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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 <dvtaylor@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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