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Dear Freesurfer experts,
I have created volumetric ROIs of entorhinal cortex regions and have registered them to subjects’ native space (T1). I now wish to register them to the subject surface in order to get information such as cortical thickness- using mri_vol2surf and mri_segstats I believe.
I was looking at your tutorial regarding this VolumeRoiCorticalThickness - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1NhD55JOKQjBEatrGH8aFF1vX2Pc2cSmUgIdVJu201vnm4tQELHhKC8hdSICHCc37zU4RhxeFcSeVly9rOphRN2XP-Hn6K3WQXbHVlzOaVeiAALFEEDsWW4Hlf1gOUgdlDeO1QVq5KumypG9Qk5hAOdZ6Othr5MGzujz9YqESMrcJREtyb3JHfB9Lq8ESK7pnmQ52E9DXwDsqbRCXXtKxYi4H1bAPwJUSTSteDzgYRyGUaGAnZcISKs0tuAXnMqHAu2AalzfMJvAfOp4Rk5KvjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness and had a few questions.
First of all- could you explain why you are going through fsaverage. Is there some kind of advantage to doing this procedure of registration, mri_vol2surf and then mri_surf2surf rather than just using mri_vol2surf with the subject space as the regheader?? When I tried through fsaverage as explained in the tutorial (following the exact same commands) the ROI appeared wrong in the surface and the thickness stats were incorrect.
Secondly, when doing the procedure as per the tutorial, do you mean that we have to register each subject's mask to the fsaverage- or only one, e.g a ROI derived from the subject-specific group template (we have one produced through ANTs).
Lastly- some explanation about how projfrac and projdist work would be very helpful. What numbers are considered best practice?
Thankyou, Marianna Pope