and Density of Human Trabecular Bone From the Major Metaphyseal Regions with Materials Testing and Computed Tomography” Journal of Orthopaedic Research, Vol. 9, No. 5 (1991) 674-682 Esses, Steven I., Lotz, Jeffrey C., and Hayes, Wilson C. “Biomechanical Properties of the Proximal Femur Determined In Vitro by Single-Energy Quantitative Computed Tomography” Journal of Bone and Mineral Research, Vol. 4, No. 5 (1989) 715-722 Harp, John H., Aronson, James, and Hollis, Marcus. “Noninvasive Determination of Bone Stiffness for Distraction Osteogenesis by Quantitative Computed Tomography Scans” Clinical Orthopaedics and Related Research, No. 301 (1994) 42-48 Hobatho, Marie-Christine, Rho, Jac Y., Ashman, Richard B. “Anatomical Variation of Human Cancellous Bone Mechanical Properties In Vitro” Studies in Health Technology and Informatics, Vol. 40 (1997) 157-173 Hvid, Ivan, Bentzen, Soren M., Linde, Frank, Mosekilde, Lis, and Pongsoipetch, Buntoing. “X-Ray Quantitative Computed Tomography: The Relations to Physical Properties of Proximal Tibial Trabecular Bone Specimens” Journal of Biomechanics, Vol. 22, No. 8/9 (1989) 837-844 McBroom, R.J., Hayes, W.C., Edwards, W.T., Goldberg, R.P., White, A.A. “Prediction of Vertebral Body Compressive Fracture using Quantitative Computed Tomography” Journal of Bone and Joint Surgery, Vol. 67-A, No. 8 (1985) 1206-1214 Rho, J.Y., Hobatho, M.C., and Ashman, R.B. “Relations of Mechanical Properties to Density and CT Numbers in Human Bone” Medical Engineering and Physics, Vol. 17, No. 5 (1995) 347-355 Taylor, W.R., Roland, E., Ploeg, H., Hertig, D., Klabunde, R., Warner, M.D., Hobatho, M.C., Rakotomanana, L., Clift, S.E. “Determination of Orthotropic Bone Elastic Constants Using FEA and Modal Anslysis” Journal of Biomechanics, Vol. 35 (2002) 767-773
Simulation The Mimics Simulation module allows you to simulate surgical p rocedures.
Overview of Simulation Function ality
Anthropometric Analysis
Simulation of surgical procedures
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Validate design of implants
Planning osteotomies and/or distractions
Easy repositioning of bone slices both with and without the use of a distractor
Note: In order to be able to use distractors in the Simulation Module, you will have to install the distractor
database. You can find this installation file on the Mimics CD or on our website at the Mimics download section.
Starting Simulation All Simulation functions are loaded immediately in Mimics after registration of the Simulation module. When the module is registered, a few extra items are visible in the interface: On the menu bar:
An extra CMF/Simulation menu, listing the different Simulation functions and Design functions is added. The softtissue simulation module is also listed here in case you also have registered the simulation module. In the Tools menu and in the Tools Toolbar, there's a Draw/Manipulate Nerve button added. In the Project Management:
Extra Simulation tab. Extra buttons on the 3D Objects tab: select a 3D Object and click on the Move or Rotate buttons to move or rotate the selected 3D Object. Note: If you're not able to start the Simulation module, you probably haven't entered the passwords yet. Go to
Options > Licenses and fill in the correct passwords.
Simulation tab
List of created Objects Name
Name of the object. By clicking on the name of the object, it can be renamed.
Visible
Lists if the object is visible or not by means of glasses. You can change the visibility by clicking on the glasses.
Contour Visible
Lists if the contour of the objectis visible on the 2D images or not by means of glasses. You can change the visibility of the contours by clicking on the glasses.
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Shows the diameter of the Nerve.
Functions on Objects New
This will show the menu of the objects you can create. You can choose between Cutting Path, Distractor, Mirror Plane and nerve.
Delete
Deletes the selected objects.
Properties
Displays the properties of the selected object:
In the properties dialog of a cutting path, you can change the name, color, depth, thickness and the extensions at the front and the end of a cutting path. You can also define if the cutting path should be closed or not. The Preview button can be used to preview the adjusted cutting path before applying the changes.
In the properties dialog of a distractor, you can change the name and color of the distractor. You can also view some information about the distractor.
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In the properties dialog of a mirror plane, you can change the thickness, width and height of the mirror plane.
In the properties dialog of the nerve, you can change the name, color and diameter of the nerve.
Simulation Menu When the Simulation module is licensed, the Simulation menu appears in the menubar. This menu lists different features of the Simulation module:
Measure and Analyze
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To launch the Measure and Analyze tool, select the corresponding option from the Simulation menu. The following window will pop up:
Analysis Overview When you click on the 'Overview' button in the Anthropometric Analysis pane, the following dialog will emerge.
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Creating a new template To create a new template simply click on ‘New’ in the overview dialog. A window will pop up allowing you to enter the desired analysis name in the ‘Analysis’ field.
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Points
When you click on the New button of the Points section, a second field in the pop-up window allows you to define landmarks for the analysis. New landmarks can be created, copied, edited or deleted. Each landmark can have some default properties that can be set when creating the landmark or by editing an existing landmark using the ‘Edit’ function. The properties that can be set are the landmark name, its color and a description. The landmark name can only be set at creation time. If you wish to import existing landmarks, refer to the relevant section in this manual.
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Planes
By clicking on the New button in the Planes section, you can add planes to the template. To define a plane you must first have defined points, or -alternatively- you can define a plane based on other planes you have already created in the template.
Measurements
In the last field, measurements can be added to the template. Distances, angles and volumes can be measured. For distance either the distance between two points or the distance between a point and a plane can be measured. As for angle, this can be measured using 3 points or using 2 lines (defined by 2 points each). A volume can be measured by selecting at least 4 points. A convex polygon will be created with those points and the volume will be measured. Note that measurements can only be done using points or planes that have already been defined in the template.
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Duplicating an existing t emplate If you wish to create a copy of an existing template, simply click in the ‘Active’ column behind the template you wish to duplicate. A green flag will appear. Now click on ‘Copy’ to create the copy. A new window will pop up allowing you to define the template in a similar way as explained under creating a new template.
Editing an existing t emplate To change the properties of an existing template, activate the template by clicking in the ‘Active’ column behind the template. A green flag will appear. Click on ‘Change’ and edit the template as desired. Note: you cannot change the default templates that are installed with the Simulation module. If you wish to edit
the properties of one of the default templates you need to first create a copy of the template and then edit the copy.
Removin g an existin g template If you wish to remove a template, activate it (the ‘Delete’.
should appear behind the template name) and then click on
Note: you cannot delete any of the templates that are installed by default with the Simulation module.
Importing Points Adding points from other templates You do not need to define existing points again if you are creating a new template. Existing points can be imported quite easily from other templates with the ‘Import’ function. Simply activate the template in which you wish to import the existing point(s) and click on the button ‘Import Points’. A new window will pop up.
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From the pull down menu choose the template where you want to import points from. All points in that template are then shown in the window, select the point(s) you wish to import en click on the ‘import’ button. If points from other templates also need to be imported select that template from the menu and repeat the steps above. To finish the import click on ‘ok’. Of course, since default templates cannot be changed it is not possible either to import points into those templates.
Getting Started The Anthropometric analysis tool allows for easy analysis and measurement based on pre-defined templates in both 3D and 2D views. To start the Anthropometric Analysis, go to the Simulation menu and choose Anthropometric Analysis. Choosing the type of analysis
Before starting the analysis you first have to choose the analysis template you wish to use from the Anthropometric analysis pull down menu.
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If you do not find a template that coincides with your requirements you can create your own template as described in the creating a new template section. When you have chosen the template you wish to use, indicate the appropriate points, planes and/or measurements as described in the following sections. a. Points of analysis
The points of the analysis pane provide you with a list of available points in the currently selected template. Points that have already been indicated on the images appear in black, the others appear in gray. The pane allows you to indicate, locate, edit or clear the points in the list. Indicating points
To place a point, first select it from the list and click on the ‘Indicate’ button. You can indicate a point in both the 2D and the 3D views. Note that you first need to indicate the point before you can use any of the other option in the pane. When you have clicked the Indicate button, the description of the point will be displayed.
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You can always move the points of the analysis after their indication. If you are not able to select the landmark points, first enable the right mouse mode by clicking on the Indicate button. Now you will be able to move the points. Locating points
If you want to easily view the image on the location where a point was placed, highlight the point and click on ‘locate’. This will move both the axial and the sagittal view to the position where the point is located. Also a short description of the point you want to locate is given. Clearing point s
If you have misplaced a point you can easily remove it by selecting the point in the list and clicking on the ‘clear’ button. Editing points
After having indicated a point you can change its properties. If you click on the ‘edit’ button you can easily change the color in which the point is shown on the images. You can also change the position of the point here by changing its coordinates.
b. Planes of analysis
The pane for the planes of analysis allows you to indicate and edit the planes defined in the template. Indicating planes
If you select the plane you want to view on the 3D image and click on ‘indicate’ a pop-up will ask you to indicate
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the different points that define the plane. If these points were already indicated the plane is shown automatically.
Editing planes
The ‘edit’ option in the planes pane allows you to change the properties of the selected plane. You can choose its thickness, change its color, width and height and select what opacity the plane should have in the image.
c. Anthropometric 3D measurements
If your current template includes measurements, a list of these measurements is provided in the anthropometric measurements plane. These measurements can be easily indicated on the images. Indicating measurements
Select the measurement you wish to indicate and click on the ‘indicate’ button. A window will pop up to guide you through the placement of the points needed by the measurement. If these points where already indicated on the images, the measurement will have been made automatically.
Viewing/exporting/printing measurement details
It is also possible to display a more detailed view of the measurements. Click on details and a new window will appear showing all measurements with there pre-operative and post-operative values for both 2D and 3D. These values can be easily referenced to a set of normal; values that can be loaded with the ‘Load normal values’
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option. This overview can be printed out or exported to a csv-file for easy importing in other programs.
d. Sagittal plane
In case the CT images were not taken with the head of the patient at a 90-degree angle to the table, 2D and 3D measurements will be off. Therefore it is possible to adjust the position of the sagittal plane to account for this.
To change the position and direction of the sagittal plane, click on ‘Change’ and draw the plane in your axial view. To return the plane to its original position, use the ‘Reset’ option.
Cut Cut Menu
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There are two different cutting tools available: Cut Orthogonal to Screen and Cut with Polyplane:
Cut with Polyplane To launch the cut with polyplane tool, select the corresponding option from the Simulation Cut menu. The following window will appear and your cursor will change in a pencil.
With this pencil you can draw your cutting path in 3D or in 2D. After drawing, you can adjust the properties of the cutting path by clicking on the Properties button.
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The cutting path will be visible in 3D and in 2D (if the option " Contour Visible" is selected)
Functions on Objects to Cut Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to
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change the visibility of the object. Contour visible
Show only selected objects Keep originals
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object. Makes the selected objects visible and the unselected objects invisible.
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Functions on Cuttin g Paths New
Allows you to create a new cutting path.
Properties
Displays the properties of the selected cutting path:
In this properties dialog you can change the depth, thickness and the extensions at the front and the end of the cutting path. You can also define if the cutting path should be closed or not. The Preview button can be used to preview the adjusted cutting path before applying the changes. Visible
Lists if the cutting path is visible or not by means of glasses. Click on the glasses to change the visibility of the cutting path.
Lists if the contour of the cutting path is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the cutting path. Cutting paths can be adjust after their creation by left-clicking on the points of the cutting path and dragging them. You can also change the angle of the cutting path by left-clicking and dragging the red arrow on the cutting path. Contour Visible
Cut with Curve By defining a contour on the 3D object you can make more complex cuts. To launch the cut with curve tool, select the corresponding option from the Simulation Cut menu. The following window will appear and your cursor will change in a pencil.
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Indicate points all around the 3D object to indicate your cutting path. When you indicate the points, a red line will appear on the 3D that represents your cutting line. You finish the cutting path by double clicking the left mouse button (or click once the right mouse button). A yellow line will appear which represents the extension of the cutting path. This extension can be adjusted in the main dialog box. Make sure that the extensions aren’t crossing the 3D object. The cut will only complete when all extensions are floating above the 3D object.
You can still adjust the control points therefore over the mouse over the cutting path. When you hover over a control point the cursor will change into a cross with circle. To select this point click your left mouse button and drag the control point to its new location. After you’ve checked the extensions click OK, the object is now cut AND split at the same time.
Functions on Objects to Cut Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects Keep originals
Makes the selected objects visible and the unselected objects invisible.
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Functions on Cutting Lines Indicate
Shows the indicate tool and enables you to indicate a cutting line.
Close
Closes the cutting line.
Delete Last
Deletes the point of the cutting line that was drawn last.
Extensions
Sets the distance between the cutting line and its extension
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Cut Orthogonal to Screen To launch the cut orthogonal to screen tool, select the corresponding option from the Simulation Cut menu. The following window will appear and your cursor will change.
You have to select an object to cut from the list before you can preview or apply the cut.
Functions on Objects to Cut Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
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If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Functions on Cutting Lines Indicate
Shows the indicate tool and enables you to indicate a cutting line.
Close
Closes the cutting line.
Delete Last
Deletes the point of the cutting line that was drawn last.
Split To launch the split tool, select the corresponding option from the Simulation menu. The following window will appear:
Functions on Objects to Split Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects All parts Largest part Two largest parts
Makes the selected objects visible and the unselected objects invisible.
This way you can choose which parts you want to keep, all cut parts, only the largest part or only the two largest parts.
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain. To split, you always need a cut first (with the cutting tool) Keep originals
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Then you select which object you want to cut and press the "Preview" and or the "Apply" button.
