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 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.