WIP: nipype_cmd - run any Interface from a command line

nipype_cmd --help

    usage: nipype_cmd [-h] module interface

    Nipype interface runner

    positional arguments:
      module      Module name
      interface   Interface name

    optional arguments:
      -h, --help  show this help message and exit

nipype_cmd nipype.interfaces.nipy

    Available Interfaces:
	    SpaceTimeRealigner
	    Similarity
	    ComputeMask
	    FitGLM
	    EstimateContrast
	    FmriRealign4d

nipype_cmd nipype.interfaces.nipy ComputeMask --help

    usage: nipype_cmd nipype.interfaces.nipy ComputeMask [-h] [--M M] [--cc CC]
                                                         [--ignore_exception IGNORE_EXCEPTION]
                                                         [--m M]
                                                         [--reference_volume REFERENCE_VOLUME]
                                                         mean_volume

    Run ComputeMask

    positional arguments:
      mean_volume           mean EPI image, used to compute the threshold for the
                            mask

    optional arguments:
      -h, --help            show this help message and exit
      --M M                 upper fraction of the histogram to be discarded
      --cc CC               Keep only the largest connected component
      --ignore_exception IGNORE_EXCEPTION
                            Print an error message instead of throwing an
                            exception in case the interface fails to run
      --m M                 lower fraction of the histogram to be discarded
      --reference_volume REFERENCE_VOLUME
                            reference volume used to compute the mask. If none is
                            give, the mean volume is used.

nipype_cmd nipype.interfaces.nipy ComputeMask /tmp/mean_volume.nii

    brain_mask = /tmp/mean_mask.nii.gz