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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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Spaces in path's name cause Too many arguments error in funcMRIQC.fMRI_HMC_afni.gen_ref #795

Closed 0rC0 closed 7 months ago

0rC0 commented 5 years ago

Version: MRIQC version 0.15.0.post1

As in object, 3dvolreg gives a FATAL ERROR: Too many arguments?! out if there are spaces in path.

A workaround is mounting with the option --bind the path somewhere else, linking the path doesn't work. 

2019-07-02 17:18:07,670 nipype.workflow:WARNING [Node] Error on "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" (/media/andreas/My Book/fMRIPrep/mriqc/tmp/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..media..andreas..MyBook..fMRIPrep..bids-dset..sub-01..func..sub-01_task-formlang_run-01_bold.nii.gz/gen_ref)
190702-17:18:08,596 nipype.workflow ERROR:
     Node gen_ref.a0 failed to run on host dr-doom.
2019-07-02 17:18:08,596 nipype.workflow:ERROR Node gen_ref.a0 failed to run on host dr-doom.
190702-17:18:08,597 nipype.workflow ERROR:
     Saving crash info to /media/andreas/My Book/fMRIPrep/mriqc/Output/logs/crash-20190702-171808-andreas-gen_ref.a0-39cd8300-24bb-49f0-a806-932ae900569c.txt
Traceback (most recent call last):
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/home/andreas/.local/lib/python3.6/site-packages/niworkflows/interfaces/registration.py", line 399, in _run_interface
    zpad=4, outputtype='NIFTI_GZ').run()
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/interfaces/afni/base.py", line 110, in _run_interface
    return super(AFNICommandBase, self)._run_interface(runtime)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/home/andreas/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
3dvolreg -Fourier -twopass -1Dfile slice.1D -1Dmatrix_save slice.aff12.1D -prefix slice_volreg.nii.gz -zpad 4 -maxdisp1D slice_md.1D /media/andreas/My Book/fMRIPrep/mriqc/tmp/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..media..andreas..MyBook..fMRIPrep..bids-dset..sub-01..func..sub-01_task-formlang_run-01_bold.nii.gz/gen_ref/slice.nii.gz
Standard output:

Standard error:
++ 3dvolreg: AFNI version=AFNI_19.0.26 (Mar 20 2019) [64-bit]
++ Authored by: RW Cox
** FATAL ERROR: Too many arguments?!  Dataset=/media/andreas/My?
** Program compile date = Mar 20 2019
Return code: 1
stale[bot] commented 5 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

oesteban commented 7 months ago

This is more of an issue in nipype. Since the OP already provides a solution, I'll consider this "wontfix".