Hi @karofinc!
I am very interested in fMRIDenoise. My data were BIDS formatted and preprocessed in fMRIPrep 1.4.0, with Ubuntu 18.04.3. When running fmridenoise, error messages were shown,
jshino@ubuntu:~$ fmridenoise /home/jshino/BIDS2/
/home/jshino/.local/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
warnings.warn(msg, category=DeprecationWarning)
190902-16:13:38,538 nipype.workflow INFO:
Workflow fmridenoise_wf settings: [‘check’, ‘execution’, ‘logging’, ‘monitoring’]
190902-16:13:38,577 nipype.workflow INFO:
Running serially.
190902-16:13:38,578 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-24HMP_aCompCor_SpikeReg_4GS.json/PipelineSelector”.
190902-16:13:38,579 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,579 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,579 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-24HMP_8Phys_SpikeReg.json/PipelineSelector”.
190902-16:13:38,580 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,580 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,580 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-ICA-AROMA_8Phys_4GS.json/PipelineSelector”.
190902-16:13:38,581 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,581 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,581 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-ICA-AROMA_8Phys.json/PipelineSelector”.
190902-16:13:38,581 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,581 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,581 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-24HMP_aCompCor_SpikeReg.json/PipelineSelector”.
190902-16:13:38,582 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,582 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,582 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-24HMP_8Phys_SpikeReg_4GS.json/PipelineSelector”.
190902-16:13:38,583 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,583 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,583 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…jshino…local…lib…python3.6…site-packages…fmridenoise-0.1.1-py3.6.egg…fmridenoise…pipelines…pipeline-Null.json/PipelineSelector”.
190902-16:13:38,583 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190902-16:13:38,583 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190902-16:13:38,584 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.BidsGrabber” in “/tmp/fmridenoise/fmridenoise_wf/BidsGrabber”.
190902-16:13:38,585 nipype.workflow INFO:
[Node] Running “BidsGrabber” (“fmridenoise.interfaces.bids.BIDSGrab”)
190902-16:13:38,652 nipype.workflow WARNING:
Storing result file without outputs
190902-16:13:38,653 nipype.workflow WARNING:
[Node] Error on “fmridenoise_wf.BidsGrabber” (/tmp/fmridenoise/fmridenoise_wf/BidsGrabber)
190902-16:13:38,658 nipype.workflow ERROR:
Node BidsGrabber failed to run on host ubuntu.
190902-16:13:38,659 nipype.workflow ERROR:
Saving crash info to /home/jshino/crash-20190902-161338-jshino-BidsGrabber-79da2314-3b9f-4e9f-9536-1e5959e115ec.pklz
Traceback (most recent call last):
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py”, line 48, in run
node.run(updatehash=updatehash)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 473, in run
result = self._run_interface(execute=True)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
return self._run_command(execute)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 649, in _run_command
result = self._interface.run(cwd=outdir)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 376, in run
runtime = self._run_interface(runtime)
File “/home/jshino/.local/lib/python3.6/site-packages/fmridenoise-0.1.1-py3.6.egg/fmridenoise/interfaces/bids.py”, line 247, in _run_interface
entity_bold = fmri_file.get_entities()
File “/home/jshino/.local/lib/python3.6/site-packages/bids/layout/layout.py”, line 65, in getattr
(self.class.name, attr))
AttributeError: BIDSFile object has no attribute named ‘get_entities’190902-16:13:38,660 nipype.workflow INFO:
190902-16:13:38,660 nipype.workflow ERROR:
could not run node: fmridenoise_wf.BidsGrabber
190902-16:13:38,660 nipype.workflow INFO:
crashfile: /home/jshino/crash-20190902-161338-jshino-BidsGrabber-79da2314-3b9f-4e9f-9536-1e5959e115ec.pklz
190902-16:13:38,660 nipype.workflow INFO:
Traceback (most recent call last):
File “/usr/lib/python3.6/runpy.py”, line 193, in _run_module_as_main
“main”, mod_spec)
File “/usr/lib/python3.6/runpy.py”, line 85, in _run_code
exec(code, run_globals)
File “/home/jshino/.local/lib/python3.6/site-packages/fmridenoise-0.1.1-py3.6.egg/fmridenoise/main.py”, line 168, in
main()
File “/home/jshino/.local/lib/python3.6/site-packages/fmridenoise-0.1.1-py3.6.egg/fmridenoise/main.py”, line 164, in main
workflow.run()
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py”, line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py”, line 71, in run
report_nodes_not_run(notrun)
File “/home/jshino/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py”, line 82, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. ’
RuntimeError: Workflow did not execute cleanly. Check log for details
Thanks a lot, Jun