We are hoping to utilize dmriprep to process our diffusion data. As a first pass, we have a small, bids-verified dataset we were hoping to test with it.
We set up the command as follows:
cd $processing_dir
for i in sub-*; do
docker run -ti --rm \
-v ${PWD}:/inputs \
-v ${PWD}/derivatives/:/outputs \
-v ${license_dir}/license:/license \
-t --user $(id -u):$(id -g) \
nipreps/dmriprep:latest \
/inputs /outputs \
participant --participant-label ${i} \
--fs-license-file /license/license.txt \
--fs-no-reconall
done
When running, we encounter the following error:
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/dmriprep/cli/workflow.py", line 85, in build_workflow
retval["workflow"] = init_dmriprep_wf()
File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/workflows/base.py", line 58, in init_dmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/usr/local/miniconda/lib/python3.7/site-packages/dmriprep/workflows/base.py", line 317, in init_single_subject_wf
force_fmapless=config.workflow.force_syn,
File "/usr/local/miniconda/lib/python3.7/site-packages/sdcflows/utils/wrangler.py", line 210, in find_estimators
for fmap in layout.get(suffix=["fieldmap", "phasediff", "phase1"], **base_entities):
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 593, in get
layouts = self._get_layouts_in_scope(scope)
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 253, in _get_layouts_in_scope
layouts = [l for l in collect_layouts(self) if l._in_scope(scope)]
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 253, in <listcomp>
layouts = [l for l in collect_layouts(self) if l._in_scope(scope)]
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 235, in _in_scope
pl_name = self.description.get("PipelineDescription", {}).get("Name")
AttributeError: 'NoneType' object has no attribute 'get'
The same issue has been reported sometime ago on the github project page, which was due to a “path issue”. I cannot figure out which path is incorrect in our command