Reposition To launch the reposition tool, select the corresponding option from the Simulation menu. The following window will appear:
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Objects to r eposition Selection of the Object to be repositioned First, select the object(s) you want to reposition.
Functions on Objects to Reposition Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show selected only
Makes the selected objects visible and the unselected objects invisible.
Keep originals
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Translation and Rotation Objects can be translated and/or rotated. For each type of manipulation the measure can be adjusted to suit your needs.
Move with mouse Objects can also be manipulated using the mouse. If the option ‘Move with Mouse’ is enabled, a box and arrows will appear around the object in both 3D and 2D views. If you grab the center of the box -marked by a yellow rectangle- you can move the object around in all views. By clicking on one of the arrows you can move the 3D object along an axis. To rotate an object, select the ‘Rotate with Mouse’ options. Rotation handles will be shown on the 3D object. You can rotate the 3D object around the X, Y and Z axis by grabbing one of the colored rotation handles. You can also rotate the 3D around the axis perpendicular to the camera view by grabbing the outer ring of the rotation tool. To change the rotation center grab and move the middle of the tool. The values of translation and rotation are shown in the statusbar.
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Restrict DOF Several restrictions on the manipulation of an object can be chosen. Possible restrictions are: translating over axis, translating over plane, rotating over an axis and rotating over a point. Off course unrestricted manipulation is also an option.
Registration With the registration function, you can move landmark points that are located on the surface of a 3D object and the 3D object will then automatically be moved according to the new position of the landmark points. If you have not created any landmark points, you can do this in the Anthropometric Analysis tool. When you click on the Registration button, you will see a list of all the indicated landmark points. Select the points you want to use from this list.
When you click on the OK button, following dialog will appear for each selected point:
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In this dialog you can move each point by specifying a Lateral, Vertical and Rostral placement. When you click on the OK button, the new position of the 3D object will be calculated and the 3D object will be moved to that position.
Switching/saving Positions A few buttons are available in this step in order to facilitate the object manipulation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’.
Motion Analysis An analysis overview of the motion will be displayed if you click on the An aly ze Mot io n button.
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Finishing the reposition If the repositioning of the objects matches the situation you want to achieve, you can click ‘finish’.
Place Distractor To place a distractor, select the corresponding option from the Simulation menu. You can place a distractor on an existing object or on a part of an object. For this, you first need to cut and split.
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By selecting 'Place Distractor' from the Simulation menu the following window will appear:
Functions on Objects to pl ace the distractor o n Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Makes the selected objects visible and the unselected objects invisible. Select on which part you want to place your distractor and click "Next". A distractor library will appear in which you can chose which distractor you want to place. Show selected only
After selecting the distractor from the library the following window will appear:
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Locate the distractor with two mouse clicks in the 3D view. The first click determines the point of the distractor on the fixed part of the bone, the second mouse click determines the point of the distractor on the moveable part of the bone.
Adjust the Distractor Position The direction of the distraction vector can be adjusted with the following window. The distractor can also be aligned to the sagittal or axial slices or to the Frankfurt plane.
You can also change the vector of the distractor by left-clicking on the red arrow originating from the distractor and dragging the arrow.
Reposition with Distractor To launch the reposition tool, select the corresponding option from the Simulation menu.
Functions on Objects to Reposition with the distractor Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
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Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show selected only
Makes the selected objects visible and the unselected objects invisible.
Translating accor ding to the Vector of the Distractor After you have selected the object to be repositioned you will be able to use the ‘Translate distractor’ option. To translate the distractor simply use the ‘-’ and ‘+’ buttons. The default translation for each step will be 1mm but this can be change by editing the field in between the two translation buttons. Of course, it is not possible to move a distractor beyond its starting or ending position, using a distraction measure that is too large will simply put the distractor in its starting, resp. ending position. The total translation of the distractor is shown underneath the translation buttons.
Switching/saving Positions A few buttons are available in this step in order to facilitate the object translation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’.
Analyze Motion An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. Note, however, that an analysis can only be made of you have first saved the position you wish to analyze.
Wizard Osteotomy Wizard
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The Osteotomy wizard will guide you through all the necessary steps to come to a good simulation. Each step will exactly tell you what needs to be done before you can go on to the next step. Like this, simulation becomes easy and fast, but take into account that the cutting paths within the wizard are simplified. If you opt to perform an osteotomy via the wizard, a number of predefined conventional procedures are available: LeFort I conventional, LeFort I trapped, LeFort II, LeFort III, Genioplasty, Sagittal split and Ramus lengthening. If none of these suite your needs you can also opt for a custom planar or a custom freeform cut. To launch the Osteotomy Wizard, select the corresponding option from the CMF/Simulation menu.
Step 1: Choosing th e type of surgery In the first step of the osteotomy wizard you must indicate the type of surgery you are about to perform. Some conventional options you can choose from are available. If you select a surgery a short description will appear in the bottom pane of the window.
Click Next to proceed.
Step 2: Select t he objects and indic ate landmarks
a. Selecting the object(s) to cut
To select the object you wish to cut simply place a mark in the column before the object you wish to cut. Multiple
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objects can be selected. Example: when you want to perform a simulation of a sagittal split surgery, you need to select the mandible as object you want to cut in.
b. Visibility of the object(s)
To take a better look at the object(s) you have selected it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. To continue the wizard click on ‘Next’, if you want to retrace your steps in the wizard you can always use the ‘Back’ button. Indicate the appropriate landmarks
The wizard will ask you to indicate the landmarks that are appropriate for the type of osteotomy you have chosen. The landmarks will appear in the cephalometric window at the right side of your screen.
If you have previously done a cephalometric analysis some or all landmarks may have already been indicated. When all landmarks have been indicated the ‘next’ button will no longer be disabled and you can continue the wizard.
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Step 3: Adjusting t he cutting path This step allows you to manipulate the cutting path that was loaded from the library to make it perfectly adjusted to the patient’s 3D model. The cutting path can be seen and adjusted both in 2D and 3D.
a. Object visibility
To take a better look at the object(s) you are working on it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. b. Adjusting cutting path position
When cutting an object it is important to make sure the cutting path cuts through the entire object. To achieve this it is possible to adjust the position of the cutting plane. Planes can either be translated or can be rotated. For both operations a measure of adjustment can be assigned to allow for easy, fast and accurate manipulation. c. Adjusting cutting path dimensions
Besides manipulating the cutting path position, it is also possible to adjust its dimensions. You can change its thickness, height and width. Of course it is also possible to reset the cutting plane to its original dimensions. d. Displaying cutting path in 2D CT views
It may be helpful to see the location of the cutting path on the axial and sagittal views. Enable the ‘Show contour’ option and the path will be made visible on the 2D images.
Step 4: Splitti ng t he 3D objects This step of the wizard will guide you through the cut itself. a. Object(s) before split
Between step 3 and 4 a copy of the object(s) you selected to be cut has been made. These objects are visible in the ‘Objects before Split’ pane. It is at this stage still possible to deselect one or more of the objects. If all objects that need to be cut are selected, click on the ‘Split’ button.
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b. Objects after split
After the split, the newly created objects will appear in the ‘Objects after Split’ pane. These will also be visible in the 3D view. The original object still exists, but will be hidden in the 3D view. You can make it visible again by clicking on the box with the color of the original object in the 3D view toolbar.
It is also possible to remove one of the new parts that have been created. To do this, simply select the object in the pane and click on ‘Remove Selected’. c. Make additional Cut
If you need to make more than 1 cut, at this stage in step 4 you are able to choose to make an additional cut. This option will restart the wizard.
Step 5: Reposit ionin g the 3D objects After having done the cut, you can reposition one or more of the newly obtained parts. Off course any motion can be easily analyzed.
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a. Selection of the Object to be repositioned
In the same fashion as you have done in the previous steps, select the object(s) you want to reposition.
Note: You can check if you selected the right object by clicking on the
. If the object that disappeared in the 3D window is the object you want to reposition, you selected the right object. Make the object visible again by clicking on the
b. Repositioning the selected Object
There are two ways of repositioning an object: with the using the keys or using the mouse. Using the keys
Objects can be either translated or rotated. For each type of manipulation the measure can be adjusted to suit your needs. Using the mouse
Objects can also be manipulated using the mouse. If the option ‘Move with Mouse’ is enabled, a box will appear around the object in both 3D and 2D views. If you grab the center of the box -marked by a dot- you can move the object around in all views. To rotate an object, grab one of its corners, the cursor will change into a rotation sign and you will be able to rotate the object around its center. This too is possible in both 2D and 3D views.
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c. Restrict the Degrees of Freedom
Several restrictions on the manipulation of an object can be chosen. Possible restrictions are: translating over axis, translating over plane, rotating over an axis and rotating over a point. Off course unrestricted manipulation is also an option. The rotation/translation point, axis or plane needs to be indicated by the use of the cephalometry. Once these point are indicated, and after selection of a restriction, you need to select them in the following window (for example when you choose “rotate around an axis”):
Click OK, select the object you want to reposition, and only the restricted movement will be enabled.
d. Registration
The registration option allows you to easily reposition objects using landmarks. Click on ‘registration’ and select the landmarks you want to reposition.
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After clicking ‘ok’, SimPlant will will take you through all the points you have selected and allow you to reposition them and the objects they are associated with.
e. Switching/saving Positions
A few buttons are available in this step in order to facilitate the object manipulation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’.
f. Motion Analysis
An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. Note, however, that an analysis can only be made of you have first saved the position you wish to analyze.
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Finishin g the Wizard Wizard If the repositioning of the objects matches the situation you want to achieve, you can finish the wizard.
Distraction Distractio n Wizard Wizard The distraction wizard will will guide you through all the necessary steps to come to a good simulation. simulation. Each step will exactly tell you what needs to be done before you can go on to the next step. Like this, simulation becomes easy and fast, but take into account that the cutting paths within the wizard are simplified. If you opt to perform a distraction via the wizard, a number of predefined conventional procedures are available: alveolar, unilateral ramus, bilateral ramus and maxillary distraction. If none of these suite your needs you can opt for a freeform way of simulating a distraction (see later). To launch the Distraction Wizard, select the corresponding option from the CMF/Simul CMF/Simulation ation menu.
Step Ste p 1: Choosing th e type of surgery In the first step of the distraction wizard you must indicate the type of surgery you are about to perform. Some conventional options you can choose from are available. If you select a surgery a short description will appear in the bottom pane of the window.
Click Next to proceed.
Step Ste p 2: Sele Select ct the objects, choos e your distr actor and positi on it i n the 3D 3D window
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a. Selecting the object
To select the object you wish to cut simply place a mark in the column before the object you wish to put the distractor on. Example: when you want to perform a simulation of a unilateral distraction, you need to select the mandible as object you want to cut in.
b. Visibility of the object
To take a better look at the object o bject you have selected it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. To continue the wizard click on ‘Next’, if you want to retrace your steps in the wizard you can always use the ‘Back’ button.
c. Choose the distractor from a library
Distractors are available from Martin, Synthes and Medicon. If the distractor that you would like to use is not available in the distractor list, please contact Materialise and we will do our best to add this distractor to the library. To choose your distractor, select it and click OK.
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d. Locate the distractor and align
After selection of a distractor your cursor will change into a pen. You can locate the distractor now with two mouse clicks in the 3D window. The first mouse click needs to be on the fixed part of the bone, the second mouse click on the part that will be distracted.
Once the distractor is indicated, the distractor can be translated or rotated and the vector can be aligned according to your needs. To translate translate the distractor, move your cursor over over the distractor in the 3D window. window. When When you get the symbol , you can translate the distractor by using using your left mouse button. When you get get the symbol you can change one of the distractor points (the fixed or the moveable one) by using your left mouse button. To rotate your distractor, you can use the available keys in the wizard dialog box.
To align the vector of the distractor, you can use the available keys in the wizard dialog box, or you can use the direction arrow. By moving your mouse to the top of the arrow, and left clicking, you can drag the arrow (the vector) towards the desired direction.
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e. Indicate the appropriate landmarks
The wizard will ask you to indicate the landmarks that are appropriate for the type of distraction you have chosen. The landmarks will appear in the cephalometric window at the right side of your screen.
If you have previously done a cephalometric analysis some or all landmarks may have already been indicated. When all landmarks have been indicated the ‘next’ button will no longer be disabled and you can continue the wizard.
Step Ste p 3: Adjusting t he cutting path This step allows you to manipulate the cutting path to make it perfectly adjusted to the patient’s 3D model. The cutting path can be seen and adjusted both in 2D (if you check
) and 3D.
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a. Object visibility
To take a better look at the object(s) you are working on it may be useful to hide all other objects in the 3D view. To achieve this, click on the ‘Show Selected Only’ button. b. Adjusting cutting path position
When cutting an object it is important to make sure the cutting path cuts through the entire object. To achieve this it is possible to adjust the position of the cutting plane. Planes can either be translated or can be rotated. For both operations a measure of adjustment can be assigned to allow for easy, fast and accurate manipulation. c. Adjusting cutting path dimensions
Besides manipulating the cutting path position, it is also possible to adjust its dimensions. You can change its thickness, height and width. Of course it is also possible to reset the cutting plane to its original dimensions. d. Displaying cutting path in 2D CT views
It may be helpful to see the location of the cutting path on the axial and sagittal views. Enable the ‘Show contour’ option and the path will be made visible on the 2D images.
Step Ste p 4: Splitti ng t he 3D objects This step of the wizard will guide you through the cut itself.
a. Object(s) before split
Between step 3 and 4 a copy of the object(s) you selected to be cut has been made. These objects are visible in the ‘Objects before Split’ pane. It is at this stage still possible to deselect one or more of the objects. If all objects that need to be cut are selected, click on the ‘Split’ button.
