Dear experts,

I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal  cortex. l did find this thread but failed to make it work on my data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). I know I could extract the signal of the ROI but also interested in this way.

Here are my questions:

1. mri_binarize should be working on the average data or the single data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants).

2. How the --match is used. I --helped the mri_binarize but did not get it. Is it for specifying the ROI by number, say the number of PFC?

3. If I could finish the mask creation and merge to label; do I have to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).

Thank you so much!