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