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b. Objects after split
After the split, the newly created objects will appear in the ‘Objects after Split’ pane. These will also be visible in the 3D view. The original object still exists, but will be hidden in the 3D view. You can make it visible again by clicking on the box with the color of the original object in the 3D view toolbar.
It is also possible to remove one of the new parts that have been created. To do this, simply select the object in the pane and click on ‘Remove Selected’.
Step Ste p 5: Reposit Reposit ionin g the 3D objects After having done the cut, you can reposition one or more of the newly obtained parts. Off course any motion can be easily analyzed.
a. Selection of the Object to be repositioned
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In the same fashion as you have done in the previous steps; select the object you want to reposition.
Note: Y You ou can check ifif you selected the right right object by clicking clicking on on the
. If the object object that that disappeared disappeared in the 3D window is the object you want to reposition, you selected the right object. Make the object visible again by clicking on the
b. Repositioning the selected Object
You can only reposition the object according to the vector and the position of the distractor. Click the + key to see the movement of the object.
c. Switching/saving Positions
A few buttons are available in this step in order to facilitate the object manipulation. It is possible to save a position and to afterwards easily return to that position. The home position of the object can always be reached by clicking on ‘Go to Home Position’. ‘Go to end position” shows the maximum distraction of that particular distractor device.
d. Motion Analysis
An analysis overview of the motion will be displayed if you click on the ‘Analysis Overview’ button. Note, however, that an analysis can only be made of you have first saved the position you wish to analyze.
Finishing the Wizard Wizard
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If the repositioning of the objects matches the situation you want to achieve, you can finish the wizard.
Soft-tissue 3D Soft tissue simulation is an extra module on top of the CMF module. An extra password is needed to activate this tool. Once activated, you can find a new menu item in the CMF/Simul CMF/Simulation ation menu, namely “Soft Tissue”.
After you simulated the maxillofacial surgery with the Simulation functions (osteotomy or distraction), you can check how the soft tissue will change according to the new bone positions. To launch a new soft tissue simulation, select the corresponding option from the Soft Tissue menu.
The following window will pop up, and the 3D objects in the 3D window will disappear.
First select the postoperative hard tissue objects. The ones you select will also become visible in the 3D window.
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Note: For optimal results of the soft tissue simulation, the spine should be included as hard tissue. If the spine is
not segmented, you can go to the segment module (if you have SimPlant Pro) and segment in a very easy way the spine. Then select the pre operative soft tissue object. The selection will become visible in the 3D window.
Click next and the soft tissue simulation will start calculating. A progress bar shows you how long the calculation will take.
Note: The calculation time depends on the performance of your computer and the size of the data. It can range
from a few seconds to a few minutes. Once the calculation is completed, the soft tissue simulation will appear on your screen. To see the simulation, click the “Play” button. The speed of the animation can be adjusted by using the Speed bar.
Ad A d v an anc c ed t o o l s
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Merge To launch the merge tool, select the corresponding option from the Simulation menu. The following window will appear:
Functions on Objects to Merge Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain. To merge, you always need select two or more 3D objects or STLs. The selected objects will then be merged to one STL by clicking on the Ok button. Keep originals
Mirror To launch the mirroring tool, select the corresponding option from the Simulation menu. The following window will pop up:
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Functions on Objects to Mirror Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects Keep originals
Makes the selected objects visible and the unselected objects invisible.
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Functions on Mirror planes Allows you to indicate a new plane. To do this, left-click three times in any 2D or 3D view. A plane will then be constructed through those three points. You can mirror a complete part of the bone, or a split part. This can be checked in 3D and in 2D. New
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Select the part you want to mirror. Then select a mirror plane or create your own by clicking on the New button and indicating three points of the plane in 2D or 3D.
With the preview button you can check the result. If the result looks ok, press Apply.
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Boolean The boolean tool allows you to do a boolean operation (Minus, Unite or Intersect) between 3D Objects, STLs or MedCAD Spheres and Cylinders. The result of the boolean operation will be put in the 3D Objects list. To launch the boolean tool, select the corresponding option from the Design menu. The following window will pop up:
Functions on Objects to Bool ean Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
Operation
The boolean operation you want to perform on object 1 and 2.
Keep originals
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Rescale The rescale tool allows you to rescale 3D Objects or STLs. The result of the rescale operation will be put in the 3D Objects list. To launch the rescale tool, select the corresponding option from the Design menu.
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The following window will pop up:
Functions on Objects to Rescale Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
Factor
You can choose the rescale factor in X, Y and Z direction.
Size
The size field displays what the size of the object will be in X, Y and Z direction with the specified factor. You can also give in a size in X, Y or Z and the rescale factor will be calculated automatically.
Uniform
If the uniform option is selected, the rescale factor will be the same for X, Y and Z direction.
Keep originals
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Smoothing The smoothing tool allows you to smooth 3D Objects or STLs. The result of the smoothing operation will be put in the 3D Objects list. To launch the smoothing tool, select the corresponding option from the Design menu. The following window will pop up:
Functions on Objects to Rescale
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Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
Iterations
You can choose how many smoothing iterations will be performed.
Smooth factor
The smooth factor determines how much smoothing is performed.
Compensate shrinkage
If the compensate shrinkage setting is enabled, the shrinkage of the object due to the smoothing will be countered.
Keep originals
If the keep originals checkbox is checked, the original objects will be kept, otherwise they will be deleted and only the cut objects will remain.
Triangle Reduction The triangle reduction tool allows you to do a triangle reduction of 3D Objects or STLs. The result of the triangle reduction operation will be put in the 3D Objects list. To launch the triangle reduction tool, select the corresponding option from the Design menu. The following window will pop up:
Functions on Objects to Rescale Visible
Lists if the object is visible or not by means of glasses. Click on the glasses to change the visibility of the object.
Contour visible
Lists if the contour of the object is visible or not by means of glasses. Click on the glasses to change the visibility of the contour of the object.
Show only selected objects
Makes the selected objects visible and the unselected objects invisible.
Reducing mode
You can choose between a Point based triangle reduction, an Edge based triangle reduction or an Advanced Edge based triangle reduction.
Tolerance
The Tolerance indicates the maximum deviation in mm that a related triangle may have, to be part of the same plane that contains the selected triangle.
Edge Angle
The Edge Angle-value defines which angle should be used to determine edges of the part that cannot be removed. Triangles deviating less than this angle will be grouped into the plane of the other triangles.
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Iterations
You can choose how many triangle reduction iterations will be performed.
Nerves toolbox This tool allows you to create a representation of nerves. Note that this is only a representation of the nerve channel as you have drawn it. The nerve is drawn manually and consists of a series of points, connected by an interpolated line. Select the nerve icon from the tools toolbar or select the Tools menu and then Draw/manipulate nerve. The nerves toolbox will appear on the screen. Each time only the relevant buttons are enabled in the toolbox. Close the toolbox by clicking on the black cross in the top right corner or by clicking again on the nerve button in the tools toolbar.
Draw a nerve This function allows you to draw the nerve. These are the steps to perform:
Select the Create nerve tool. The cursor will change to a pencil.
Start drawing the nerve: for every change in direction along the nerve, you need to click (press and release the left mouse button) once to define the course of the nerve. In order to terminate the nerve, double click the left mouse button or click the right mouse button.
While drawing the nerve you can scroll through the images with the cursor keys and follow the nerve channel if needed.
Fine adjustments can be made by dragging the points to a new location. The nerve can be moved entirely by dragging the orange line.
Select a nerve Select the cursor tool and click on a nerve to select it. The points of a selected nerve are in white. The points of a non-selected nerve have the same color as the lines of the nerve. The action you do is always performed on the selected nerve.
Delete a nerv e Select the nerve you want to delete and click on the Delete nerve button.
Add a point to a nerve Click on the add point to nerve button, hover the mouse over the nerve segment were you want to add the point. The cursor will change into a pencil, click your left mouse button to add a point.
Remove a point from a nerve
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Click on the point of the nerve you want to delete. The selected point will be colored green. Click on the Remove point from nerve button to delete the point.
Show the list of nerves Click on this button to display the Nerves tab on the project management.
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Mimics Tutorial In Mimics, you can set a general default working directory (Options > Preferences). Copy the demo files to this working directory. Make sure that you have read and write permissions in this directory. If you have chosen to install the demo files during the Mimics installation procedure, only two of the files used in this tutorial would be put in the MedData folder. All the other ones can be found on the CD or from our website. To download the tutorial files from our website, surf to http://www.materialise.com/software/download_ENG.html and register. You can then choose Mimics and then the link for Tutorial Datasets. The extra tutorial files are a self-extracting zip-file. To unpack the file, double click on it and choose your MedData folder as destination folder. The following tutorials are available: Chapter 1: Import Chapter 2: Mimi
Tutorial that shows how you can import images in Mimicis Tutorial that shows how to do a basic segmentation and 3D calculation. Chapter 3: Simon Tutorial that shows some advanced segmentation functions to remove artefacts. Chapter 4: Hip Tutorial that shows how to use the MedCAD module. Chapter 5: Obturator Tutorial that shows how to make a mold of a cavity by segmenting the soft tissue around the cavity. Chapter 6: Manual Import Tutorial that shows how to use the manual import function. Chapter 7: FEA Tutorial Tutorial that shows how to use the FEA module. Chapter 8: Simulation Tutorial Tutorial that shows how to use the Simulation module. Chapter 9: CFD Tutorial Tutorial that shows how to use the FEA module for linking to CFD. Note: In Mimics you have the possibility to use both Hounsfield and Grey Values. This is very important when setting a threshold and when you use the Profile Line function. To switch between these two possi bilities, go to Options > Preferences, General tab and select the Pixel unit you want to use. Most tutorials need one or more modules of Mimics (STL+, RP Slice or MedCAD). If you wish to try that section of the tutorial and you don’t have the required module(s) installed, an evaluation period of that module can be obtained on request.
Import The goal in the first part of this chapter is to teach you how to import images and convert them i nto a Mimics project. The second part will illustrate how to organize the images in the project you made. In this tutorial we will discuss three topics:
How to do an Automatic Import
How to organize images
How to do a Semi-Automatic Import
Note: To import images from a tape you need to use the Dump Tape function Note: There are 3 ways to import images, depending on their format: automatic import, when the format of the files is known to Mimics semi-automatic, e.g. Bitmap or Tiff images manual import (Case 6), when the file type is unknown and you need to specify some parameters manually
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Automatic import To start the Import wizard, first select File and then choose Import Images. An Import Project Wizard will be displayed where you can select where the images to be imported can be found (STEP 1). In the import wizard, browse to the MedData folder and sel ect the folder called “Import1”. A list of files will be displayed in the Filename column and all the files will be automatically selected. Click the Next button. If the format of the images is known to Mimics (see the general help fil es for a list of known formats), you can select the images and press the Next button. If you click on the displayed containing the correct path and format of the images.
button, an import message will be
Note: In this case the file type is recognized, but in some cases the message log tells you that one or more images are of an unknown fil e type. If this happens, you have to perform a manual import (see Case 6).
Note: If you want to keep all the files, press the Next button, otherwise first change the selection of images to fit your needs. This selection can be done in two different ways: either you can click on the first file and then on the last one you want to include while keeping down the Shift button (this way you will include all files in the interval) or you can select the files one by one while keeping down the Ctrl button. After clicking on the Next button you will reach the second step of the Import Project Wizard, in which you need to select the studies to be converted. The study you have just imported is already selected by default. In this window some information about the project can be found, such as the number of images, pixel size, patient name, orientation parameters, etc.
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Now you can click the Convert button and you will see a progress bar during the conversion process, the project will be opened automatically di splaying the Change Orientation window since one or more of the orientation strings were missing in the original images.
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Now you need to set the Orientation Parameters that were missing and change the ones that are incorrect. Actually if you look at the axial image you see the orientation strings L and R, which stand for Left and Right respectively together with A and P which stand for Anterior and Posterior. In the coronal and sagittal image two red Xs are displayed instead of the above mentioned orientation strings. Move the mouse cursor to the top X in the sagittal or coronal image. The cursor shape changes to a hand and if you right-click, a menu appears with all possible orientation strings. Select “Top”. Note that all the other orientation strings are completed automatically. If the orientation of the images is right you can click OK and your Mimics project will be opened. Now you can process your images using the tools explained in the tutorials dealing with Case 2 and Case 3 (Threshold, Region Growing, Edit, etc..)
Organizing images Once you have opened your project, you can decide to exclude some images if they are not good or if you don’t need all of them. For example, we can decide to delete the images of the project Simon.mcs that don’t include parts of mandible or that don’t contain any information. To access the Organize Images window, go to File and then choose Organize Images.
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First of all you can get a better look at the images changing the preview size to Medium or Large by clicking on the arrow on the left side. If you look at the images you will notice that the ones that correspond to table positions –49.5 and –48.5 do not contain any information about mandibular bone. So you can click on these two images to unselect them, the red mark will disappear and the image will be unchecked in the list on the left. On closer inspection you can also notice that the image at table position –1.5 is the last one that contains information about the mandible. Right-click on the image at position –1.5 and choose Unselect after this. All the consecutive images will be unselected also. Press OK and scroll through the axial images to check if the correct ones are visible in the project, you should not see the ones you unselected. You can now save your Mimics project with the name “Organizing Images.mcs” going to File and then Save As. After you have done this you can make a segmentation following the next tutorial (Case 2)
Semi-automatic import Now we will try to import the Bitmap images you can find in your MedData directory in the "Import2" subdirectory. Again select File > Import Images and browse to the \MedData\Import2\ directory. If you press the Next button, a new window will be displayed.
