External Email - Use Caution

Hello FreeSurfer Developers,

I was attempting to execute the mkheadsurf script to process MRI data and encountered some errors.

1. The first error message is "subjdir: Undefined variable.". After reading through the mkheadsurf script, I realized that is a temporary variable used in a script. Having no idea why this was required in the beginning, I manually entered export subjdir=/Volumes/Lab/SA/MRI/ForMNE/subj01 to circumvent that problem.

2. Indeed the script started running afterwards, but there were two errors at step 1. (Creating a dense scalp tessellation with mkheadsurf) First, mris_smooth -n 10 -b /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/area.seghead -c \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/curv.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead resulted in error: MRISwriteCurvature: could not open lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.curv.seghead

Second, mris_inflate -n 10 -sulc /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/sulc.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead.inflated resulted in error: MRISwriteCurvature: could not open /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.sulc.seghead

Please note that the weird output paths have the output folder repeated twice in different positions. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the mkheadsurf.log in case it's of any use.

1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOSX 10.13.6 3) uname -a: Darwin localhost 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 4) mkheadsurf.log: see attached

Sincerely, -- Yong-Jun Lin Postdoctoral Associate Department of Psychology New York University 6 Washington Place, Room 955 New York, NY 10003