Hi,
Your $SUBJECTS_DIR should be pointed to the directory where your subjects' data live. To symlink your $SUBJECTS_DIR to $FREESURFER_HOME/subjects/fsaverage be sure to have sourced FREESURFERhttps://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer, set your SUBJECTS_DIR, then
cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage
If this does not solve the issue, please send the command you are using and the recon-all.log file.
Best, Jocelyn
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fatemeh Ahmadi one.ahmadi@yahoo.com Sent: Sunday, January 10, 2021 3:42 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all , fsaverage ?
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Hi Dear Dr.,
I run recon -all and get an ERROR reading /media/sf_shared/fsaverage/label/lh.BA1.label
I saw that you answered similar questions as follows:
It should be symlinked from you $SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage.
How do I do this?
Thank you in advance,
--------------------- Fatemeh Ahmadi, PhD Student in Computer Science, Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran Email: f.ahmadi@aut.ac.ir