using dMRIprep for the first time
Closed this issue · 3 comments
- dmriprep version:dMRIPrep v0.5.0
- Python version:3.8
- Operating System:ubuntu
Description
Hello
I am converting the data to BIDS format.
I tried the following command line:dmriprep /home/besma/Desktop/test/sub-099S6632/ /home/besma/Desktop/test/Dmri/ participant -w work/
I got this error:bids-validator does not appear to be installed
210328-17:42:45,157 nipype.workflow IMPORTANT:
Running dMRIPrep version 0.5.0:
* BIDS dataset path: /home/besma/Desktop/test/sub-099S6632.
* Participant list: ['099S6632'].
* Run identifier: 20210328-174226_bd41ca82-18fa-4ea5-a898-7a0df6c0bee3.
* Output spaces: run.
Process Process-2:
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/besma/.local/lib/python3.8/site-packages/dmriprep/cli/workflow.py", line 85, in build_workflow
retval["workflow"] = init_dmriprep_wf()
File "/home/besma/.local/lib/python3.8/site-packages/dmriprep/workflows/base.py", line 58, in init_dmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/home/besma/.local/lib/python3.8/site-packages/dmriprep/workflows/base.py", line 313, in init_single_subject_wf
fmap_estimators = find_estimators(
File "/home/besma/.local/lib/python3.8/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/lib/python3.8/dist-packages/pybids-0.12.4-py3.8.egg/bids/layout/layout.py", line 593, in get
layouts = self._get_layouts_in_scope(scope)
File "/usr/local/lib/python3.8/dist-packages/pybids-0.12.4-py3.8.egg/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/lib/python3.8/dist-packages/pybids-0.12.4-py3.8.egg/bids/layout/layout.py", line 253, in
layouts = [l for l in collect_layouts(self) if l._in_scope(scope)]
File "/usr/local/lib/python3.8/dist-packages/pybids-0.12.4-py3.8.egg/bids/layout/layout.py", line 235, in _in_scope
pl_name = self.description.get("PipelineDescription", {}).get("Name")
AttributeError: 'NoneType' object has no attribute 'get'
If anyone can help me. I would be grateful.
Thank you.
What I Did
Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.
I had a path problem and now it's solved
cordially
Sorry for missing this @Meryam1985. Glad that you were able to figure it out and hopefully we can respond sooner to any future issues.
Sorry for missing this @Meryam1985. Glad that you were able to figure it out and hopefully we can respond sooner to any future issues.
sorry I have a same issue, can you tell me how to solve it?