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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
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NodeExecutionError: #2933

Closed juansanchezpena closed 1 year ago

juansanchezpena commented 1 year ago

What happened?

I saw fmriprep / nipype NodeExecutionError #3415 but did not see any comments.

Node: fmriprep_22_1_wf.single_subject_patensasc0089_wf.func_preproc_ses_1385_task_rest_run_05_wf.unwarp_wf.resample Working directory: /tmp/work/fmriprep_22_1_wf/single_subject_patensasc0089_wf/func_preproc_ses_1385_task_rest_run_05_wf/unwarp_wf/resample

Node inputs:

in_coeff = in_data = in_xfms = num_threads = 8 pe_dir = ro_time =

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/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 resample.

What command did you use?

Running fMRIPrep version 22.1.0+0.gce344b39.dirty

docker service create --replicas 1 --reserve-cpu 8 --reserve-memory 16g --mode replicated --restart-condition none  --mount type=bind,source=$indir,destination=/input,readonly=true --mount type=bind,source=$outdir,destination=/output  --mount type=bind,source=/MRI_DATA/bin/freesurferlicense.txt,destination=/opt/freesurfer/license.txt,readonly=true  nipreps/fmriprep:22.1.0  /input /output participant $addarg

What version of fMRIPrep are you running?

22.1.0

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.

230111-08:36:34,445 nipype.workflow ERROR:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     could not run node: fmriprep_22_1_wf.single_subject_patensasc0085_wf.func_preproc_ses_1173_task_rest_run_04_wf.unwarp_wf.resample
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 230111-08:36:35,519 nipype.workflow CRITICAL:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     fMRIPrep failed: Traceback (most recent call last):
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |   File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     result["result"] = node.run(updatehash=updatehash)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |   File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     result = self._run_interface(execute=True)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |   File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     return self._run_command(execute)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |   File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     raise NodeExecutionError(msg)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node resample.
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | Traceback:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    concurrent.futures.process._RemoteTraceback: 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    """
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    Traceback (most recent call last):
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        r = call_item.fn(*call_item.args, **call_item.kwargs)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/process.py", line 202, in _process_chunk
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        return [fn(*args) for args in chunk]
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/process.py", line 202, in <listcomp>
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        return [fn(*args) for args in chunk]
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/sdcflows/interfaces/bspline.py", line 624, in _b0_resampler
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        if unwarp.fit(distorted_img):
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/sdcflows/transform.py", line 99, in fit
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        wmat = grid_bspline_weights(spatialimage, moved_cs)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/sdcflows/transform.py", line 417, in grid_bspline_weights
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        colloc_ax = BSpline.design_matrix(x, t, 3)[:, (2 + pad_left):-(2 + pad_right)]
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/scipy/interpolate/_bsplines.py", line 416, in design_matrix
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        raise ValueError(f'Out of bounds w/ x = {x}.')
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    ValueError: Out of bounds w/ x = [ 3.62616494  4.12461877  4.6230726   5.12152642  5.61998025  6.11843408
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      6.61688791  7.11534173  7.61379556  8.11224939  8.61070322  9.10915704
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      9.60761087 10.1060647  10.60451853 11.10297235 11.60142618 12.09988001
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     12.59833384 13.09678766 13.59524149 14.09369532 14.59214915 15.09060297
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     15.5890568  16.08751063 16.58596446 17.08441828 17.58287211 18.08132594
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     18.57977977 19.07823359 19.57668742 20.07514125 20.57359508 21.0720489
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     21.57050273 22.06895656 22.56741039 23.06586421 23.56431804 24.06277187
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     24.5612257  25.05967952 25.55813335 26.05658718 26.55504101 27.05349483
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     27.55194866 28.05040249 28.54885632 29.04731014 29.54576397 30.0442178
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     30.54267163 31.04112545 31.53957928 32.03803311 32.53648694 33.03494076
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     33.53339459 34.03184842 34.53030225 35.02875607 35.5272099  36.02566373].
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    """
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    The above exception was the direct cause of the following exception:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    Traceback (most recent call last):
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        runtime = self._run_interface(runtime)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/site-packages/sdcflows/interfaces/bspline.py", line 373, in _run_interface
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        ) = zip(*outputs)
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        for element in iterable:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        yield fs.pop().result()
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/_base.py", line 439, in result
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        return self.__get_result()
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      File "/opt/conda/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |        raise self._exception
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |    ValueError: Out of bounds w/ x = [ 3.62616494  4.12461877  4.6230726   5.12152642  5.61998025  6.11843408
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      6.61688791  7.11534173  7.61379556  8.11224939  8.61070322  9.10915704
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |      9.60761087 10.1060647  10.60451853 11.10297235 11.60142618 12.09988001
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     12.59833384 13.09678766 13.59524149 14.09369532 14.59214915 15.09060297
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     15.5890568  16.08751063 16.58596446 17.08441828 17.58287211 18.08132594
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     18.57977977 19.07823359 19.57668742 20.07514125 20.57359508 21.0720489
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     21.57050273 22.06895656 22.56741039 23.06586421 23.56431804 24.06277187
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     24.5612257  25.05967952 25.55813335 26.05658718 26.55504101 27.05349483
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     27.55194866 28.05040249 28.54885632 29.04731014 29.54576397 30.0442178
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     30.54267163 31.04112545 31.53957928 32.03803311 32.53648694 33.03494076
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     33.53339459 34.03184842 34.53030225 35.02875607 35.5272099  36.02566373].
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 230111-08:37:07,839 cli ERROR:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     Preprocessing did not finish successfully. Errors occurred while processing data from participants: patensasc0085 (1). Check the HTML reports for details.
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    | 230111-08:37:07,839 cli ERROR:
peaceful_wozniak.1.1f50cdq7sjk0@plisskenmri.nyspi.local    |     Preprocessing did not finish successfully. Errors occurred while processing data from participants: patensasc0085 (1). Check the HTML reports for details.

Additional information / screenshots

This also happened with a subsequent subject in the last resting state run as well.

effigies commented 1 year ago

This should be fixed in 22.1.1.

effigies commented 1 year ago

See https://github.com/nipreps/sdcflows/issues/323

juansanchezpena commented 1 year ago

Thanks Chris, I will use the 22.1.1 on same data and report back

From: Chris Markiewicz @.> Sent: Wednesday, January 11, 2023 12:58 PM To: nipreps/fmriprep @.> Cc: Sanchez, Juan (NYSPI) @.>; Author @.> Subject: Re: [nipreps/fmriprep] NodeExecutionError: (Issue #2933)

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juansanchezpena commented 1 year ago

worked without errors on 21.1.1 Thanks Chris