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neurospin / pypreprocess

Preprocessing scripts for neuro imaging
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Error running an examples/easy_start/nipype_preproc_spm_auditory.py with Nipype >0.13 #288

Open KamalakerDadi opened 6 years ago

KamalakerDadi commented 6 years ago 
2018-01-26 15:09:46,326:INFO: found SPM directory to be "/home/kamalakar/opt/spm8/spm8/spm8_mcr/spm8"
2018-01-26 15:09:46,326:INFO: using SPM version: 8
2018-01-26 15:09:46,326:INFO: setting SPM MCR path to "/home/kamalakar/opt/spm8/spm8.sh" and "use_mcr" to True
2018-01-26 15:09:46,326:INFO: SPM configuration succeeded using SPM MCR.
Traceback (most recent call last):
  File "examples/easy_start/nipype_preproc_spm_auditory.py", line 52, in <module>
    subject_data = do_subjects_preproc(jobfile, dataset_dir=dataset_dir)[0]
  File "/home/kamalakar/Kamalakar/work/pypreprocess/pypreprocess/nipype_preproc_spm_utils.py", line 1715, in do_subjects_preproc
    subject_data, **preproc_params) for subject_data in subjects)
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 779, in __call__
    while self.dispatch_one_batch(iterator):
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 625, in dispatch_one_batch
    self._dispatch(tasks)
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 588, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/_parallel_backends.py", line 111, in apply_async
    result = ImmediateResult(func)
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/_parallel_backends.py", line 332, in __init__
    self.results = batch()
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/sklearn/externals/joblib/parallel.py", line 131, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/home/kamalakar/Kamalakar/work/pypreprocess/pypreprocess/nipype_preproc_spm_utils.py", line 1298, in do_subject_preproc
    software=realign_software
  File "/home/kamalakar/Kamalakar/work/pypreprocess/pypreprocess/nipype_preproc_spm_utils.py", line 319, in _do_subject_realign
    jobtype=jobtype, **kwargs)
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/nipype/caching/memory.py", line 74, in __call__
    interface.inputs.trait_set(**kwargs)
  File "/home/kamalakar/.local/lib/python2.7/site-packages/traits/has_traits.py", line 1544, in trait_set
    setattr( self, name, value )
  File "/home/kamalakar/miniconda2/envs/pypreprocess/lib/python2.7/site-packages/nipype/interfaces/base/traits_extension.py", line 335, in validate
    value = super(MultiPath, self).validate(object, name, newvalue)
  File "/home/kamalakar/.local/lib/python2.7/site-packages/traits/trait_types.py", line 2337, in validate
    return TraitListObject( self, object, name, value )
  File "/home/kamalakar/.local/lib/python2.7/site-packages/traits/trait_handlers.py", line 2313, in __init__
    raise excp
traits.trait_errors.TraitError: Each element of the 'in_files' trait of a RealignInputSpec instance must be an existing file name, but a value of [u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_004.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_005.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_006.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_007.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_008.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_009.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_010.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_011.img', u'/home/kamalakar/nilearn_data/spm_auditory/pypreprocess_scratch/sub001/cache_dir/nipype_mem/nipype-interfaces-spm-preprocess-SliceTiming/0f1bac640d9cea8dadaf57a6dfdcdc0c/afM00223_012.img', 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I am currently experiencing problem running this example with more recent versions of Nipype. I can open an issue there to ask.

Meanwhile, please let me know if you know why ?

KamalakerDadi commented 6 years ago

FYI Issue is reported to Nipype team here https://github.com/nipy/nipype/issues/2406

KamalakerDadi commented 6 years ago

For now, I think we can add a small note in readme document to be cautious of running examples (which are broken) with more recent Nipype versions.

I will issue a PR.

dohmatob commented 6 years ago

Ok, thanks for looking into this.