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The only information you need to provide/change is the slice distance and the pixel size. This information should be collected by someone who i s familiar with the machine used to make the CT-Scan. It is very important to insert the exact values since the dimensions of the volumes and the 3D depend on them. If the data is accurate, you can press OK to continue with the second step of the Import Project Wizard. Now the import continues in similar a similar way to the automatic import. You will need to select the study you wish to convert and your Mimics project will be created after clicking on the Open button. Now you should be able to set the orientation parameters as described in the previous paragraph and calculate a good 3D.
Mimi In the second case of this tutorial we will show you some basic features of Mimics. The topics that will be discussed are:
Opening the Project
Windowing
Thresholding
Region Growing
Creating a 3D representation
Displaying a 3D representation
STL+ Procedures
Generating a STL file
RP Slice procedures
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Generating a contour file
Generating supports
View of the end result
Opening the project From the File menu, select Open (Ctrl+O). The Open dialog box shows all projects in the working directory. Double click on the mimi.mcs file (Mimics project file). All images are loaded and displayed in three views. The view on the right shows the images as they are exported by the scanner (xy-view or axial view). The upper left corner is a reslice of these images in the xz-direction (xzview or coronal view) and the bottom left is a reslice i n the yz-direction (yz-view or sagittal view). The different colors of the intersecting lines (dashed lines) refer to the colors of the contour lines of each view so every line refers to the slice in the corresponding view. You can easily navigate through the images by clicking on any point of the CT images in any view: the intersecting lines will move crossing each other in the point you clicked and all the views will be updated showing the corresponding slices.
If you need to change the orientation of a view, go to File > Change Orientati on. This will open a window in which you can change the orientation parameters simply by clicking on i t with the right mouse button (see tutorial Case 1).
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Every indicator can be turned off by selecting View > Indicators in the Menu Toolbar. In the right border of the window you will see a slider that allows you to scroll thro ugh the images from the active view. In our current project (Mimi), all images are correct. If, however, you have an image set from which you want to remove some images, go to File > Organize Images. There you can add or remove images (see tutorial Case 1).
Windowing First of all, we have to adjust the contrast of the images displ ayed in the different views. Contrast enhancement is a very good tool for selecting parts with different intensities, e.g. bone vs. brain tumor. This action can be performed at any time. You can change the contrast in the corresponding tab of the Project management. The contrast tab shows the histogram of the project with a li ne representing the “window”. The gray values or Hounsfield units below the start point of the line will be displayed in black. All gray values above the end point of the line will be displayed in white. The gray values in between the window will be mapped on a shade of gray. You can change the window size by clicking your left mouse on one of the points and dragging it to its new location. To move the window select the line and drag it to its new position. You can also choose one of the predefined “windows” by selecting the appropriate scale from the menu on the bottom of the tab. The following steps will describe the necessary actions to achieve a nice segmentation mask. A segmentation mask is a collection of pixels of interest that constitute an object you wish to work on. One can create several dependent or independent - masks, each displayed with their own identifying color. Usually several masks will be needed to obtain a final segmentation object that contains the information that is needed.
Thresholding Thresholding means that the segmentation object (visualized by a colored mask) will contain only those pixels of the image with a value higher than or equal to the threshold value. Sometimes an upper and l ower threshold is needed; the segmentation mask contains all pi xels between these two values. For example:
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A low threshold value makes it possible to select the soft tissue of the scanned patient. With a high threshold, only the very dense parts remain selected. Using both an upper and a lower threshold is needed when the nerve channel needs to be selected. Defining a good threshold value also depends on the purpose of the model. If you ust want a nice looking model, a lower threshold value is recommended since this results in a model with less holes. On the other hand, when the model serves for modeling prostheses a higher threshold value is preferred. Click the Threshold button
.
To change the threshold value, press the left mouse button on a slider in the Threshold Toolbar and move the slider by moving the mouse (while still holding the left mouse button). Some tips for selecting an adequate threshold value: Look at different images. You can change images of any view by:
using the arrow keys, the page up and page down keys
using the slider on the right in the window border
moving the slice indicators
Click the Profile button
.
Draw a line (with your mouse) in the main window. Along this line an intensity profile is generated (figure 2-1). The straight horizontal line is your current threshold value. Click on Start Thresholdin g and drag the straight-line up/down to set a good threshold. If you want a good visualization model, select a threshold slightly above the intensity plateau of the soft tissue. If your model will serve for modeling prostheses, place the l ine between the soft tissue plateau and the top value of the bone. If a p roper threshold is set, click on End Thresholdin g to save the current value.
Zoom in on a part you’re interested in. First, from the pull-down menu next to the zoom button, select Box. Click the Zoom-button
: the mouse is displayed as a loupe. Click the left mouse button on the image and drag for
creating a zoom rectangle, release for zooming. To return to the whole image, click the Unzoom-button
.
A good threshold value for Mimi is about 270 (Hounsfield scale). The threshold value is displayed in the Min. box of the Threshold toolbar. To end thresholding, click the Ap pl y button. After the thresholding operation a green mask will be created. In a project you can have different masks but you can use the segmentation tools only on the active mask. To choose the active mask, select it in the mask tab in the project management. In case the project management isn’t active, select the project management button in the main toolbar.
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You can also hide any mask by clicking on the glasses of the corresponding color.
Region growing The region growing tool makes it possible to split the segmentation created by thresholding into several objects and to remove floating pixels. Click the Region gro wing button Growing window is on the screen.
or press Ctrl + R. The mouse is now cross-shaped and the Region
Select the Source (= Green) and Target mask (= New Mask). Click the left mouse button on one point in the green area of the object of i nterest (which is a part of the current segmentation object, i.e. part of the skull). The program starts to calculate the new segmentation, all points in the current segmentation object that are connected to the marked point will be used to form a new mask. The new segmentation is colored yellow. Click the Close button to close the Region growing window. To make this new mask active, select "Yellow" in the Visualization toolbar. Clicking on the green glasses will hide the green mask. Clicking the button again will make the green mask visible. Check the mask on different images. When we check the images, we see that everything looks fine. It’s time to build a 3D representation. Note: Thresholding needs to be done before region growing, since all previous work is lost after changing the threshold value.
Creating a 3D representation In the mask tab you see all created masks listed with their respective threshold. The names of these masks are Green and Yellow. Selecting one mask will make it active. Now, you still know that the Yellow mask contains the skull, but after a month, when you reload a project, it might be difficult to know in which mask your end result was stored. Therefore, it may be interesting to rename the mask (in Project Management, Masks tab). Click on the name Yellow so that it becomes editable; replace Yellow with a more telling name like ‘skull’.
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.
The "Calculate 3D Models" Dialog box is displayed. Here you can mark (with a green dot in the column called “Selected”) which masks you want to visualize and calculate the 3D by clicking on the Calculate button (if you made segmentations of different objects, like skull and teeth, you can calculate them together and go to lunch in the mean time). Select "Skull" from the list. You can set the visualization quality of your model. This is only the visualization on the screen; this parameter doesn’t need to have any impact on the model that you will actually build on an RP machine!!! Of course, the lower the quality, the less time the program needs to calculate the 3D i mage and the less memory is needed to load the 3D image afterwards.
Displaying a 3D representation If you are in 3-panes layout, click the 3D button coronal images (left corner at the bottom).
to display the 3D representation. It will take the place of the
In the vertical 3D toolbar on the right, you can set the visibility of the different calculated 3Ds. This can also be done in the Project Management's 3D Objects Tab, by clicking on the glasses. Once the 3D image is loaded, different operations are available:
rotate the model with the button button
on the right of the window or moving the mouse pressing the right
select different standard views, like Top, Front, Bottom, by clicking on the button window zoom with the buttons
on the right of the
or Pan with the
change the color of your model and background by clicking the right mouse button and selecting the option “Color”
The model can also be displayed transparent. To do so, push the Toggle Transparency button
. You can
switch between different degrees of transparency (high-medium-low-opaque) by clicking the square button the transparency column.
in
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To change the background color, go to View > 3D Background Color and select the color you prefer.
STL+ procedures The intermediate file between Mimics and STL+ can be one of the following:
“.3dd” file
Masks
3D Objects
You can create a skull.3dd file by clicking the Export 3dd button in the Project Management’s Masks Tab or with the option Export > 3dd in the main toolbar. After clicking the Save button the .3dd files will be placed in the MedData folder. This step is not always necessary. Calculation of the machine files can be done directly on the masks or on 3D objects. Click on the STL+ button in the Masks Tab of the project Management. Press the STL+ button and a window will pop up on the screen with 3 different tabs for each option. Choose the Masks tab, select the mask called “skull” and click the Ad d button. Choosing the 3D tab would have enabled you to select a 3D object. Please note that multiple 3Ds or masks can be selected and added to the list but it is not possible to add both masks and 3Ds. If you're interested in creating files for Rapid Prototyping or exporting an STL or VRML file, pl ease continue this tutorial. After selecting the mask or the .3dd file and pressing the Ad d button, the file appears in the output area. If you wish, you can rename the output file to “skull” (in the same way as you would in Windows Explorer). Select the output format. Depending on the type of output fil e format, there are different possible formats, like STL or VRML.
Generating a STL file Click the Next button: the Conversion to STL Dialog box is displayed. You can use the parameters as they are displayed in the screenshot. Further details about these parameters can be found in the STL+ Reference guide. Fill in the appropriate values like in the dialog box and click the Finish button. The calculation starts and an STL file is generated.
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RP Slice procedures RP Slice procedures Note: It is also possible to generate slice files for Stratasys machines. Instructions on how to use these files in Quickslice are also provided (read the STL+ Reference Guide). The file generated in this tutorial will be used in the RP Slice procedures. Within the RP slice dialog you are able to generate a contour file from a mask or a 3dd and you can also generate a support file from a contour fil e.
Generating a contour file Go to Project Management, Masks tab and choose the RP Slice button. Choose the mask called “skull” from the list in the Masks tab of the RP Slice window that just opened and press the Ad d button, the mask will appear in the area below. Select the SLI Output format. Click the Next button, the Conversion to RP format Dialog Box is di splayed. You can use the following parameters in the RP Slice Parameter dialog box.
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Click the Next button to proceed; the Calculation Parameters dialog box is displayed. Fill in the values as displayed below.
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Further details about these parameters can be found i n the STL+ Reference guide. Click the Finish button; the calculation starts and an SLI file is generated. For calculating the support structures, please continue this tutorial.
Generating suppor ts For building the object with Stereolithography, a support is generated directly from the slice file with RP Slice module . Go to the RP Slice window, Contour files tab and set the .SLI file option in the Input format field. Select the file you created in the previous section and press the Ad d button.
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When one contour file is selected, the Next button in the “RP slice – Mask/3dd/contour file selection” window opens the window displayed below.
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Note: It is also possible to generate slice files for Stratasys machines. Instructions on how to use these files in Quickslice are also provided (read the STL+ Reference Guide). The program defaults to full height, so that the whole model is supported. This isn’t always necessary. Check the slices from bottom to top and search for new ‘islands’. To prevent that these islands start floating during the building process, they certainly need support. In the case of "Mimi", a support till layer height 50.00 is sufficient (depending on the resin used). Press the Finish button to start the support generation; an SLI file is created. You now have a model and support file, good luck with the building of the model !!
View of end result
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Simon The Simon case is an example of a dental segmentation. The mandible of the patient was partially edentulous and needed a prosthesis. First, a scan prosthesis was made that resembled the new teeth to be implanted. The patient had this prosthesis at the correct position in his mouth during the CT scan. Because scan prostheses are made out of barium sulfate, an opaque material, they are clearly visible in a CT image. The result is that you see both the bone and the prosthesis in one image, well positioned against each other. Such a procedure with a scan prosthesis gives better esthetic results and the surgeon is able to make a better planning. The images in the Simon project are CT scans of the jaw together with the scan prostheses. It will be your job to do the segmentation of the mandible and the prosthesis. The topics that will be discussed are:
Opening the Project
Preparation of the data o
Windowing
o
Thresholding
o
Region growing
o
Editing
o
Artifacts
o
Multiple particles
o
Scan prosthesis
Boolean Operations
View of the end result
Opening the project In the File menu, select Open (Ctrl+O). Double click the Simon.mcs file.
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Preparation of the data Windowing For correct windowing see the windowing procedures in " Mimi" (Case 2).
Thresholding Go to an axial image where the mandible (without the teeth) is visible (for example, at position -30, 50). Press the Profile line button and draw a line over the bone. The figure below shows a profile line and the corresponding profile dialog box. Press Start thresholdin g and drag the threshold line to a value of about 538 (Hounsfield scale). End the thresholding and save your settings. Close the dialog box.
Profile line over the bone (upper image) and the corresponding profile dialog box
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Region gr owing Press the Region Growing button
and click on the bone of the skull to start the region growing. The skull is
now added to a new mask. Click on the Project Management icon . In the Masks tab, double click the name of the mask and change it to “skull”. Make the previous mask invisible (make sure the skull mask is active before making the first mask invisible).
Editing - Thresholding Separating maxill a and mandible To separate the mandible from the maxill a, we have to disconnect them manually. The trick we will use is the one explained in the Obturator case (Case 5) further on in this tutorial. We first erase a layer from the active mask somewhere between the mandible and the maxilla. Then we perform a region growing on the mandible. The result is that both mandible and maxilla will be in a different mask and thus separated. Look at the sagittal image and place the horizontal indicator between the maxilla and the mandible. Note that it will not be possible to separate them completely in every image, so we have to find the best possible position.
