Dear all,
i’ve run my bids data with a script in docker mode but i have this error:
180427-16:11:24,48 workflow WARNING:
[Node] Error on "fmriprep_wf.fsdir" (/root/src/fmriprep/work/fmriprep_wf/fsdir)
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 339, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/bids.py", line 352, in _run_interface
copytree(source, dest)
File "/usr/local/miniconda/lib/python3.6/shutil.py", line 353, in copytree
raise Error(errors)
shutil.Error: [('/opt/freesurfer/subjects/fsaverage/surf/rh.white_avg', '/out/out/freesurfer/fsaverage/surf/rh.white_avg', '[Errno 5] Input/output error')]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==1.0.11', 'console_scripts', 'fmriprep')()
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 274, in main
fmriprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 190, in run
self._send_procs_to_workers(updatehash=updatehash, graph=graph)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 347, in _send_procs_to_workers
'traceback': traceback
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 339, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/bids.py", line 352, in _run_interface
copytree(source, dest)
File "/usr/local/miniconda/lib/python3.6/shutil.py", line 353, in copytree
raise Error(errors)
shutil.Error: [('/opt/freesurfer/subjects/fsaverage/surf/rh.white_avg', '/out/out/freesurfer/fsaverage/surf/rh.white_avg', '[Errno 5] Input/output error')]
my bash/docker script:
docker run -it --rm \
-v /media/DATA/BIDS/test/test_project:/data:ro \
-v /media/DATA/BIDS/test/test_project/derivatives/fmriprep:/out \
-v /media/DATA/BIDS/test/license.txt:/opt/freesurfer/license.txt \
poldracklab/fmriprep:latest \
/data /out/out \
participant \
--participant-label sub-0001 \
--write-graph \
--nthreads 4 \
--mem_mb 6000 \
--write-graph \
--fs-license-file /opt/freesurfer/license.txt