fMRI Characterization for the Study of Cortical Reorganization

fMRI Characterization for the Study of Cortical Reorganization in Acute Nerve Inflammation fMRI data analysis Ashish Uthama Ashish Uthama Supervisor: Dr. Rafeef Abugharbieh Department of EECE Collaborator: Dr. Anthony Traboulsee Department of Neurology http://bisicl.ece.ubc.ca/ 1 Introduction

MRI studies anatomy. Functional MRI (fMRI) studies brain function. Source: Jody Culhams fMRI for Dummies web site Ashish Uthama http://bisicl.ece.ubc.ca/ 2 Introduction 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/ 3 Clinical Objective Multiple Sclerosis: Permanent damage to the nerves in the CNS 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) Track the changes in the visual response of the brain during and after an attack of mono ocular ON for re-adaptation 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/ 4

Setup Source: Jody Culhams fMRI for Dummies web site Ashish Uthama http://bisicl.ece.ubc.ca/ 5 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/ 6 Tools Data format conversion from scanner native format to more process friendly format (Using MRIcro www.sph.sc.edu/comd/rorden/mricro.html ) SPM2

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/ 7 Data Analysis Steps Re-Orientation Re-Alignment (Motion Correction)

LMS based realignment of each volumes to a single reference volume (Usually the first volume of the scan) Normalize 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 A 4mm*4mm*4mm Gaussian 3-D kernel used to smoothen the volumes Increases SNR

Part of the GRF approach Ashish Uthama http://bisicl.ece.ubc.ca/ 8 Data Analysis Steps Raw data Ashish Uthama Pre-Processed data http://bisicl.ece.ubc.ca/ 9 Data Analysis Steps Stimulus

Voxel-wise parameter estimation (4-D to 1-D) Uses GLM (Generalized Linear Model) approach A Design matrix needs to be specified Includes expected response (HRF compensated) Other Explanatory variables (Motion, Drift ) Activation Detection GRF (Gaussian Random Field) statistics Threshold the parameter map to detect activation 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 Expected response http://bisicl.ece.ubc.ca/ 10 Results for activation detection Both eye open Ashish Uthama http://bisicl.ece.ubc.ca/ 11 Results for activation detection Left hemi field activation*

Ashish Uthama http://bisicl.ece.ubc.ca/ 12 Things to do More data! (Specially patient scan data) How does it deviate from normal? Ethics proposal and patient recruitment Statistics of comparison between groups A robust shape characterization technique for the activation region

which should be able to discriminate between the volumes of patients and control 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/ 13 Q&A Does anybody have some free time in Dec?? I Need Volunteers for a scan!!!

Special 575 offer: 1 Brain Scan absolutely free with every Question!!!! No conditions! Ashish Uthama http://bisicl.ece.ubc.ca/ 14

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