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Dear Freesurfer experts,
After running the -qcache option to extract thickness data for every subject, I tried pulling all the data together in order to get a matrix of subjects x vertices containing thickness data (for a given hemisphere) in all vertices of the brain.
I noticed that for some small areas, particularly medial temporal, thickness data equals to 0 for some subjects, and has values for other subjects. May this be of concern? If so, would you have any idea why this is happening?
Another, perhaps related question is: when I try to use a subject's individual thickness mgh as an overlay in tksurfer, I obtain the outputs attached to this email (I am not modifying any overlay min max or threshold values). I am wondering if these grey zones in the map (around occipital and parietal areas specifically; not for subcortical areas) are to be expected, or if they may reflect some processing problem? If so, what problem could it be?
Thank you in advance for your help,
Best regards,
Joëlle van der Molen
