The SUBJECTS_DIR is where you want the result of the freesurfer analysis to go. This is usually not /usr/local/freesurfer/subjects because you usually don't have write permissions. Try setting it to a place where you have some space, then run recon-all something like
recon-all -s yoursubject -i /Desktop/Allimages/MRIscan... and the full path till DICOM/dicomfile
the output will then be in $SUBJECTS_DIR/yoursubject
doug
Janani Dhinakaran wrote:
My data is on the desktop. The subjects directory is under usr/local/freesurfer/subjects. I tried setting desktop as SUBJECTS_DIR by using 'export SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till DICOM" ' but apparently it didn't work because when I tried to run recon, it says SUBJECTS_DIR /Desktop/Allimages/MRIscan/.../....DICOM does not exist
If I can't get SUBJECTS_DIR to change to Desktop path, how can I introduce my data into usr/local/freesurfer path? I notice Bert has everything in order. If I mkdir Mine in SUBJECTS_DIR and put my MRI files in there , will it work?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer