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Dear FreeSurfer Developers,
I am trying to analyze functional connectivity using Freesurfer. When I checked FSFAST tutorial, it says: Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface self lh -fwhm 5 -notask -nuisreg vcsf.dat 1 -nuisreg wm.dat 1 -mcextreg -polyfit 5 -nskip 4 -fsd fsrest -TR 4.5 -per-run" -mcextreg means that only top 3 components (I checked it was first 3 columns of mcprextreg) are used out of total 6 components. And indeed there are only 3 motion regressors in X.mat file. Freesurfer uses AFNI program to get motion correction parameters and AFNI uses all 6 components. (https://secure-web.cisco.com/12TJnsSiUh4nUlS0evLlfL-8nA36tqM4rfztjSsg7-3om9_...) Do you have any reasons for having 3 as default?
Kind Regards, Andy Junghyun Kim