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--cifti-output + --fs-no-reconall produces confusing error messages #3071

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effigies opened this issue Aug 14, 2023 · 0 comments
Open

--cifti-output + --fs-no-reconall produces confusing error messages #3071

effigies opened this issue Aug 14, 2023 · 0 comments
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bug effort: low Estimated low effort task impact: low Estimated low impact task
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@effigies
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What happened?

I think this can be resolved by setting some metadata in the argument parser, but we can also just check for this.

What command did you use?

docker $bids_root_dir $bids_root_dir/derivatives \
    participant \
    --participant-label $subj \
    --cifti-output  91k\
    --task-id probabilisticclassification \
    --skip-bids-validation \
    --md-only-boilerplate \
    --fs-no-reconall \
    --output-spaces MNI152NLin6Asym:res-2\
    --nthreads $nthreads \
    --stop-on-first-crash \
    --mem_mb $mem_mb

What version of fMRIPrep are you running?

23.1.4

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

230814-13:34:28,492 nipype.workflow WARNING:
         [Node] Error on "fmriprep_23_1_wf.single_subject_4_wf.func_preproc_ses_timepoint2_task_probabilisticclassification_run_02_wf.bold_fsLR_resampling_wf.select_surfaces" (/tmp/work/fmriprep_23_1_wf/single_subject_4_wf/func_preproc_ses_timepoint2_task_probabilisticclassification_run_02_wf/bold_fsLR_resampling_wf/_hemi_L/select_surfaces)
230814-13:34:28,492 nipype.workflow WARNING:
         Storing result file without outputs
230814-13:34:28,494 nipype.workflow WARNING:
         [Node] Error on "fmriprep_23_1_wf.single_subject_4_wf.func_preproc_ses_timepoint2_task_probabilisticclassification_run_02_wf.bold_fsLR_resampling_wf.select_surfaces" (/tmp/work/fmriprep_23_1_wf/single_subject_4_wf/func_preproc_ses_timepoint2_task_probabilisticclassification_run_02_wf/bold_fsLR_resampling_wf/_hemi_R/select_surfaces)
230814-13:34:28,822 nipype.workflow ERROR:
         Node select_surfaces.a0 failed to run on host 969bf52d0d4d.
230814-13:34:28,832 nipype.workflow ERROR:
         Saving crash info to /out/sub-4/log/20230814-133313_96c84b56-2d5e-42a5-9923-e4c12c29d096/crash-20230814-133428-root-select_surfaces.a0-e200706d-4cb0-46f9-b0d2-781c34a2c2b4.txt
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node select_surfaces.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
            out = function_handle(**args)
        TypeError: _select_surfaces() missing 3 required positional arguments: 'surfaces', 'morphometrics', and 'spherical_registrations'

Additional information / screenshots

No response

@effigies effigies added bug impact: low Estimated low impact task effort: low Estimated low effort task labels Aug 14, 2023
@effigies effigies added this to the 24.0.0 milestone May 9, 2024
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