Hello everyone,
I'm new to FreeSurfer and this question might sound a bit stupid: I'm trying to get the volumetric measures, surface area and cortical thickness of brain regions of three groups of subjects (patient group 1, group 2 and healthy controls), and I was wondering whether the morphometric variance across subjects (gender, shape of brain, etc) unrelated to the neurological condition has been corrected automatically within the recon-all pipeline using the default options.
That is, given that the groups are age-, gender- and otherwise matched, after segmentation and calculation of these values with FreeSurfer, the morphometric differences we are looking at could be attributed to the neurological condition itself, instead of other factors.
From what I read, the step Talaraich which computes the affine transform from the orig volume to the MNI305 atlas (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Talairach.28-.3Cno.3Etalairach.29) seems to be one of the steps that does what I need, and we are therefore safe using the default recon-all for pre-processing and extraction of morphometric data. Otherwise, please let me know what I could do.
Thanks very much for your information and help in advance!