Hi Rick,
Thank you! I understand how to make the FS_vent, and FS_white based on the Freesurfer note.
I guess the final confusion lies in the input Freesurfer anatomy. You have it labeled as " FT_SurfVol.nii" Is this equivalent to the "T1.mgz" file that is created by Freesurfer?
Also, Freesurfer creates an "fsaverage" folder and a "${subject}.fs folder. Both contain an mri folder with all the aseg files and a T1.mgz file. Does it matter whether I take from fsaverage or ${subject}.fs?
Given that the "_rank" file is not used in the analysis, should I remove that step entirely?
Thanks for getting me going!
Emily
