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

2. Ashish Uthama http://bisicl.ece.ubc.ca/2 MRI studies anatomy. Functional MRI (fMRI) studies brain function. Introduction… Source: Jody Culham’s fMRI for Dummies web sitefMRI for Dummies

3. Ashish Uthama http://bisicl.ece.ubc.ca/3 Introduction… Stimulus causes activation of the corresponding part of the brain Activation needs oxygen Oxygen supplied by localized blood inflow Blood with O 2 and without O 2 have different magnetic properties Blood Oxygen Level Dependent response to magnetization Process of stimulus perception to change in O 2 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

4. Ashish Uthama http://bisicl.ece.ubc.ca/4 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

5. Ashish Uthama http://bisicl.ece.ubc.ca/5 Setup Source: Jody Culham’s fMRI for Dummies web sitefMRI for Dummies

6. Ashish Uthama http://bisicl.ece.ubc.ca/6 Data collection Time 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 30 sec ActivationBaseline One volume every 2.4 seconds

7. Ashish Uthama http://bisicl.ece.ubc.ca/7 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 (www.fil.ion.ucl.ac.uk/spm/spm2.html)  A Matlab toolbox for fMRI data analysis Matlab

8. Ashish Uthama http://bisicl.ece.ubc.ca/8 Data Analysis Steps… Re-Orientation  6 parameter rigid transformation of all volumes to the same orientation as a template Re-Alignment (Motion Correction)  LMS based realignment of each volumes to a single reference volume (Usually the first volume of the scan) Normalize  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

9. Ashish Uthama http://bisicl.ece.ubc.ca/9 Data Analysis Steps… Raw data Pre-Processed data

10. Ashish Uthama http://bisicl.ece.ubc.ca/10 Data Analysis Steps… 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 … ) Stimulus Expected response

11. Ashish Uthama http://bisicl.ece.ubc.ca/11 Results for activation detection Both eye open

12. Ashish Uthama http://bisicl.ece.ubc.ca/12 Results for activation detection Left hemi field activation*

13. Ashish Uthama http://bisicl.ece.ubc.ca/13 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 …

14. Ashish Uthama http://bisicl.ece.ubc.ca/14 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!