Getting this error message when running fMRIPrep.
I’m running in a virtualenv…I think maybe its an environment problem??
(fmriprep)slab@freewill:/net/pizza/BPReward_BIDS$ fmriprep-docker /net/pizza/BPReward_BIDS/ /net/pizza/BPReward_BIDS/derivatives/ --fs-license-file /usr/local/freesurfer/freesurfer_6.0.0_centos6/license.txt --nthreads 8 --ignore slicetiming --use-syn-sdc --no-freesurfer
RUNNING: docker run --rm -it -v /usr/local/freesurfer/freesurfer_6.0.0_centos6/license.txt:/opt/freesurfer/license.txt:ro -v /net/pizza/BPReward_BIDS/:/data:ro -v /net/pizza/BPReward_BIDS/derivatives/:/out poldracklab/fmriprep:1.0.6-2 /data /out participant --nthreads 12 --ignore slicetiming --use-syn-sdc --no-freesurfer
Process Process-2:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 249, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.6/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 370, in build_workflow
os.makedirs(log_dir, exist_ok=True)
File “/usr/local/miniconda/lib/python3.6/os.py”, line 210, in makedirs
makedirs(head, mode, exist_ok)
File “/usr/local/miniconda/lib/python3.6/os.py”, line 220, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: ‘/out/fmriprep’
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==1.0.6.post2’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 247, in main
fmriprep_wf = retval[‘workflow’]
File “”, line 2, in getitem
File “/usr/local/miniconda/lib/python3.6/multiprocessing/managers.py”, line 772, in _callmethod
raise convert_to_error(kind, result)
KeyError: ‘workflow’
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues