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/home/siegfriedwagner/virtual_enviroments/fmridenoise/bin/python -m fmridenoise compare /home/siegfriedwagner/Downloads/fmriprep_dummy/dummy -d fmriprep
201219-16:29:17,747 nipype.workflow INFO:
[Node] Setting-up "BidsValidate" in "/tmp/tmprm8sxop8/BidsValidate".
201219-16:29:17,749 nipype.workflow INFO:
[Node] Running "BidsValidate" ("fmridenoise.interfaces.bids.BIDSValidate")
201219-16:29:19,805 nipype.workflow WARNING:
Storing result file without outputs
201219-16:29:19,805 nipype.workflow WARNING:
[Node] Error on "BidsValidate" (/tmp/tmprm8sxop8/BidsValidate)
Traceback (most recent call last):
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/siegfriedwagner/git/fmridenoise/fmridenoise/__main__.py", line 236, in <module>
main()
File "/home/siegfriedwagner/git/fmridenoise/fmridenoise/__main__.py", line 228, in main
compare(args)
File "/home/siegfriedwagner/git/fmridenoise/fmridenoise/__main__.py", line 177, in compare
workflow = init_fmridenoise_wf(input_dir,
File "/home/siegfriedwagner/git/fmridenoise/fmridenoise/workflows/base.py", line 455, in init_fmridenoise_wf
result = bids_validate.run()
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 434, in run
runtime = self._run_interface(runtime)
File "/home/siegfriedwagner/git/fmridenoise/fmridenoise/interfaces/bids.py", line 387, in _run_interface
layout = BIDSLayout(
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/bids/layout/layout.py", line 161, in __init__
self.add_derivatives(
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/bids/layout/layout.py", line 469, in add_derivatives
deriv_paths = validate_derivative_paths(paths, self, **kwargs)
File "/home/siegfriedwagner/virtual_enviroments/fmridenoise/lib/python3.8/site-packages/bids/layout/validation.py", line 138, in validate_derivative_paths
raise BIDSDerivativesValidationError(
bids.exceptions.BIDSDerivativesValidationError: Every valid BIDS-derivatives dataset must have a PipelineDescription.Name field set inside 'dataset_description.json'.
Example: {'PipelineDescription': {'Name': 'Example pipeline'}}
Process finished with exit code 1
Problem is connected (partialy) with another resolved issue #74
This problem is still present, but now not in our project but in a roots of pybids.
bids-standard/pybids#640
For now I will recommend not using datasets in BIDS 1.4 standard because there are no tools to interact with it
Until this problem is resolved in pybids it will be hard to support latest BIDS standard
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