In the corresponding axial image all pixels have to be removed from the active mask. The position of the axial image corresponding to the position of the horizontal indicator in the figure above, is -4,50. Go to this image an d press the Edit masks button . Select the Erase mode, choose a big square as type of cursor and remove all pixels from the active mask. Make sure you don’t forget any! Go to a lower image in the data set and do a region growing of the mandible (do not activate the Leave Original Mask option). Now you have two masks, o ne for the mandible and another for the maxilla. Note: In the region growing toolbar, if you activate the Leave Original Mask option, the pixels selected with region growing will be put into a new mask, but they will also remain in the original mask. If the result of the region growing is not satisfying, you still have the complete original mask and you can start over. If this option is not activated, the pixels selected during region growing are removed from the original mask. In this case you can’t do the region growing again from the same origi nal mask. Change in the Project Management the name of the two masks to “mandible” and “maxilla” respectively. In figure below, these two masks are shown and the red line in between indicates the layer that was removed from the active mask. But be careful! Because it was not possible to perform the separation 100% correct, we will still have to edit the images and make sure that all the pixels that belong to the mandible are really in the mandible mask.
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Scroll through the coronal images and check if every pixel that belongs to the mandible is in the proper mask. Do you notice at position 64,50 that some pixels (at the left side in the image) from the maxilla are wrongly put in the mask of the mandible?
Move both indicators until their point of intersection indicates the wrong pixels (figure above). It concerns two layers of pixels, belonging to a tooth of the maxilla. In the two corresponding axial images (position -6,50 and 5,50), erase the tooth from the mask of the mandible. You cannot be mistaken, because that tooth is also indicated with the point of intersection of the indicators (figure below). If the two layers of pixels are shown in grey values in the coronal image, you can be sure you erased the whole tooth from the mandible mask. If not, move the indicators again in the coronal image so their intersection points to the wrongly colored pixels. In the axial image, remove the pixels that are i ndicated by the indicators from the active mask.
Axial images (position: left -5,50, right -6,50): the indicators point out the tooth that does not belong to the mandible mask. In the sagittal image at position 87,25 (or the coronal image at position 43,25) another collection of badly masked pixels is visible. But now it’s the opposite situation! Three layers of pixels that belong to the mandible are not in the mandible mask. Two layers belong to the maxilla mask and the other layer is the one we erased in the beginning to make the disconnection. Again, mark these pixels with the indicators as it is done in the figure below.
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In the corresponding axial images (at positions -4,50 and -3,50 and -2,50) the pi xels (of a tooth) should be added to the mandible mask. We will make use of a local threshold to do this. To make this threshold clear, a short intermezzo is inserted below.
Indicators point to pixels that should belong to the mandible mask (sagittal view). Local threshold: In the obturator case i t is mentioned that there are three modes to choose from in the Edit toolbar, i.e. draw, erase and threshold. The threshold mode (ctrl + T) is used to set a local threshold. This means that if you apply a local threshold in a particular area of one image, this threshold doesn’t apply to the other images in the project. Remark that the threshold we’ve set in the beginning of this case was global and it applied to every image in the dataset. When you activate this mode, the box with the two default threshold values is shown on your screen. To set a different local threshold, press one of the two arrow buttons and double click on a threshold value. After you changed the value, press Enter. When you move the square over the image while p ressing the left mouse button, every pixel that comes to lie within the square and has a threshold in the threshold range you just set, will be added to the active mask. On the other hand, all the pixels that already belonged to the active mask and that don’t have a grey value within the range will be removed from the mask.
The local threshold range For the moment we don’t have to change the threshold values, but it will be used later on in this case to remove artifacts out of the image. Maybe you now wonder why we will add the pixels of the teeth that belong to the mandible with this local threshold method and not with the draw mode we will use in the obturator case. With the draw mode, can’t you also add pixels to a mask? Yes, that’s true, but there is a difference! With the draw mode you add every pixel you touch with your cursor. With the threshold mode you do the same, but there is one more condition before they are really added: their HU values must li e in the range shown in the box (figure 3-7). In this case, it’s much safer to add pixels by taking into account their grey values. Our segmentation will be more accurate. Press Ctrl + T. The Edit toolbar shows up and the threshold mode is already selected. Choose a circle as type of cursor and make it more or less the same size as a tooth. Make sure that the mandible mask is the active mask. Press the left mouse button and go over the tooth with your cursor. Make sure you got the tooth completely. You can check this very easil y by looking at the sagittal or coronal image: if the wrongly masked l ayers (figure 3-6) now have the color of the mandible mask it’s alright, otherwise you’ve forgotten some pixels. Suppose you added too much pixels, just press E (or select the Erase mode with your mouse) and erase them. If you repeat the thresholding in the necessary axial images (see before to know their positions) you should become a sagittal image like in the figure below. Now we can say that the whole mandible is in the mandible mask.
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Sagittal image after local thresholding
Arti facts The images still don’t look nice, because of all the artifacts. We are going to get rid of them by again performing a local threshold, but not the default one like we just used to add the pixels. To enter the Edit mode, press Ctrl + T. The threshold mode is already selected. Click on the top arrow of the threshold range box (figure 3-7) and double click the threshold 1 value. Change this value to 3000 (if you are working in Hounsfield Units) and press Enter. Because the Hounsfield Units of the artifacts are lower than the ones of the teeth. Go with your cursor over the artifacts and notice that they disappear. Why do we use this high local threshold? Because the HU values of the artifacts are lower than the ones of the teeth. So by setting a very high threshold the artifacts will be removed from the mask because their grey values are not in the range. Moreover, if you accidentally go with your cursor over the teeth, their pixels will remain in the mask, except for the edges (their HU are lower). If you removed the edges from the mask, don’t panic. Set the threshold range back to the default one by cli cking once on the lowest arrow and move your cursor over the tooth again to restore the edges. So, this is the way you should work. Scroll through the axial i mages and remove all the artifacts from the mask of the mandible.
The artifacts in the left image are removed with a local threshold. The right image shows the result
Multiple particles Let’s calculate the 3D image of the mandible. Press the Calculate 3D button and select the mandible mask to be calculated (choose low quality). You get the message that the mask consists out of multiple parts. Answer with “Yes”.
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Visualize the 3D by pressing the 3D button. Rotate the model and remark that there are little particles floating around the mandible. That caused the message you got about the multiple parts. The particles are due to the editing you’ve done to remove the artifacts. To avoid this you have to do a region growing before calculating the 3D. Press the 3D view button again to g et back the sagittal image. Press the Region grow ing button and click into the mandible. Change the name of this new mask to “Total mandible”. Now calculate and visualize the 3D model of the final mandible. You can delete the first 3D (with the particles) li sted in the 3D tab of the Project Management.
Scan prost hesis Can you distinguish between the natural teeth and the scan prostheses in the 3D model of the mandible? It’s quite simple; the natural teeth are connected to the bone, while the scan prostheses are not. There are 3 teeth of the scan prostheses at the patient’s left side and one at his right side. In the figure below, the scan prosthesis (axial view) is marked with rectangles.
Axial image indicating the prosthesis in the boxes. We would like to have the mandible without the prosthesis and the prosthesis itself into two different masks. There are two ways to achieve this. The first one is to proceed with the segmentation of the final mandible an d to remove the prosthesis from the active mask. The second option is to perform a segmentation of the prosthesis. We opt for the latter. We will do a region growing of the prosthesis twice, once at either side. But, we first have to make sure that the prosthesis is completely disconnected from the natural teeth. The intention is to remove (from the final mandible mask) the pi xels surrounding the prosthesis and the pixels connected to the prosthesis. The goal is to get the prosthesis nicely isolated in every image. Keep the following advice into account: remove enough pixels in the surrounding of the prosthesis, because sometimes in 2D it looks like there is no connection, but there is still one in 3D. So a 3D model can be very tricky!
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Project Management – Masks tab Make the mask of the final mandible active and press the Duplicate button in the Masks tab of the Project Management window. This way a backup mask i s created that we can use to do the segmentation of the prosthesis, while the original Final mandible mask is left unchanged. The last one will be used later on to perform Boolean operations. Proceed with this backup mask (if you don’t like the color, press the Color button in the masks tab and choose the color you like). Scroll through the axial images and remove (enough!) pixels surrounding the prosthesis from the active mask. In the figure below it is shown for the axial image at position 11,50. If you think you disconnected the prosthesis completely, press the Region Growing button. Make sure your target mask is a new mask (if not, select “new mask” from the drop down list) and that you activate the Leave Original Mask option. This last option is very important!
The prosthesis is disconnected in this layer Click on the left or the right prosthesis. If you disconnected the prosthesis entirely, only the prosthesis should be shown in the color of the target mask. If this is not the case, make the previous mask active again, delete the last mask in the list (generated for the regi on growing) and remove more surrounding pixels from the backup mask. Also in the layers where you don’t see the prosthesis it can be useful to remove some pixels belonging to the teeth next to the prosthesis. repeat these actions for the prosthesis at the other side. Give the masks of both prostheses proper names.
Boolean Operations Let’s examine what we’ve obtained so far: the final mandible (with prosthesis), the left prosthesis and the right prosthesis in three different masks. That’s nice, but we said earlier that we would like to have the mandible without prosthesis. We can achieve this with some Boolean operations we can achieve this. Press the Boolean operations button
. Let's use the following calculation:
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Mandible without prosthesis = total mandible – left prosthesis – right prosthesis Follow the steps below:
Mask A: final mandible Operation: minus Mask B: left prosthesis Result: new mask (called mask C for reference) After these options are set, press the Ap pl y button. Mask A: mask C (obtained in the first step) Operation: minus Mask B: right prosthesis Result: new mask
After these options are set, press the Ap pl y button. Press the Close button. The last mask (the one that should be active now) contains the pixels of the mandible without the prosthesis. Calculate and view the 3D of this mask. Show also the left and right prosthesis. The other 3Ds can be set invisible. You should have a model that looks like this one.
View of end result
Hip In the fourth tutorial we will discuss some of the possibilities of the MedCAD module. To finish this tutorial you will have to have a license for the MedCAD module. The topics that will be discussed are:
Opening the Project
Preparation of the data
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o
Thresholding
o
Region growing
Calculation of the Polylines
Patching of the contours
Creation of MedCAD objects
Visualization possibilities
Opening the project The objective for this part is the creation of a file ready to use in all CAD-systems supporting the IGES-interface. The part of the "Hip" we’ll focus on is the right femur of the patient (left in the images). In this IGES-file a basic reference system calculated on the data as well as a partial modeling of the outer contours using freeform surfaces will be present. It is strongly advised to first follow the tutorial of Case 2 to obtain the necessary skills for segmentation and image processing. In the File menu, select Open (Ctrl+O). The Open dialog box shows all projects in the working directory. Double click the hip.mcs file (Mimics project file).
Preparation of the data Thresholding A good minimum threshold value for this case is 1235 (Grey Values) or 211 (Hounsfield values). Set this threshold in your base mask and apply it. The procedure is explained in more detail in Case 2.
Region gr owing We want to make a model of the right femur (left in the image set). Therefore use the following steps:
Click the Region Grow button or press Ctrl + R. Set the Source to Green (if this is your base mask) and Target to New Mask. Check the Multiple layer box. Click the left mouse button on one point of the right femur (left on the images). The right femur has now been grown into a new mask (Normally if you have started fresh the femur will be in the yellow mask now).
To calculate your 3D, go to Project Management, Masks tab, select the yellow mask and press the Calculate 3D button. The yellow mask will be automatically selected in the Calculate 3D window, but you need to set the qual ity to “high” and press the Calculate button. The 3D view will replace the sagittal view. You can find more details about this in Case 2.
Calculation of the Polylines Go to the Project Management.
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Project Management - Masks tab Select the yellow mask and click on the action button, select the Calc Polyline option from the action list. The Create Polylines dialog box appears with the Yellow mask already checked; click OK. The borders of your yellow mask will be calculated and displayed as a polyline in both 2D and 3D images. In 2D you can see the polylines right away: they're displayed together with the images and your masks. You can also calculate polylines by clicking the
button in the segementation toolbar.
To see them in 3D, press the 3D View button. Make the 3D invisible by clicking on the yellow cube in the right toolbar. Now you will only see the polylines. When you rotate the polylines and switch on the depth shading (check box in the bottom part of the screen), you should see something like the image below.
3D view of the polylines
Patching of contours Since we are only interested in the outer contours, we need to select these out and grow them to a new set of polylines. Go to layer -523 and zoom i n on the right femur in the 2D image (xy plane). Click the Polyline Growing button
in the MedCAD toolbar.
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Set all parameters as displayed in the image below: i.e. the set to start from, the set that will contain the grown polylines, ... .. In order to select a polyline, you need to draw a rectangle over it. Hold the l eft mouse button down, drag it to the opposite corner of the rectangle and then release the left mouse button.
The growing of the polylines stopped at layer -513 because of a small extension on the bone (scroll through the images pressing the Ctrl + Arrow keys). This needs to be removed in layers –513 and -511. Next the polylines need to be updated and then we can proceed with the polyline growing:
Click the Edit masks button and go to the erase mode or press Ctrl + E
Make sure that the Yellow mask is Active
Erase the extension on the bone
Press the Ctrl + U key or the Update Polylines button in the Edit toolbar
Repeat this for the following images.
Scroll back to image -513 and click the Polyline Growing button. Set "selection 1" as the target polyline and use 96 % as matching parameter. Select the polyline. Scroll to image –485 (figure below).
Image –485 of the Hip At this slice you see a cavity in the contour. If you want to restore this with editing, keep in mind that it will be the yellow contours that will be updated, so we need to remove the pink polyline first. Do a Polyline Growing from Selection 1 to a New Set ; be sure to turn Auto Multi-Select off. You can delete this set by selecting it in the Project management and then pressing the Delete button. Lose the cavity by drawing in the mask and updating the polyline (Ctrl + U). Similar editing and updating of the polylines needs to be done on slices: -483 till -479, -475, -471 (on the femur head). Don't forget to update for every image. When all corrections have been made, the polyline growing can continue. Go back to layer -485 and perform the Polyline Growing (from Set 2 to Selection 1, matching parameter 95 %, Auto Multi-Select on)
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When all editing was performed properly, all layers until -477 are now stored in Selection 1. The femur head and the greater trochanter will be grown into new selection sets. The end result should look li ke the figure below.
