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