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fMRI Characterization for the Study of
Cortical Reorganization in Acute Nerve
Inflammation
fMRI data analysis
Ashish Uthama
Ashish Uthama
http://bisicl.ece.ubc.ca/
Supervisor:
Dr. Rafeef Abugharbieh
Department of EECE
Collaborator:
Dr. Anthony Traboulsee
Department of Neurology
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Introduction…
MRI studies anatomy.
Functional MRI (fMRI)
studies brain function.
Source: Jody Culham’s fMRI for Dummies web site
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Introduction…
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Stimulus causes activation of the corresponding part of the brain
Activation needs oxygen
Oxygen supplied by localized blood inflow
Blood with O2 and without O2 have different magnetic properties
Blood Oxygen Level Dependent response to magnetization
Process of stimulus perception to change in O2 concentration is called that
Haemodynamic Response Function (HRF)
Controlled stimulus can be used to activate
certain parts of the brain and the resulting
change in Oxygen concentration can be
picked up by an MRI machine : fMRI
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Clinical Objective
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Multiple Sclerosis: Permanent damage to the nerves in the CNS
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Optic Neuritis: One of the symptoms of MS effecting vision. Usually a
temporary condition where visual acuity is lost in one or both eyes
(Temporary: Brain recovers part of the functionality despite physical damage)
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Track the changes in the visual response of the brain during and after an
attack of mono ocular ON for re-adaptation
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Does the volume (strength) of activation change?
Does the distribution/shape of the activation volume change?
Collect fMRI data on patients with MS over a duration of time using optic
stimulation
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Setup
Source: Jody Culham’s fMRI for Dummies web site
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Data collection
Activation
Baseline
30 sec
Time
One volume every 2.4 seconds
• 164 volumes collected (2.4 sec per volume) in each scan (~7 minutes)
• Each volume is 128*128*45 voxles (2mm*2mm*4mm)
• Currently have one pilot data set containing 4 scans of a normal person
•Left hemi field activation (Both eyes open)
•Left eye activation (Right eye closed)
•Right eye activation (Left eye closed)
•Both eyes open
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Tools
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Data format conversion from scanner native format to more process
friendly format (Using MRIcro www.sph.sc.edu/comd/rorden/mricro.html )
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SPM2
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Statistical Parameter Mapping using SPM2
A Matlab toolbox for fMRI data analysis
(www.fil.ion.ucl.ac.uk/spm/spm2.html)
Matlab
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Data Analysis Steps…
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Re-Orientation
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Re-Alignment (Motion Correction)
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LMS based realignment of each volumes to a single reference volume (Usually
the first volume of the scan)
Normalize
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6 parameter rigid transformation of all volumes to the same orientation as a
template
12 parameter affine transformation of all volumes to the standard space
Required for multi subject comparisons
Smooth
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A 4mm*4mm*4mm Gaussian 3-D kernel used to smoothen the volumes
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Increases SNR
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Part of the GRF approach
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Data Analysis Steps…
Pre-Processed data
Raw data
Ashish Uthama
http://bisicl.ece.ubc.ca/
9
Data Analysis Steps…
Stimulus
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Voxel-wise parameter estimation (4-D to 1-D)
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Uses GLM (Generalized Linear Model) approach
A Design matrix needs to be specified
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Includes expected response (HRF compensated)
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Other Explanatory variables (Motion, Drift …)
Activation Detection
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GRF (Gaussian Random Field) statistics
Threshold the parameter map to detect activation
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Determination of the Threshold level is the key
Activation volumes at a given p value (a p values
denotes the chances of wrongly classifying a voxel as
activated. Usually p values are <.05. Highly dependent
on nature of pre-processing, number of volumes,
number of subjects, cluster size … )
Ashish Uthama
http://bisicl.ece.ubc.ca/
Expected response
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Results for activation detection
Both eye open
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Results for activation detection
Left hemi field activation*
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Things to do…
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More data! (Specially patient scan data)
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How does it deviate from normal?
Ethics proposal and patient recruitment
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Statistics of comparison between groups
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A robust shape characterization technique for the activation region
which should be able to discriminate between the volumes of
patients and control
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Should provide for a measure of similarity between two volumes
Should take into consideration possibility of discrete globules
Might have to represent phase delay in the response
Robust, Accurate, Reproducible …
Ashish Uthama
http://bisicl.ece.ubc.ca/
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Q&A
Does anybody have some free time in Dec??
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I Need Volunteers for a scan!!! 
Special 575 offer:
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1 Brain Scan absolutely free with every Question!!!! … No conditions!
Ashish Uthama
http://bisicl.ece.ubc.ca/
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