Dear Freesurfer, The data that I'm using as a part of my study contains only the patients' T1 images and we have not collected any control subjects yet. I want to compare the cortical thickness of these subjects with a template (instead of a control subject), but I'm confused which volume I need to choose. When I run recon-all, does it transform the slices based on the fsaverage? Is fsaverage based on Talairach template or MNI or something else?
Would you please guide me with the question and inform me what template volume is the best for me to use instead of my control subjects? Best Regards, Mahtab.
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