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.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