Neuroimaging Informatics Vanessa Sochat 05/08/2013
Brains, the Final Frontier! Neuroimaging Informatics
Neuroimaging Informatics computational methods and infrastructure for understanding the structure and function of the brain
Neuroinformatics FTW!
tools and databases methods for analysis computational models
I have burning… questions! Neuroscience!
I’ll take any question to prove my method!
I just want to understand the visual system
I will build you a new spaceship!
I just discovered a new nebula!
Captain’s Log A Brief History 1989
What to do with this data?
Captain’s Log A Brief History 1989 1991 Here are some ideas! What to do with this data?
Captain’s Log A Brief History 1989
1991 1993 Here are some ideas!
What to do with this data?
Fine! Here’s Neuroinformatics! grant $$$
Captain’s Log A Brief History 1989
1991 1993
2006
Here are some ideas! What to do with this data?
Fine! Here’s Neuroinformatics! grant $$$
INCF
Captain’s Log A Brief History 1989
1991 1993
2006
Here are some ideas! What to do with this data?
Fine! Here’s Neuroinformatics! grant $$$
2013
Mission • The Human Brain • How do we image brains? • How do we build tools?
UNCHARTED TERRITORY HOW TO EXPLORE NEUROINFORMATICS
Mission • The Human Brain • How do we image brains? • How do we build tools?
BACKGROUND DATA METHODS
The Uncharted Territory: The Human Brain
The Uncharted Territory Central Nervous System (CNS)
Peripheral Nervous System (CNS)
BACKGROUND
DATA
METHODS
The Human Brain
BACKGROUND
DATA
METHODS
The Human Brain
3 pounds <> 109 neurons <> 1015 synaptic connections BACKGROUND
DATA
METHODS
The Human Brain
BACKGROUND
DATA
METHODS
Anatomical Directions DORSAL SUPERIOR
ANTERIOR
POSTERIOR
ROSTRAL DORSAL
VENTRAL INFERIOR
BACKGROUND
CAUDAL
DATA
METHODS
Slice it up!
CORONAL
BACKGROUND
SAGITTAL
AXIAL
DATA
METHODS
How to Explore: Neuroimaging Methods
SPATIAL RESOLUTION
We study brains with Neuroimaging
TEMPORAL RESOLUTION
BACKGROUND
DATA
METHODS
We don’t want to cut people open!
BACKGROUND
DATA
Oh?
METHODS
We collect data to answer a biological question structure and function
? Population
Protocol
What happens to the structure of region X as we get older? What is my brain doing when I see pictures of cats? Which regions are working together?
BACKGROUND
DATA
Data
Public Repository
METHODS
We collect data to answer a biological question structure and function
? Population
Protocol
Data
Public Repository
BACKGROUND
DATA
METHODS
We like to identify biomarkers in our images
?
Public Data
Why?
Feature Extraction
Process
Analysis / Machine Learning
Disorder diagnosis Classification of subtypes of disease Improved filtering methods Understanding human connectome
BACKGROUND
DATA
METHODS
We measure structure and function Invasive
Non-invasive Structure
Function
sMRI
fMRI
CT
PET
DTI
EEG MEG
BACKGROUND
DATA
METHODS
We measure structure and function Invasive
Non-invasive Structure
Function
sMRI
fMRI
CT
PET
DTI
DTI
sMRI
MEG CT
EEGPET fMRI
EEG
MEG BACKGROUND
DATA
METHODS
What imaging modalities do we use to measure structure?
Computed Tomography tumors bones! infarction calcifications
CT
BACKGROUND
DATA
METHODS
Magnetic Resonance Imaging
sMRI
T1
gray matter white matter cerebrospinal fluid
T2
BACKGROUND
DATA
METHODS
Diffusion Tensor Imaging white matter integrity
DTI
BACKGROUND
DATA
METHODS
What imaging modalities do we use to measure function?
Functional Magnetic Resonance Imaging neural activity blood flow oxyhemoglobin MR signal
fMRI
BACKGROUND
DATA
METHODS
Positron Emission Tomography
PET
BACKGROUND
DATA
METHODS
Electroencephalography
EEG
BACKGROUND
DATA
METHODS
Magnetoencephalography
MEG
BACKGROUND
DATA
METHODS
What data do I need to measure… I want to measure…
Imaging Modality
Some tissue volume
sMRI (T1)
Tumor, bone, or fluid
CT, sMRI (T2)
Cortical Thickness
sMRI (T1)
White Matter Integrity
DTI
Brain Function
fMRI, with sMRI (T1) for registration
Superficial Activity
EEG, MEG
Neurotransmitter-specific Activity
PET
BACKGROUND
DATA
METHODS
What does my data look like?
What does my data look like?
TIME
BACKGROUND
DATA
METHODS
What does my data look like?