Polyline sets
Creation of MedCAD objects On the great trochanter and on the l ower part of the femur we will fit a Free Form Surface, on the femur head, we will fit a sphere. In the Project Management on the Polylines tab, you will find a button Fit Surface. Choose Selection 1 and press the Fit Surface button. The following dialog box will appear.
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Surface Fit Parameters You can accept these default values and a Free Form Surface will be fitted on Selection 1. Note: Some caution in increasing the number of control points is advised. The basis of a B-spline is a polynomial and a polynomial has the tendency to wave. So, if the number of points is too high, the fit on the polyline will become worse. Repeat this set on Selection 3. The Free Form Surfaces are visible in 3D as a shaded surface and in 2D you will see a cross-section on every layer of this Free Form Surface. To fit a Sphere on Selection 2, go to the MedCAD menu and select Sphere > Fit on Polylines. Choose the correct polyline set. The result of all these fittings should look like following figures:
Objects fitted on the Polyline sets
Imported STL files
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Visualization possibilities When a prosthesis is designed, the STL file can be loaded in Mimics. One can rotate and move this prosthesis to obtain the best fit of the prosthesis onto the femur and check the design related to the bone structures. You can import an STL file in the Project Management from STLs tab. Click the Load... button. The STL file will be visible both in 2D (as cross-sections) and in 3D. To adjust the position of the STL file, click the Move button to move the STL file or the Rotate button to rotate it. Both actions can be performed in 2D as well as in 3D.
Obturator In the previous cases we have segmented bone structures, whereas in this project we are going to make a softtissue model. An interesting application is the modeling of the soft tissue around the cavity of the mouth. Such a model can be used as a mold for obturator prostheses. In the case study following this introduction we will do just that. How are we going to model this soft tissue? Since we are only interested in the area around the cavity, we need to limit the model to the region of interest. By erasing one layer from the active mask in every direction, the cavity and the soft tissue around it will be separated from the rest of the image. This way the region of interest is captured in a 3D box delimited by the removed layers. Next we perform a region growing that starts in the region of interest. Because this region is separated from the active mask, only this area will be put into a new mask after the region growing is done. From the new mask a 3D model can be calculated which will contain just the cavity of the mouth and the soft tissue surrounding it. The topics that will be discussed in this tutorial are:
Case Study
Preparation of the data o
Windowing
o
Orientation
o
Thresholding
Editing
Region growing
View of the end result
Case study Obturator prosthesis for oncologic patients Case presented by Dr. L.L. Visch from Daniel den Hoed Kliniek Rotterdam. The first picture shows the cavity in the mouth of the patient after resection of a tumor. In order to protect the tissue weakened by irradiation and to be able to breathe and eat normally, this hole needs to be filled by an implant.
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A CT-scan of the patient was made. The soft tissue around the cavity, clearly visible on the scans, was modeled. This model served as a direct mold for the implant.
The implant, called an obturator prosthesis, was cast from the mold in a bio-compatible sil icone.
Absolutely no surgery was needed to implant the obturator prosthesis. As the silicone prosthesis is plastic deformable, it can be implanted very easily. The prosthesis fits the cavity much better than ever could have been achieved by using conventional impression techniques. These traditional techniques produce a master of the obturator prosthesis by making an impression of the cavity in a deformable plastic material.
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The prostheses cast from such masters are always less accurate because of the presence of undercuts (the impression technique is not sensitive to local internal broadening of the cavity) and can severely damage the sensitive and vulnerable surrounding tissue. The soft prosthesis is fixed by means of magnets on a hard dental implant. This makes it possible to take it out for inspection and to replace it afterwards.
Preparation of the data Preparation of t he data In the File menu, select Open (ctrl+O) or click the button
. Double click the obturator.mcs project.
Windowing For correct windowing see the windowing procedures in " Mimi" (Case 2).
Orientation When the project is loaded, a Change Orientation window pops up. In the axial image you see the orientation strings L and R, which stand for Left and Right respectively. In the coronal and sagittal image several Xs are displayed instead of the orien tation strings. Move the mouse cursor to the top X in the sagittal or coronal image. The cursor is changed to a hand and when you right-click, a menu appears with all possible orientation strings. Select “Top ”. Remark that all other orientation strings are completed automatically. Do the same to set the Anterior-Posterior orientation parameter looking at the image displayed.
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You can always change your orientation parameters, going to File > Change Orientatio n.
Thresholding A reliable way to define an appropriate threshold is to make use of a profile line (see also Case 2). Press the Profile line button
and draw a line in the axial image over the cavity.
Profile line over the cavity of the mouth See the figure above (axial image on position 374) to have an idea where to place the profile line. You get a profile like shown in the image below. You can clearly see the transition from the soft tissue to the cavity. Press the Start thresholding button. To visualize all the soft tissue in the mask, drag the lowest threshold line to the value –444 (Hounsfield scale). Press again the End thresholding button and answer yes to the question whether
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you want to save the threshold value or not. Close the window.
Editing In the axial image, go to position 387,00. Press the Edit masks button . The edit toolbar is displayed on your screen. Your cursor has become a little square. If not, go to Type and sel ect a square from the drop down li st. Notice that the length and the width of the square are displayed and can also be altered. The easiest way to change the size is to press the control key and your left mouse button simultaneously and to move to the right/left to make the square bigger/smaller.
The three modes available are listed below. To make a mode active, just click in the little circle on the left of the mode or press the first letter of the desired mode. When the edit mode is not yet selected and you use the shortcuts between parentheses below, the edit toolbar appears and the associated mode is activated.
Draw (Ctrl + D): Every pixel that lies within the shape of your cursor, while pressing the left mouse button, will get the color of your active mask. In other words, you add pixels to the active mask by going over the pixels with the square. Erase (Ctrl + E): This mode is the opposite of the draw mode. You remove all the pixels from the active mask by moving the square (keeping the left mouse button pressed) over the pixels i n the image. Threshold (Ctrl + T): This mode is used to set a local threshold. This means that if you apply a local threshold in a particular area of one image, this threshold doesn’t apply to other images in the project. Remark that the threshold we’ve set in the beginning of this case was global and it applied to every image in the dataset.
When you activate this mode, a box with the two default threshold values is displayed on your screen. To set a local threshold, press one of the two arrow buttons and double click on a threshold value. After you have changed the value, press Enter. When moving the square over the image while pressing the left mouse button, every pixel that comes to lie within the square and has a threshold within the threshold range you set, will be added to the
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active mask. On the other hand, all the pixels that were already part of the active mask and that don’t have a grey value within the range will be removed from that mask.
For the current case we are only going to use the draw a nd the erase mode. In the Simon case we already illustrated the threshold mode. Working on the axial i mage in position 387 activate the Erase mode (Ctrl + E) and set a very large square (for example, 200 by 200). Press your left mouse button and wipe off all the color in the image. Be sure not to forget any pixels! Close the Edit toolbar.
Notice in the sagittal image that one layer is shown in grey values. In the figure below, the sagittal image is displayed and the arrow points to the layer that has been removed from the active mask (the slice indicator is moved down to see this).
To see the result of erasing the mask in one layer, we will now perform a region growing . Select the axial image at a position lower than 387,00, (= the position of the image we removed from the active mask). Press the Region Growing button, a window will be displayed on the screen.
Check both the Multiple Layer and Leave Original Mask checkboxes and click on an arbitrary position in the active mask. You see that all the i mages at a position lower than 387,00 are put into a new mask (yell ow mask in figure below). Close the region growing toolbar.
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Why are the images above this position not included into the new mask? As you already know, a region growing looks for pixels that are connected to each other and puts them into a new mask. But, because we have disconnected the lower images from the higher ones, we have limited the area of the region growing. This will be the trick we will use to get our region of interest into a separate mask. How will we proceed? In the same way as above, we are going to erase a complete layer from the active mask on every side so that our region of interest is completely surrounded by these removed slices. After we perform a region growing within that region, we should have the oral cavity and the surrounding tissue in one mask, like we wanted. Activate the axial image. Go to position 362,00 and press Ctrl +E (or press the Edit masks button and select the erase mode). Make a big square and erase all the pixels from the active mask. Take a loo k at the sagittal image. Two horizontal lines are shown in grey values. The top and the bottom of our box are now defined. To set the left and righ t boundaries of the box, you have to remove two layers from the mask in the sagittal image. Try to visualize the situation and make sure you understand why we will now operate in the sagittal image. Erase all pixels from the active mask at position 126,49 (left boundary) and 42,05 (right boundary) in the sagittal image. In the axial image two vertical lines in grey values are visible. To close our box, a separation still has to be made on the posterior side. Activate the coronal image and remove all pixels from the active mask at position 76,61. In the axial image the removed layer is visible. Setting a boundary on the anterior side is not necessary. In figure 5-10 you can see the boundaries of the obturator on the yellow mask.
Region growing Now that the box is delimited by the layers removed from the active mask, a region growing can be performed to get the obturator into a new mask. Go to an axial image that has a position between 362,00 and 387,00. Thi s is to make sure that the starting pixel for the region growing lies within the region of interest. Press the Region growing button and click in the axial image within the box.
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Boundaries of the obturator in the axial image. The obturator is now within a ne w mask. In the figure below you clearly see the obturator within the active (blue) mask from the axial and the sagi ttal viewpoint.
Axial and sagittal view of the obturator Because we disconnected the pixels of the obturator from the other pixels in the origin al mask, the region growing was confined to the region of interest. Press the Calculate 3D button and select the mask of the obturator. Choose custom quality and press the Calculate button. The processing of the 3D model is started.
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To visualize the 3D image, make the axial image active and press the 3D View button
.
Note that the model will always be visualized in the sagittal view, unless you select to view it in a fourth pane in Option s > Preferences > Visualization > View. On the right of the 3D obj ect you see a toolbar and a button where you can select some predefined viewpoints for your 3D model
. If you press the bottom view you
should obtain a model as shown in figure 5-12. You can also enable transparency using the
button.
View of end result
Manual Import In this case we will show you how you can use the manual import function to import any image data you want. The topics that will be discussed in this tutorial are:
Importing images
Manual Import
o
Parameters
o
Preview the images
o
Choosing the right parameters
Convert the images
Importing images The goal of this chapter is to teach you how to i mport images with the Manual Import option and convert them to a Mimics project. Select Import Images form the File menu. An Import Project Wizard will be displayed where you need to point to the "MedData\Import3" directory (STEP 1)
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There are 3 ways to import images, depending on their file format: automatic, semi-automatic and manual import. Only the manual import will be explained in detail, because the other ways are more straightforward to use and are mentioned already in the tutorial Case 2. Note: When you press the Next button, all the project files listed will be converted. Select only the files you want to convert and leave the others unselected.
Manual import Manual impo rt In the first step of the wizard, browse to the following path: \MedData\convert\. The images will be selected automatically. Select the Manual Import button and press Next. A new window is displayed on your screen. The most important parameters are explained in the next paragraph.
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Parameters File header si ze The file header size is calculated automatically, based on the file size, the resolution of the images and the pixel type. Typically a file contains both a file header and the image itself (in some rare cases also a footer is present). The file header can contain information about pixel size, patient data, … The image is a matrix of pixels. The horizontal (or vertical) image size is equal to the number of pixels in that direction.
Structure of a fil e Common sizes of images are: 256 * 256
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512 * 512 1024 * 1024 The number of bytes per pixel depends on the type of the pixel. Some examples of pixel types and their respective sizes (note that these types can be either signed or unsigned, however, this does not affect their size):
Byte: 1 byte
Short: 2 bytes
Long: 4 bytes
Float: 4 bytes
Image size = horizontal image size * vertical image size * number of bytes per pixel In this example, the images have a resolution of 256*256. If you fill these values in, you will see that Mimics will set the file header size to 8432 bytes.
Exam information Fill in an appropriate name for the patient name. This will be the name that is used for your project.
Image information In the Image Information frame you see that the value for the image size is still 512*512. Correct the size to 256 * 256 pixels. The default val ues for the other parameters are correct in this case.
Pixel properties Select Signed Short for the parameter Type and Low Byte First for the parameter Byte Swapping.
Preview the images Press the Show Preview button and take a look at the images to check whether the parameters we filled in were correct. On the left side, the first of the 8 images is displayed. Scroll through the images by moving the arrow on the right (or use your mouse wheel if you have one). For each image a histogram is displayed that gives you information about the range of grey values that are present in the image and their respective quantity. If you want to know the amount of al l the different grey values in the entire dataset (and not just in one image), you have to press the Sample button on the right. Notice that the title of the middle frame has changed to Sampled. What if you have a very large dataset? Don’t worry, you can restrict the amount of images that is used for this calculation. For example, fill in the number 2 for the interval. Now only 4 images are taken into account, namely the first, the third, the fifth and the seventh image.
Press the OK button to close this window.
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Choosing the right p arameters Let’s experiment a little bit with the different parameters. The examples will help you fill in the right parameters when the image does not look like you expected it to.
File header si ze: Set the file header size back to zero. Select the Show Preview button. Notice that all the pixels are shifted. Fill in the correct value and click the Update button to adjust the preview. Pixel Type: Select Unsigned Short for the pixel type and preview the images. Remark the loss of information due to the restriction to positive grey values. Select the correct type and click the Update button to adjust the preview. Byte Swapping: Choose High byte first for the byte swapping and preview the images. You can see that there are local distortions all over the image, because the data is read in the wrong order. Fill in the correct value and click the Update button to adjust the preview.
