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?
Hi Courtney
Can you send us your command line and a recon-all.log?
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Wednesday, December 2, 2020 9:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error
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?
freesurfer@nmr.mgh.harvard.edu
-
Courtney Haswell -
Fischl, Bruce