Hmmm. I’m getting a problem with templateflow, error below. I feel like I’ve seen stuff like this on Neurostars, but searching didn’t yield anything useful.
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
190607-15:01:09,47 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.4.1rc2:
* BIDS dataset path: /mnt.
* Participant list: ['CBPD0142'].
* Run identifier: 20190607-150108_7a1900d7-3648-40a8-af17-3351dc673405.
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIPediatricAsym/cohort-2/tpl-MNIPediatricAsym_cohort-2_res-1_T1w.nii.gz
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 608, in build_workflow
work_dir=str(work_dir),
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 259, in init_fmriprep_wf
use_syn=use_syn,
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 551, in init_single_subject_wf
skull_strip_template=skull_strip_template,
File "/usr/local/miniconda/lib/python3.7/site-packages/smriprep/workflows/anatomical.py", line 230, in init_anat_preproc_wf
normalization_quality='precise' if not debug else 'testing')
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/anat/ants.py", line 188, in init_brain_extraction_wf
tpl_target_path = get_template(in_template, **template_spec)
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 39, in get
_s3_get(filepath)
File "/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py", line 139, in _s3_get
with filepath.open('wb') as f:
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1176, in open
opener=self._opener)
File "/usr/local/miniconda/lib/python3.7/pathlib.py", line 1030, in _opener
return self._accessor.open(self, flags, mode)
OSError: [Errno 30] Read-only file system: '/opt/templateflow/tpl-MNIPediatricAsym/cohort-2/tpl-MNIPediatricAsym_cohort-2_res-1_T1w.nii.gz'
Command is:
unset PYTHONPATH;
echo 'job is running'
singularity run --cleanenv -B ${BIDS_folder}:/mnt ${tools_dir}/fmriprep-1-4-1rc2.simg \
/mnt/ /mnt/derivatives/fmriprep_test \
participant \
-w /tmp/utooley${subject} \
--participant-label ${subject} \
--fs-license-file $HOME/license.txt \
--skull-strip-template MNIPediatricAsym:cohort-2 \
--output-spaces MNIPediatricAsym:cohort-2:res-2 T1w template fsaverage5 \
--nthreads 1 \