3 Dec
2020
3 Dec
'20
9:52 a.m.
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?