Just a guess: if you are using a Mac, the path for the directory should be something like
/Users/yourname/Desktop/ etc. instead of just /Desktop/ etc. hope this helps, roberto On Thu, Feb 18, 2010 at 10:15 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
