MAINT: Use PyBIDS 0.9.2+ via niworkflows PR

[effigies]

Closes #776.

[effigies]

Travis failure is just whining about the URL in setup. Will be resolved once niworkflows has a release.

[effigies]

@oesteban I suspect this is something you'll know more about:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/bin/mriqc_run.py", line 418, in init_mriqc
    wf_list.append(build_workflow(dataset[mod], mod, settings=settings))
  File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/workflows/core.py", line 25, in build_workflow
    workflow = fmri_qc_workflow(dataset, settings=settings)
  File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/workflows/functional.py", line 111, in fmri_qc_workflow
    ema = epi_mni_align(settings)
  File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/workflows/functional.py", line 718, in epi_mni_align
    template_resolution=2, ),
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/mixins/reporting.py", line 32, in __init__
    super(ReportCapableInterface, self).__init__(**kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/mni.py", line 100, in __init__
    super(RobustMNINormalization, self).__init__(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 175, in __init__
    self.inputs = self.input_spec(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/specs.py", line 67, in __init__
    super(BaseTraitedSpec, self).__init__(**kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py", line 172, in error
    value )
traits.trait_errors.TraitError: The 'moving' trait of a RobustMNINormalizationInputSpecRPT instance must be 'T1w' or 'boldref', but a value of 'bold' <class 'str'> was specified.

We can naively replace bold with boldref here:

https://github.com/poldracklab/mriqc/blob/f38b344655e37b25e7e8f6af373f8c361874a7b8/mriqc/workflows/functional.py#L710

But I'm not sure if that's actually appropriate.

[oesteban]

It is actually necessary - nipreps/niworkflows#368

I forgot to check on MRIQC when merged that PR.

[effigies]

It is actually necessary - poldracklab/niworkflows#368

I forgot to check on MRIQC when merged that PR.

To be clear, I should change that to boldref, or we need to restore bold to the interface options?

[oesteban]

It is boldref now, you have to change it. Sorry for the confusion

…

On Fri, Jul 12, 2019, 10:15 Chris Markiewicz ***@***.***> wrote: It is actually necessary - nipreps/niworkflows#368 <nipreps/niworkflows#368> I forgot to check on MRIQC when merged that PR. To be clear, I *should* change that to boldref, or we need to restore bold to the interface options? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#796>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAESDRV2BRBM3VQ4WWGTJC3P7C325ANCNFSM4H7F2ZEA> .