SLICE VOXEL
BACKGROUND
DATA
METHODS
What does my data look like? 3D • .nii (one file) • .img / .hdr combo 4D • .nii.gz (compressed file) • .nii (uncompressed) • .img/.hdr combos
Header P Files
Nifti Imaging Data
BACKGROUND
DATA
METHODS
What are those numbers?! • Structural – Gray and white matter volume – White Matter Integrity – Cortical Thickness
• Functional – Functional connectivity – Blood flow
How we build tools: Neuroimaging Informatics Methods
“What I want!”
computational methods and infrastructure for understanding the structure and function of the brain “What I do!” develop and apply new methods for acquisition, representation, and analysis of neuroimaging data and knowledge BACKGROUND
DATA
METHODS
Neuroimaging Informatics Pipeline
1
2
IMAGE ACQUISITION
3
PREPROCESSING
PROCESSING
ANALYSIS
Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools
BACKGROUND
DATA
METHODS
Neuroimaging Informatics Pipeline
1
2
IMAGE ACQUISITION
3
PREPROCESSING
PROCESSING
ANALYSIS
Data + Knowledge Representation + Infrastructure = Sharing, Knowledge, Tools
BACKGROUND
DATA
METHODS
Pre/Processing Prepares for Analysis
Realign and Reslice
Coregister
Normalize
Smooth
Segment
Segment
BACKGROUND
DATA
METHODS
Realignment for Motion Correction
translation
Realign and Reslice
rotation
Coregister
BACKGROUND
zooming
Normalize
DATA
Smooth
shearing
Segment
METHODS
Coregistration
Realign and Reslice
Coregister
BACKGROUND
Normalize
DATA
Smooth
Segment
METHODS
Normalization
Realign and Reslice
Coregister
BACKGROUND
Normalize
DATA
Smooth
Segment
METHODS
Smoothing
No smoothing
Realign and Reslice
Coregister
BACKGROUND
Normalize
DATA
4 mm kernel
Smooth
Segment
METHODS
Segmentation Priors
Tissue Types
GM
Realign and Reslice
WM
Coregister
BACKGROUND
CSF
Brain/skull
Normalize
DATA
Smooth
Segment
METHODS
Segmentation
Realign and Reslice
Coregister
BACKGROUND
Normalize
DATA
Smooth
Segment
METHODS
Neuroimaging Informatics Pipeline
1
2
IMAGE ACQUISITION
3
PREPROCESSING
PROCESSING
ANALYSIS
Data driven approaches Hypothesis drive approaches
BACKGROUND
DATA
METHODS
Two Analysis Approaches
I’m getting bigger! Can we address my burning question now?
BACKGROUND
DATA
?
METHODS
What are commonly used apriori methods?
VOXEL BASED MORPHOMETRY (VBM)
?
What are structural characteristics (e.g. gray matter volume, density) within a brain region of interest in a subject population? sMRI
SEGMENT NORMALIZE MODULATE SMOOTH VOXEL-WISE STATISTICS
BACKGROUND
DATA
METHODS
TRACTOGRAPHY (DTI)
?
How are two or more brain regions of interest connected anatomically in a subject population?
BACKGROUND
DATA
METHODS
GENERAL LINEAR MODEL (GLM)
?
Which brain regions show neural activity during a function of interest?
sMRI and fMRI
REALIGN AND RESLICE SEGMENT REGISTER NORMALIZE FIT to GLM
BACKGROUND
Brain regions responding “active” to biological motion
DATA
METHODS
CORRELATIONS
?
What is the brain network underlying a function of interest?
IDENTIFY ROI EXTRACT SIGNAL NETWORK CONNECTIVITY
Brain network underlying hand movement
BACKGROUND
DATA
METHODS
What are commonly used datadriven methods?
INDEPENDENT COMPONENT ANALYSIS (ICA)
?
What is the brain network underlying a function of interest?
nxm
S X
=
BACKGROUND
nxn
nxm
A-1 X X S DATA
METHODS
MULTI VOXEL PATTERN ANALYSIS (MVPA)
?
How and which set of brain regions cumulatively represent an experimental stimuli?
fMRI
BACKGROUND
DATA
METHODS
How do I use informatics to extend my analyses?
Databases to Distribute Resources Processed Images
Demographics Raw Images Publicly available Brain DBs: fMRIDC Allen Brain Atlas BIRN Neurosynth ADNI NDAR Human Connectome
BACKGROUND
Imaging Protocol
DATA
METHODS
Atlas: Terms for Spatial Characteristics
Brodmann Atlas
BACKGROUND
ICBM Atlas
DATA
METHODS
Knowledge Representation FMA
NIFSTD
XCEDE
BACKGROUND
DATA
METHODS
Challenges, Captain! Take that, poor resolution!
Complex, noisy data! Arg!
Where are the standards?!
BACKGROUND
DATA
METHODS
The Journey Continues…
PAST
BACKGROUND
PRESENT
DATA
FUTURE
METHODS
[email protected] I have questions…
