dcm2niix

[NPann]

Summary

dcm2niix interface failed with FileNotFoundError exception with following flags:

    converter = Dcm2niix()
    converter.inputs.single_file = True
    converter.inputs.compress = 'n'
    converter.inputs.output_dir = '/some/directory/'
    converter.inputs.source_names = ['/some/input/file.dcm']
    converter.inputs.bids_format = False
    converter.inputs.out_filename = 'filename'
    converter.run()

Fails with:
FileNotFoundError: File/Directory '[u'/some/directory/filename.nii.gz']' not found for Dcm2niix output 'converted_files'.

_parse_stdout is currently not taking into account compression arg and expected output file extension is .nii.gz.

Actual behavior

Interface Dcm2niix failed to run.

Expected behavior

Dcm2niix run

Platform details:

{'nibabel_version': '2.1.0', 'networkx_version': '1.11', 'numpy_version': '1.12.0', 'sys_platform': 'linux2', 'sys_version': '2.7.13 (default, Mar 20 2017, 09:17:50) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-17)]', 'commit_source': u'(none found)', 'commit_hash': u'', 'pkg_path': '/usr/local/lib/python2.7/site-packages/nipype', 'sys_executable': '/usr/local/bin/python', 'traits_version': '4.6.0', 'scipy_version': '0.18.1'}
0.13.0-rc1