1. fMRI: Biological Basis and Experiment Design Lecture 21: Anatomical ROIs Cortex-based analysis Cortex reconstruction Registration Distortion 1 light year = 5,913,000,000,000 miles?

2. Cortex-based analysis Theory: signal changes we care about are in gray matter –White matter dilutes responses –CSF and vessels add noise Method: define gray matter and restrict analysis Problem: how do we define gray matter?

3. Following examples taken from: Cortex reconstruction Plenty of available software packages –Brain Voyager –Free Surfer –…

5. Identification of gray matter Reconstruction of cortical surface

6. Visualization on inflated and flattened brains Bar et al PNAS 2006 Hasson et al Science 2004

7. Translating data & ROIs: misalignment = missed data

8. Successful selection of gray matter ROI

9. Functional - anatomical alignment Standard procedure –Acquire 3 data sets reference anatomy (not necessarily same scan) EPI “inplane anatomy” (T 1 -weighted FLASH or T 2 -weighted TurboSE, with same slice prescription as EPI) –Align “inplane anatomy” with reference anatomy –Use this alignment information to

10. Functional - anatomical alignment Better procedure –Acquire 2 or 3 data sets reference anatomy (not necessarily same scan) EPI Optional: “inplane anatomy” (T 1 -weighted FLASH or T 2 -weighted TurboSE, with same slice prescription as EPI) –Either Align EPI to reference anatomy Align EPI to inplane anatomy and then inplane to reference –Use this alignment information to

13. Dealing with EPI distortion in defining ROIs EPI aligned to reference anatomyEPI aligned to distorted reference anatomy

14. Cortex reconstruction on distorted anatomy (the hard way to solve the problem)