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?