Hi Lisa
Is the subject fsaverage symlinked in your SUBJECTS_DIR? Also, the argument to
-s is typically just an identifier, not a path then and identifier. That is, it
should be more like:
recon-all -s subid
instead of
recon-all -s imagedir/subid
I’m not sure if this is the source of your problem, but certainly recon-all is
failing to find some of the files as it throws errors like:
SUBJECTS_DIR /dfs6/pub/ltaylor2/downs
FREESURFER_HOME /data/opt/apps/freesurfer/6.0.1
Loading source label.
Invalid argument
ERROR reading /dfs6/pub/ltaylor2/downs/fsaverage/label/lh.BA1_exvivo.label
So check to see if /dfs6/pub/ltaylor2/downs/fsaverage exists and that your
SUBJECTS_DIR is /dfs6/pub/ltaylor2/downs. If it does not exist you can create a
symlink from $FREESURFER_HOME/subjects/fsaverage to your SUBJECTS_DIR.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa Marie
Sent: Wednesday, July 14, 2021 11:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Taylor, Derek <dvtay...@hs.uci.edu>
Subject: [Freesurfer] Freesurfer not creating specific files
External Email - Use Caution
Hi everyone,
I could really use some help with figuring out an issue I've been struggling
with the last few months. It seems that when I run recon-all on over 20 of my
participants, not all freesurfer files are created. But I am not understanding
why, and my technical capabilities are limited. Particularly, it seems there's
an issue reading the lh.BA1_exvivo.label. I will attach the recon-all log file
for any other information that it can provide.
Also, I run a script for recon-all and these are the arguments: srun
${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all
-hippocampal-subfields-T1 -brainstem-structures -qcache
Not sure if this is pertinent, but our HPC has been updated, but I am unaware
if that can impact how freesurfer is run.
Thank you for any insight you can provide!
Lisa
(I previously sent an email with screen shots, but the email was waiting to be
approved due to size)
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