fMRIdnoise RuntimeError: Workflow did not execute cleanly

alado · May 20, 2021, 8:52am

Hi!

I’m trying to run fmridenoise on Linux.
If I use the command: fmridenoise compare -p 24HMP8PhysSpikeReg /home/alado/datasets/RBH/preprocessed/
where the path is the path to the bids folder (after fmriprep)
I get an error: fmridenoise compare: error: the following arguments are required: bids_dir
Am I using it incorrectly?

If I use the following command: fmridenoise compare /home/alado/datasets/RBH/preprocessed/
I get the following error message:
`[Node] Finished “BidsValidate”.
210520-10:39:19,600 nipype.workflow INFO:
Workflow fmridenoise_wf settings: [‘check’, ‘execution’, ‘logging’, ‘monitoring’]
210520-10:39:19,652 nipype.workflow INFO:
Running serially.
210520-10:39:19,652 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-24HMP_8Phys_SpikeReg_4GS.json/PipelineSelector”.
210520-10:39:19,653 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,653 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,653 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-24HMP_aCompCor_SpikeReg_4GS.json/PipelineSelector”.
210520-10:39:19,654 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,654 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,654 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-24HMP_aCompCor_SpikeReg.json/PipelineSelector”.
210520-10:39:19,654 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,654 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,654 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-ICA-AROMA_8Phys.json/PipelineSelector”.
210520-10:39:19,655 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,655 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,655 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-24HMP_8Phys_SpikeReg.json/PipelineSelector”.
210520-10:39:19,655 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,655 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,655 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-ICA-AROMA_8Phys_4GS.json/PipelineSelector”.
210520-10:39:19,656 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,656 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,656 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path…home…alado…anaconda3…lib…python3.8…site-packages…fmridenoise…pipelines…pipeline-Null.json/PipelineSelector”.
210520-10:39:19,656 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
210520-10:39:19,656 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
210520-10:39:19,656 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.JoinPipelines” in “/tmp/fmridenoise/fmridenoise_wf/JoinPipelines”.
210520-10:39:19,660 nipype.workflow INFO:
[Node] Outdated cache found for “fmridenoise_wf.JoinPipelines”.
210520-10:39:19,663 nipype.workflow INFO:
[Node] Running “JoinPipelines” (“nipype.interfaces.utility.base.IdentityInterface”)
210520-10:39:19,666 nipype.workflow INFO:
[Node] Finished “fmridenoise_wf.JoinPipelines”.
210520-10:39:19,666 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.GroupConn” in “/tmp/fmridenoise/fmridenoise_wf/GroupConn”.
210520-10:39:19,667 nipype.workflow INFO:
[Node] Running “GroupConn” (“fmridenoise.interfaces.connectivity.GroupConnectivity”)
210520-10:39:19,668 nipype.workflow WARNING:
Storing result file without outputs
210520-10:39:19,668 nipype.workflow WARNING:
[Node] Error on “fmridenoise_wf.GroupConn” (/tmp/fmridenoise/fmridenoise_wf/GroupConn)
210520-10:39:19,668 nipype.workflow ERROR:
Node GroupConn failed to run on host sandvik.
210520-10:39:19,668 nipype.workflow ERROR:
Saving crash info to /home/alado/crash-20210520-103919-alado-GroupConn-237fe7c6-12d4-427a-bc38-b4ea94add680.pklz
Traceback (most recent call last):
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py”, line 46, in run
node.run(updatehash=updatehash)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 1004, in _run_command
return super(JoinNode, self)._run_command(execute, copyfiles)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 434, in run
runtime = self._run_interface(runtime)
File “/home/alado/anaconda3/lib/python3.8/site-packages/fmridenoise/interfaces/connectivity.py”, line 112, in _run_interface
entities = parse_file_entities_with_pipelines(self.inputs.corr_mat[0])
IndexError: list index out of range

