Hi Courtney
Can you send us the recon-all.log file and the full screen output from one job
that failed?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Courtney Haswell
Sent: Thursday, December 3, 2020 9:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all issues debugging
External Email - Use Caution
I am trying to debug why all of our T1's are failing Freesurfer recon-all. It
seems that most of the files are being created but it isn't getting to the
stats steps to output those files. In the recon-all log it does say "recon-all
-s 13265 exited with ERRORS."
I looked in the recon-all.error file and the only thing in that is "CMD
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix."
Would this be the step where the error is happening?
I have checked the T1 thoroughly and it is good quality. What is the best way
to debug why this is happening with our scans?
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