Influence of the file header size
Influence of the pixel type (signed/unsigned)
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Influence of the byte swapping (high first/low first)
Convert the images If the images look good in the preview, click the OK button in the Manual Conversion Options window. In the wizard window you should see the name of the patient and some other i nformation about the data. Select the project you want to convert and check the box. Press the Open button, the project will be saved in the default folder (usually MedData). A Mimics project is created from the data and it will be opened automatically showing you the Change Orientation window.
FEA Tutorial In the FEA Tutorial we will explain the work-flow for making a FEA analysis on a model of the Femur. We will start with a dataset of a Femur a nd explain how to do the segmentation, how to calculate the 3D, how to remesh the 3D and how to assign materials to the 3D. The FEA and STL+ module have to be licensed to be able to conclude this tutorial. The topics that will be discussed in this tutorial are:
Opening the Project
Calculating a 3D
Remeshing the 3D
Exporting the remeshed 3D object
Material Assignment
Exporting the Volumetric Mesh
Opening the project In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Femur.mcs file.
Calculating a 3D There is already a Green mask available in this dataset that will be used to calculate a 3D object. In the Calculate 3D dialog select the High quality setting and click on calculate.
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Remeshing the 3D In the next step we will remesh the 3D to make it optimal for FEA purposes. Start the remesher by going to the FEA menu and choose Remesh, select the calcul ated 3D and click on the remesh button.
This will open the remesher with the part already loaded:
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There are several quality parameters available to measure the quality of the triangles. For this example we will use the height/base parameter. This parameter measures the ratio between the height and the base of a triangle and normalizes the value. A perfect equilateral triangle has a quality of 1 and a very bad triangle has a quality of 0.
Make sure the Part Quality Sheet is on in the remesher (View menu: Part Quality Sheet):
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This quality histogram shows the amount of triangles that have a certain quality. Then drag the green slider to 0,40. This is the quali ty threshold we will use for our project. Below the histogram you can see three values:
Value 1 is number of triangles that have a quality below the minimum quality threshold. Since the minimum quality threshold is 0 in our project, there are 0 triangles with a lower quality Value 2 is the number of triangles that have a quality between the minimum and maximum threshold. In this case we have 170 triangles. We will try to increase the quali ty of all those triangles. Value 3 is the number of triangles that have a higher quality as our quality threshold. In this case 56618.
For more information about the remesher in general and quality in specific, please have a look at the Remesher Help file.
Remeshing Protocol Below is a description of the remeshing protocol that you can use to remesh the Femur. The values given are those used for the Femur example and will have to be adapted if your part has a different scale (i.e. geometric error, maximum triangle size and, to a l esser degree, smallest edge length). The protocol can be divided in three big steps: 1.
Reduce the amount of detail
2.
Reduce the amount of triangles of your object
3.
Improve the quality of the triangles of your object
4.
Reduce the amount of triangles while preserving the quality
5.
Remove extra shells
In between these steps measures will be taken to make sure that the object has no intersecting triangles and has no bad edges. STEP A: Because the 3D object will be used for FEA only, you can reduce the amount of detail by applying a
Mimics Tutorial
smoothing to the 3D object. Go to Tools -> Smoothing (or select the smoothing icon toolbar).
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on the top of the
Perform a global smoothing and use the following parameters: Smooth Factor 0.5, Shrinkage Compensation Factor 0.5 and 3 iterations. Step B: The 3D object contains too much triangles for an FE Analysis. To reduce the amount of triangles, go to Tools -> Global Remeshing -> Triangle Reduction -> Normal (or use the Normal triangle reduction i con on the top toolbar ) and use following parameters for the normal triangle reduction: geometric error: 0.1, 5 iterations, angle 15 degrees. Do this 2 times, once point-based and once edge-based.
STEP C: You can now optimize the quali ty of the triangles with the Auto Remeshing tool. This tool uses parameters as the Min edge length and Max edge length. You can get a n idea of the edge lengths present in the mesh by selecting the inspection parameter Smallest edge length and Largest edge length. In the Quality histogram select I to show the histogram of the selected inspection parameter.
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You will notice that most of the triangles have a smallest edge bigger then 2mm and a largest edge bigger then 3mm. To Auto Remesh the 3D object, make sure that the height/base parameter is selected as quality parameter. Go to Tools -> Global Remeshing -> Auto Remesh Part -> Split-based Method (or use the Split-based remesh icon on the top toolbar ) and use the following parameters: quality threshold: 0.3, geometric error: 0.1, minimal edge length 2.5, 3 iterations, 1 move iteration, maximum edge length of 4 mm, preserve initial mesh on.
STEP D : You can now reduce the amount of triangles while preserving the achieved quality of the mesh. Go to Tools -> Triangle reduction -> Qualtiy preserving and use the following parameters: Quality threshold 0.3, number of iterations 3, Max Geometry error 0.05 mm, Max edge length 5 mm.
STEP E: Call the self-intersection test. No intersections should be found. When you are satisfied with the quality of the mesh, go to File -> Exit meshing module and click on Yes when the remesher asks you if you want to save the changes to the mesh. You will then return to Mimics and the remeshed surface mesh can then be exported.
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Exporting the remeshed 3D object Now you can export the remeshed 3D object in Mimics to a Patran neutral, Abaqus or Ansys file. To do this go to the FEA menu and choose Export. Select the 3D, choose the correct format and export the mesh:
This remeshed surface mesh can then be used to generate a volumetric mesh in your FEA preprocessor. We have provided a Patran neutral volume mesh in the tutorial files so this will be used further on. It is of course also possible to use your own volume mesh of the jaw.
Material Assignment When you have created a vol umetric mesh in your FEA preprocessor from your remeshed object, you can load this volume mesh in Mimics for material assignment. Patran, Abaqus and Ansys volume meshes are supported (see also supported files). We have provided an example volume mesh for the Femur project which we will use. To load the volume mesh of the Femur go to the FEA menu and choose Import. Browse to the directory where the tutorial files are i nstalled and select the femur_volume_mesh.out file. You can see the mesh lis ted in the FEA mesh tab. This mesh is invisible by default, so make it visible. If the surface mesh of the Jaw is still visible, make it invisible.
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Note: We will use grayvalues for this tutorial, so if you are working in Hounsfield units, please change this by going to the Options menu, choose Preferences and change the Pixel Unit in the General tab. With the FEA mesh of the Femur selected, click on the Materials button. Mimics will display a message that the grayvalues for this mesh have to be calculated before you can do a material assignment. Choose Yes to continue. After the calculation you will see following dialog box:
Mimics shows for each grayvalue the amount of elements that were assigned that particular value. We will then convert this grayvalue to material properties. In this tutorial we will use the uniform method. STEP A: If the uniform method is not selected, click on the radio button next to Uniform. STEP B: Enter the number of materials in the edit box. We will use 10 materials for this tutorial. The FEA module will now divide the range of grayvalues that occur in the volume mesh into 10 equally sized intervals that each represent a material. You can see this di scretization by choosing the Materials histogram:
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STEP C: Enter a density expression to convert the grayvalue of each material to a density. For this tutorial we will use following expression: Density = -13.4 + 1017 * Grayvalue. STEP D: Choose to write out only the E-Modulus material properties in the exported file by deselecting the selection boxes before Density and Poisson Coefficient. We will use following expression for the E-Modulus: EModulus = -388.8 + 5925 * Density. STEP E: Check the values for the materials that will be assigned in the material editor:
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STEP E: Press the OK button to assign the materials to the FEA mesh. The elements of the FEA mesh will be colored according to their materials:
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This volumetric mesh can then be exported together with the material assignment (in this case only the EModulus).
Exporting the Volumetric Mesh The volumetric mesh, together with the material assignment can be exported to Ansys, Patran Neutral and Abaqus files and can then be used to do FEA analysis on the mesh. To export the mesh go to the FEA menu and choose Export. Then go to the FEA tab, a dd the correct mesh to the export list, choose the required format and export directory and click on the OK button.
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Simulation Tutorial In the Simulation Tutorial we will explain some of the functions that are available in the Simulation module. We will start with a dataset of a skull with a hole in it and explain how to do the segmentation, how to calculate the 3D, how to cut, split and reposition a custom implant.. The Simulation module has to be licensed to be abl e to conclude this tutorial. The topics that will be discussed in this tutorial are:
Opening the Project
Windowing
Thresholding
Region Growing
Calculating a 3D
Cutting
Splitting
Mirroring
Repositioning
Opening the project
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In the File menu, select Open (Ctrl+O). Browse to the directory where you have installed the extra Tutorial Files and double click the Skull_with_hole.mcs file.
Windowing For correct windowing see the windowing procedures in " Mimi" (Case 2).
Thresholding Go to an axial image where the skull is vi sible (for example, at position 18,94). Press the Profile line button and draw a line over the bone. The figure below shows a profile line and the corresponding profile dialog box. Press Start thresholdin g and drag the threshold line to a value of about 1250 (Grayvalue scale). End the thresholding and save your settings. Close the dialog box.
Profile line over the bone (upper image) and the corresponding profile dialog box
Region Growing Now we will use the region growing tool to separate the skull from the artifacts and noise in the images:
Click the Region Grow button or press Ctrl + R.
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Set the Source to Green (if this is your base mask) and Target to New Mask. Check the Multiple layer box.
Click the left mouse button on one point of the skull. The skull has now been grown into a new mask.
Calculating a 3D Go to the Project Management by clicking its icon
and choose the Masks tab.
You'll see all created masks listed with their respective threshold. Selecting one mask will make it active and it will appear in the Active Mask field in the visualization toolbar automatically. It is possible to hide/show a mask by clicking on the glasses.
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Click on the Calculate 3D button.
The "Calculate 3D Models" Dialog box is displayed. Here you can mark (with a green dot in the column called “Selected”) which masks you want to visualize and calculate the 3D by clicking on the Calculate button. Select the "Skull" mask if it is not already selected and click on the Calculate button.
Cutting After the calculation of the 3D you will see a 3D representation of the Skull mask. To be able to make a cut that fits well, make the skull transparent by clicking on the button and choose to view the skull from the Right view. Now you can pan and zoom so you can see the hole clearly.
If you then zoom and pan, you can clearly view the hole in the skull through the intact side.
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This way we can easily draw around this hole. To do this, select the Cut with Polyplane tool from the Simulation menu (CMF/imulation -> Cut -> With Polyp lane). You will see following dialog:
Select the 3D from the skull in the Objects to Cut list. The New button is already enabled so we can immediately start drawing a cutting path. Do this by clicking several times with your left mouse button around the hole like below. To end the drawing, double click with your left mouse button.
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You can see that a cutting path has been added to the cutting path list. You can now make the 3D opaque again by clicking on the not:
button. You can then rotate the 3D to determine if the cut went through the whole skull or
As you can see, it would be best if we adjust the depth of the cutting path. You can do this by clicking on the Properties button while the cutting path is selected. This will open the cutting path properties dialog:
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Adjust the Depth of the cutting path from 20.0mm to 30.0mm and enable the Closed checkbox (this will close the cutting path). Click on Preview to view the result. When you are happy with the result, close the Cutting Path Properties by clicking on the OK button. Enable the Keep Originals checkbox (since we want to keep the original 3D) and finish the cut by clicking on the OK button of the Cut with Polyplane tool. You can see in the 3D objects list that a new 3D object was added.
Splitting The next step is to split the two cut parts of the newly generated 3D. To do this, go to the CMF/Simulation Menu and choose Split.
Select the freeform object, choose to keep all parts and disable the Keep Originals checkbox. You can then click on Preview to preview the split and then on OK to apply the split.
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As you can see, two different objects were created and have been given a different color. You can make the largest part invisible since we will only need the small part to fix the defect in the skull.
Mirroring To mirror the part to the other side of the 3D, we will need a mirror plane. The Mimics simulation module generates a default sagittal plane, but we will have to adjust this plane a bit to make sure it's suitable for this dataset. To do this, go to the Simulation Layout (by pressing F5 or by going to the View menu, choose Layouts and then Simulation Layout). Then make the original skull visible and go to the CMF/Simulation menu and choose Measure and Analyse .
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You can see in the right dialog that you can change the Sagittal Plane. Click on the Change button and adjust the Sagittal plane (by dragging the white po ints with your left mouse button) in the axial images to make sure the sagittal plane goes through the center of the nose.
After this, close the Measure and Analyse tool by going to the Simulation Menu and choosing Measue and Analyse again. Then mirror the part by going to the Simulation Menu, from the advanced Tools select Mirror . Select the correct part and mirror plane and disable the Keep Originals checkbox and click on the OK button to apply the mirroring.
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As you can see, the part is mirrored, but not correctly positioned. We will reposition this part in the next section of the help.
Repositioning To reposition the part, got to the CMF/Simulation menu and choose Reposition. This will open following dialog:
Select the Mirrored part and start the repositioning. The easiest way to do this, is to first reposition the part with the mouse and then do some fine-tuning with the parametrical translation and rotation tools. So click on the Move with Mouse button and reposition the part. You can translate the part by dragging the center point with your left mouse button and rotate the part by dragging the corners of the selection box with your left mouse button. Keep in mind that you can also reposition in the 2D views so this makes it a lot easier to get a real nice fit. During repositioning it is also possible to scroll through the axial images to make sure the fit is optimal on all slices.
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When you are happy with the fit, you can click on the An aly ze Mot io n button to see the final translation and rotation of the part.
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To apply the reposition, click on the OK button. If you have a license for STL+, you can then export the part and the skull to STL files and continue working on the custom implant in your design software.
