Question about Cortical Thickness - Freesurfer

6 Oct 2016

      I have a few questions regarding the instructions at:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
The instructions assume that there is an ROI in the same space as the 
T1.mgz map. Then they do the following:
1) Register the T1 to fsaverage
2) resample the ROI to the cortical surface of fsaverage
3) map the thickness data of the subject to fsaverage
4) measure the thickness data
Why is the registering to fsaverage helpful? It seems as if this 
computation could be done in the native space. Why couldn't one make the 
following changes:
1) in mri_vol2surf, the reg option could be replaced with regheader MYSUB.
2) Then the surf2surf command becomes unnecessary.
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Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

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