C) When running mri_surf2surf, I get an error saying that file/surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log file from make_average_subject so i don’t know if it gave any errors.. It's extremely helpful to have command lines ...Sorry, my commands were: make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 --tval lh.thickness.10.mgh
It might be a version problem. You can create a symbolic link from lh.white_avg to lh.white
Under fsaverage/surf there is both an lh.white and an lh.white_avg file, while under average/surf there's only lh.white_avg. I repeated the mri_surf2surf command above with "--s fsaverage" instead of "--s average" (since I understand in this case it's the same thing), and then it ran to completion.
Also, it's not clear from the wiki what flag should an ROI's label/mask be specified into mri_surf2surf with, prior to a ROI analysis. The --cortex flag seems to always be required anyway, and --sval seems to be design-related ("--sval lh.gender_age.thickness.00.mgh" in the group tutorial)! Should the same flag then also be used to specify the ROI in mri_glmfit, the command that follows mri_surf2surf?
Thanks!