External Email - Use Caution
Dear Freesurfer developers,
I am trying to run the longitudinal processing pipeline of our data on our HPC cluster (SGE based) and it crashes at the 3rd step - generating the longitudinal runs. The exact command is 'recon-all -long tp1dir basedir -all'. There is no error message on the screen, it just says that it exited with errors.
The recon-all.log file has no error information either, other than the statement that it exited with errors. It seems to have stopped after mri_nu_correct.mni step and looking further it looks like it crashed at the beginning of orig_nu step, since orig_nu.log has this error message:
/usr/bin/time: /dev/stdout: Not a directory
Please see attached log files.
Additional information:
Freesurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
uname -a:
Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
lsb_release -a: LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.6 (Final) Release: 6.6 Codename: Final
What is interesting is that running it on the headnode directly without qsub works fine. The headnode has the same OS and tcsh versions.
In my rather poorly informed opinion, it looks like fs_time is the culprit. For a quick fix, is it safe to assume that using fs_time from Freesurfer 6 wont affect the processing pipeline in any way?
Thank you!
Best regards, Renat.