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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. (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni05_regression.pdf)

Do you have any reasons for having 3 as default?

Kind Regards,

Andy Junghyun Kim