Hello Daniel,
The docker container may not be properly supporting symbolic links, i.e., apparently you can write files inside the container, but in your log that error is the first instance of the ln command.
Could you try running it w/o using a container and see if it gets past the ln command? If so, then I would ask someone at your facility to look at the docker configuration. The fix for that error message in some docker postings is to upgrade to a newer version of docker.
- rob
On Jul 11, 2018, at 11:06 AM, Daniel Kimmel <danielkimmel@gmail.commailto:danielkimmel@gmail.com> wrote:
External Email - Use Caution
Hello,
I'm attempting to run basic preprocessing with reconstruction using fmriprep-docker.py and freesurfer. The fmriprep process completes when excluding freesurfer, but encounters a fatal error when including freesurfer. There error is:
recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018
For more details, see the log file /out/freesurfer/sub-18042401/scripts/recon-all-rh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error: ln: failed to create symbolic link 'rh.white.H': Operation not supported Return code: 1
180711-01:39:51,447 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:51,452 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:54,738 cli WARNING: Errors occurred while generating reports for participants: 18042401 (2).
The call to freesurfer is made by fmriprep, which is doing so within a docker container, so unfortunately I don't know the exact version of freesurfer. I'm using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux box: uname -a: Linux xxx.xxx.xxx.columbia.eduhttp://xxx.xxx.xxx.columbia.edu/ 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
I've attached: 1) the complete terminal output from fmriprep (which is reporting the output of freesurfer) 2) recon-all-status-rh.log 3) recon-all.log
Thanks very much for your help! Best, Daniel
<fmriprep-docker-terminal-output-12 - freesurfer.txt><recon-all-status-rh.log><recon-all.log>