search

nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://www.nipreps.org/dmriprep
Apache License 2.0
63 stars 24 forks source link

using dMRIprep for the first time #160

Closed Meryam1985 closed 3 years ago

Meryam1985 commented 3 years ago

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.
Meryam1985 commented 3 years ago

I had a path problem and now it's solved cordially

josephmje commented 3 years ago

Sorry for missing this @Meryam1985. Glad that you were able to figure it out and hopefully we can respond sooner to any future issues.

chengyu89527 commented 2 years ago

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?