Fmriprep: Permissions Error (?) with FreeSurfer Processing and -u Flag in 20.0.6

[jrussell9000]

Using fMRIPrep 20.0.6, via docker (fmriprep-docker) with the -u $UID flag. During at the start of FreeSurfer processing, fMRIPrep crashes with what appears to be a permissions error. No other preceding errors and everything to that point comes out owned by my user account (as desired).

Node: fmriprep_wf.fsdir_run_20200424_173701_c73b53cd_29a6_4755_b77b_ac5e10a68752
Working directory: /tmp/work/fmriprep_wf/fsdir_run_20200424_173701_c73b53cd_29a6_4755_b77b_ac5e10a68752

Node inputs:

derivatives = /out
freesurfer_home = /opt/freesurfer
overwrite_fsaverage = False
spaces = []
subjects_dir = freesurfer
Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/bids.py", line 684, in _run_interface copytree(source, dest) File "/usr/local/miniconda/lib/python3.7/shutil.py", line 359, in copytree raise Error(errors) shutil.Error: [('/opt/freesurfer/subjects/fsaverage/label', '/out/freesurfer/fsaverage/label', "[Errno 1] Operation not permitted: '/out/freesurfer/fsaverage/label'"), ......]

(ellipses added at the end)

[mgxd]

can you share the full command you are using? and verify that /out/freesurfer/fsaverage/label is owned by the same UID you are passing in?

[jrussell9000]

The fsaverage folder and contents aren't owned by the UID I'm passing (they're owned by root), which appears to be the problem. My command is below...

fmriprep-docker --fs-license-file ~/license.txt ./BIDS_Master/ ./fmriprep/ participant --ignore fieldmaps --n_cpus 32 -u $UID

[oesteban]

@mgxd with that command line (without --fs-subjects-dir), should not the freesurfer folder be pointing to $PWD/fmriprep/freesurfer ?

[mgxd]

@oesteban the output directory, in this case ./fmriprep, is remapped to /out within the container, so /out/freesurfer seems correct.

@jrussell9000 did the output folder exist before running the wrapper? this looks similar to https://github.com/poldracklab/fmriprep/issues/2098

in any case, we could add a check to the wrapper warning users about permission issues when mounting non-existing directories.

[jrussell9000]

In this case the output directory structure did not exist prior to starting the wrapper. I'd second a permissions check...I didn't realize I needed to create those directories. I'll create the fmriprep and freesurfer directories (owned by my UID) before running again and update this issue with the results.

[mgxd]

This should be fixed in #2106