210520-10:39:19,669 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.GroupConf” in “/tmp/fmridenoise/fmridenoise_wf/GroupConf”.
210520-10:39:19,670 nipype.workflow INFO:
[Node] Running “GroupConf” (“fmridenoise.interfaces.confounds.GroupConfounds”)
210520-10:39:19,671 nipype.workflow WARNING:
Storing result file without outputs
210520-10:39:19,672 nipype.workflow WARNING:
[Node] Error on “fmridenoise_wf.GroupConf” (/tmp/fmridenoise/fmridenoise_wf/GroupConf)
210520-10:39:19,672 nipype.workflow ERROR:
Node GroupConf failed to run on host sandvik.
210520-10:39:19,672 nipype.workflow ERROR:
Saving crash info to /home/alado/crash-20210520-103919-alado-GroupConf-c152fe77-0ecd-4b2e-af32-830ac219f2bd.pklz
Traceback (most recent call last):
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py”, line 46, in run
node.run(updatehash=updatehash)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 1004, in _run_command
return super(JoinNode, self)._run_command(execute, copyfiles)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 434, in run
runtime = self._run_interface(runtime)
File “/home/alado/anaconda3/lib/python3.8/site-packages/fmridenoise/interfaces/confounds.py”, line 260, in _run_interface
entities = parse_file_entities_with_pipelines(self.inputs.conf_summary_json_files[0])
IndexError: list index out of range

210520-10:39:19,673 nipype.workflow INFO:
***********************************
210520-10:39:19,673 nipype.workflow ERROR:
could not run node: fmridenoise_wf.GroupConn
210520-10:39:19,673 nipype.workflow INFO:
crashfile: /home/alado/crash-20210520-103919-alado-GroupConn-237fe7c6-12d4-427a-bc38-b4ea94add680.pklz
210520-10:39:19,673 nipype.workflow ERROR:
could not run node: fmridenoise_wf.GroupConf
210520-10:39:19,673 nipype.workflow INFO:
crashfile: /home/alado/crash-20210520-103919-alado-GroupConf-c152fe77-0ecd-4b2e-af32-830ac219f2bd.pklz
210520-10:39:19,673 nipype.workflow INFO:
***********************************
Traceback (most recent call last):
File “/home/alado/anaconda3/lib/python3.8/runpy.py”, line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File “/home/alado/anaconda3/lib/python3.8/runpy.py”, line 87, in _run_code
exec(code, run_globals)
File “/home/alado/anaconda3/lib/python3.8/site-packages/fmridenoise/main.py”, line 238, in
main()
File “/home/alado/anaconda3/lib/python3.8/site-packages/fmridenoise/main.py”, line 230, in main
compare(args)
File “/home/alado/anaconda3/lib/python3.8/site-packages/fmridenoise/main.py”, line 207, in compare
workflow.run()
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py”, line 632, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py”, line 70, in run
report_nodes_not_run(notrun)
File “/home/alado/anaconda3/lib/python3.8/site-packages/nipype/pipeline/plugins/tools.py”, line 97, in report_nodes_not_run
raise RuntimeError(
RuntimeError: Workflow did not execute cleanly. Check log for details`

However, runtime.log is empty.
The following archives are created:
crash-20210520-101754-alado-GroupConf-5c8b39a2-5b35-4c44-b185-98561ee5e6e6.pklz
crash-20210520-101754-alado-GroupConn-6b0eca95-8862-4488-952e-50a03d1b6225.pklz

Maybe I use the wrong commands?

Best,
Anastasia

alado · June 3, 2021, 8:15pm

Hi!
If anyone is running into the same problems as I was

2nd question: I didn’t have AROMA outputs from fMRIPrep. That’s why I was getting the error. At least, it disappered after I re-run fMRIPrep with AROMA.

1st question: from the website Usage — fmridenoise documentation I assumed that you run fmridenoise like: fmridenoise compare [arguments] <bids_dir>. However it gives an error fmridenoise compare: error: the following arguments are required: bids_dir.
But when I change the command to fmridenoise compare <bids_dir> [arguments] it executes successfully.

But now I’m running into a new problem: if I specify the session number I get fmridenoise.interfaces.bids.MissingFile: missing file(s) for {'subject': '02', 'task': 'nback', 'session': 'ses-1', 'run': 1, 'extension': 'tsv', 'suffix': ['regressors', 'timeseries'], 'desc': 'confounds'} (check if you are using AROMA pipelines)
But I have the file sub-02_ses-1_task-nback_run-1_desc-confounds_regressors.tsv.

Does anybody know what may be the problem?
If I don’t specify the session number, everything executes correctly, but since I don’t have the same number of sessions for all subjects, subjects who lack one session are just skipped.

Best,
Anastasia