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?
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Douglas N. Greve, Ph.D.
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