CFD Tutorial In the CFD Tutorial we will explain the workflow for creating a 3D model of the throat that is suitable to do a CFD analysis on. This tutorial will explain how to link between Mimics and Fluent. We will start with a dataset of a head and explain how to do the segmentation, how to calculate the 3D and how to remesh the 3D. The FEA module has to be licensed to be able to follow this tutorial. The topics that will be discussed in this tutorial are:
Importing the images
Doing a segmentation
Calculating a 3D Object
Remeshing the 3D Object
Exporting to a Fluent mesh
Importing the mesh in Fluent
Importing the images In the File menu, select Import Images. Browse to the directory where you have install ed the extra Tutorial Files and go to the Airway directory.
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The images in the Airway directory will be selected automatically, so click on the Next button to accept this selection. In the next step you will see the properties of the project. Make sure that the skip images setting is 0 and that you use CT as compression method. By clicking on the Convert button, the images will be imported and a Mimics project will be created in your default working folder.
Doing a segmentation After the import of the images, we can start doing a segmentation of the air in the throat. Create a new mask with a lower threshold value of – 1024HU and an upper threshold value of –500HU.
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As you can see, this will create a mask that contains all the air in the project. We will now cut of a part of this segmentation to make sure we only have a small part of the throat. To do this, go to the segmentation menu, choose Edit Mask and choose the erase function. Make sure that your cursor is big enough by pressing the CTRL key and drag the left mouse button. Then go to axial sli ce 48.30/10.80 and remove the green mask from that sli ce with the manual editing tools. Then do the same for the axial slice 92.70/55.20.
Before manual editing
After manual editing
Before manual editing After manual editing Next we will isolate the throat from the other parts in the dataset. To do this, go to axial slice 63.30/25.80, then go to the segmentation menu and choose the Region Growing tool. Select the Green mask as the source mask and a new mask as the target mask. Then click with the left mouse button on the throat as indicated on the screenshot below.
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Calculating a 3D Object This will result in a second mask that only contains the throat. You can now calculate a 3D Object. To do this, go to the segmentation menu and select the Calculate 3D Object item. Select the Yellow mask from the list, choose Custom Quality and then click on the Options button. This will open the Calculate 3D Parameters dialog where you should use the same settings as below:
This will result in following 3D:
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This 3D Object is quite coarse because we are not using any smoothing. We will do this smoothing in the Remesher to make sure that we can contain the sharp edges at the top and bottom of the throat.
Remeshing the 3D Object This 3D Object now has to be remeshed in the Mimics Remesher. To do this, go to the FEA m enu and choose Remesh. This will show following dialog:
Choose the Yellow 3D Object and click on the OK button. This will open the Mimics Remesher with the 3D Object loaded. Make sure your interface is looking like the screenshot below and that the triangle visualization mode is selected:
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Smoothing We will first do a smoothing operation. Since we don’t want to loose the sharp edges at the in and out surface, first select the in and out surface by selecting the surface selection tool in the mark toolbar and left clicking on the in and out surface:
Then select only the mantle by clicking on the Toggle button on the mark toolbar
.
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Next, do a local smoothing by going to the Tools menu and selecting the Smoothing operation. Make sure that local is selected in the Smoothing dialog:
Unmark all triangles by clicking on the Unmark button
in the mark toolbar.
Improve quality Next we will improve the quality of the triangles. Make sure that the quality parameter is selected in the quality histogram and that you have selected Skewness as quality parameter and Sharp geometry as inspection parameter:
Set a value of 0.4 as the maximum quality measure. As you can see we have 149 triangles with a qu ality that is below 0.4.
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Hint: The skewness parameter in the Mimics remesher and the Fluent softwares are inverses. So a quality of 0.4 in the Mimics Remesher is actually a quality of 1-0.4=0.6 in Fl uent. We will try to remove these with the Split Based Remeshing operation
. Use following settings and click on OK:
Then apply the Split Based Remeshing operation again with following settings:
This will result in following 3D Object and quality histogram:
As you can see, there are no more triangle with a quality below 0.4.
Sharp Geometry Next we will check for sharp geometries in the part. To do this, select the Inspection parameter in the Quality histogram and put the Maximum quality threshold to 0.8:
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Then enable the Group checkmark and the Show All checkmark and set a Boundary level of 2. Click on the Mark Group button to select all the triangles that are now on the screen (all triangles that have a sharp geometry that is lower than 0.8 + their 2 neighbors).
We will refine the mesh where sharp geometry is occurring. You can do this by calling the Split Based Remeshing algorithm again and by setting a minimum edge length of 0mm and a maximum edge length of 0.5mm.
Then, again go to the Inspection Parameter and click the Mark Group button. Now, we want to smooth the parts were sharp geometry is occurring, but we don’t want to change the sharp edges of the i n and outlet surfaces. Select the Shell button on the mark toolbar and left click on the in and outlet surfaces.
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Now select the Smoothing function again, make sure that the local mode is selected and apply the smoothing:
Click on the Unmark button in the mark toolbar again to unmark all triangles. Go again to the Quality parameter in the quality histogram and you will see that a couple of bad triangles were created during the previous operations. Remove them by using the Split Based Remeshing algorithm again with following settings:
Areas with high curvature There are still two areas with high curvature. It is best to select the triangles in this area (with the mark window button ) and do a local split based remeshing with a maximum triangle size of 0.5mm and leave the other settings as before.
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Areas with sharp edges During our segmentation we have created an in- and outlet surface with a very sharp angle. This sharp angle can be removed if needed during the segmentation or by moving the points causing this sharp angles with the move point tool
.
Split up in surfaces Mimics will split up your mesh, based on the wireframe of your 3D Object. All surfaces with a closed wireframe will be split up to a separate surface. All wireframe that is not closed, will be ignored. So we will first l ook if the in and outlet surface have a closed wireframe and then if there are other closed wireframes. Make sure that, in the preferences, the wireframe angle setting is set to 30 degrees:
Choose Wire as display mode:
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As you can see, both in and outlet surface have a closed wireframe (with the wireframe angle setting on 30 degrees) and they are the only closed wireframes. If this would not be the case, you can create and delete wireframe by using the manual remeshing functions and the smoothing function. If you set the wireframe to a higher setting, you will notice that the noise wireframe is removed while the wireframe for the in and outlet surfaces still remains. If you put the wireframe on e.g. 50 degrees you will see that all noise wireframe is removed, but that the wireframe of the in and outlet surface is still closed.
Export to a Fluent mesh The remeshing of the airway is complete, so we can go back to Mimics by closing the remesher. The remesher will ask you if you want to save your changes, so choose Yes. You will see a new 3D Object in Mimics that is called Remeshed_Yellow 1_1. You can export this object to a Fluent mesh by going to the Export menu and choosing Fluent. This will show following dialog:
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Select the Remeshed file and add i t to the export list. When you click on the OK button, Mimics will ask for a Split Angle. Use the same value of 50 degrees as you have used as wireframe angle in the remesher. The resulting .msh file can then be imported in Gambit or Tgrid and a volume mesh can be created.
Import the mesh in Fluent You can then import this fluent file in fluent by using following parameters:
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System Requi rements Mimics runs under Windows 2000 and XP. It operates on any Pentium class personal computer as long as the video memory is at least 4MB so that it supports a 1024x768 resolution with 24 bit colors. The monitor should be a high quality, non-interlaced color monitor to ensure sharp and accurate images. We recommend a fast 3D video card that supports OpenGL to speed up the complex 3D calculations used by Mimics. If you intend to purchase a computer for Mimics, we strongly urge you to use the Recommended Specifications as a guide. If you are installing Mimics on an existing computer system, please refer to the Minimal Specifications to ensure that Mimics will operate on your computer.
Software Requirements: Minimal:
Windows 2000
Internet Explorer 5.0
Recommended:
Windows 2000 or XP
Internet Explorer 6.0
Hardware Requirements: Minimal:
Intel Pentium II 300 MHz or equivalent
256 MB RAM
Graphics card supporting 1024x768 and 16-bit color with 4 MB RAM
Non-interlaced 15" color monitor
Recommended:
Intel Pentium 4 3,0 GHz or equivalent
1 GB RAM
ATI RADEON or NVIDIA GeForce card with 128 MB RAM
Non-interlaced 19" color monitor or 17” flat panel monitor
Resolution of 1280x1024 or higher
Optical mouse with a scroll wheel
Note: To ensure smooth operation of Mimics, make sure to update your graphic card drivers. You can find the latest drivers on the ATI an NVIDIA
website.
Frequently Asked Questions Import module 1. Mimics does not recognize the MOD device.
The drivers are installed together with the Mimics software. Our drivers operate with the OD and they take care of reading and converting of the data. In order to do this, the drive has to be connected correctly. It's also important that the user has administrator rights, in order to access the SCSI devices. The following questions help to detect the problem: When you start the PC, do you see the drive displayed in the list? This is important to know whether the PC recognizes the drive. If this is not the case, the drive is not correctly connected. A bad wire, a terminator problem, the dipswitch settings, or the SCSI address (0,1 or 7) can be the causes for this problem.
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Are there other devices connected to the PC, like a tape drive, a ZIP drive? If yes, try without any of these other drives connected. If the SCSI device is listed during start-up, start Mimics and choose "Advanced SCSI" in the Options menu. Start testing the SCSI devices. If you don't see the drive in the list, see our troubleshooting page in the help files (via General, CT-Convert, Trouble Shooting). 2. Each time I select Import images from t he File menu, my computer reboots.
When importing images, Mimics tries to contact the connected SCSI devices. The reason why it causes problems is that one (or more) of these devices give error messages. In mimics there is a function to block the messages from certain devices, so that this problem doesn't occur anymore. Open Mimics and select from the file menu: Options --> Advanced SCSI. In the dialog box that appears, disable the Ënable SCSI”checkbox. Click OK, restart Mimics and try to import again. 4. When I convert Tiff images I got no-contrast i mages, even though the preview window looked good.
In the Manual import dialog you see at the right bottom corner "Maximum Image Value". If this value is a lower than the real maximum value in the dataset, it may cause images without contrast, once they are converted. 5. When I import images, the maximum pixel value is 4096, while the interval should be 0...65000.
When importing data in Mimics, all gray values are scaled/translated to the range of 0 - 4095. This comes from our medical background and also allows more compression on the data (12 bit data). 6. When I impor t images and use CT compression, I get no-contrast images in Mimics. When using loss l ess compression, the images look fine.
CT compression is a lossy compression. When you select CT compression during conversion, the first 200 gray values in the data set will be changed to the Hounsfield unit -1024. This CT compression is useful in datasets with a wider range of gray shades, where it will filter out the noise in the air. Mimics also provide a loss less compression. If you have a dataset with a narrow gray value range, most of these gray values will be put on -1024 HU and this may cause images without contrast. 7. When tryi ng to import DICOM images, the message "Cannot process DICOMDIR" is show n and nothi ng is read.
It's probably a DOS formatted disk with DICOM images that is being read. On these disks there's normally a file called DICOMDIR that lists all the images on disk. If this file can't be found, then Mimics can't import the images and gives you this warning. Check if the disk is not empty, because it's very strange for the DICOMDIR to be missing... 8. Are data sets wit h varying sli ce distances supported?
If the file format is supported, the images are automatically read and converted. The table position is read from the header of the file and used afterwards in the Mimics, so varying distances are supported. You can simply read the table position on the axial view in Mimics. When a manual import is needed (because the file format is not known), the situation is a bit more complicated but not impossible. You will need to know all parameters upfront, so also which image is on which table position. This info should be stored in a txt file that has to load via the "Import table positions from" function in the Manual conversion window. When you know this, you can create a dataset based on these images. If there are groups of images with the same size (= sets of succeeding images), each of these sets can be imported, set per set. But you have to make sure that you adjust the "first table position" parameter for every set. Like this, you can pile up all images again at the correct position. You can make the combination again of all sets with the "organize images" function. 9. How to r ead images from Unix f ormatted disks?
Unix formatted disks can be read like other optical disks in Mimics 7.2 and later versions. The images need to be uncompressed. A TAC Helicoidal Marconi Twin is an example of a scanner that writes UNIX formatted disks. 10. Input of Mimics
The Raw data is the data as it comes off the scanner in Fourier space. It is unreconstructed. The reconstructed images slices are input for Mimics, not the volume data/RAW data without header. Mimics can read all images that are parallel, have the same size and contain gray values. If the images are binary, it's no problem for Mimics to read them, but it will not be possible to generate a nice 3D model. If the scanner and/or file format is unknown, it can be implemented/supported if we get the help of the customer. Since the scan site is customer, it is easier for them to obtain the information about disk formatting and file formatting from the scanner manufacturer. Having this information makes it easier for us to implement this. 12. When I import images from an MOD, my patient is not listed.
First check both sides of the optical disk. If it's a Picker MOD, then you must know that only 1 data block can be read from this MOD. This means that only 1 patient can be read at a time. In order to read all patient data, they have to put each patient data on a different Picker MOD.
STL+ 13. When I export an STL file, I can’t fi nd the fi le in th e target folder.
Make sure you have the permission to write to the target folder. It could be that only users with administrator rights have the permission to write to certain folders. Also check if the option "hide file extensions for known types" is unchecked in Windows Explorer > View Menu > Folder Options. Make also sure that there is enough space on the hard disk. 14. The size of the STL file becomes so high that it's v ery difficul t to handle in Li ghtYear soft ware.
You should use the direct interface: in the RP Slice module you can calculate SLC files that can be loaded in the Lightyear software. This method has 3 advantages: 1. No problem with big file sizes, because it is already sliced. 2. Cubical interpolation can be applied. The model will look less stair-stepped. 3. High resolution can be kept. Once the SLC file is loaded in Lightyear, you just have to click "prepare". Also calculate the support file with RP Slice! MEDCAD
General
