Description
Summary
When in a pipeline allineate does not generate filenames. This is using a version after the allineate fix.
Actual behaviour
The allineate call now fails with a runtime error.
Expected behaviour
Allineate to generate an output file name
How to replicate the behaviour
Run a script with an input 1D file and an input file to motion correct
Script/Workflow details
moco = pe.MapNode(interface=afni.Allineate(), name='moco', iterfield=['in_file', 'in_matrix'])
moco.inputs.outputtype = 'NIFTI_GZ'
preprocphase.connect([(inputspec, img2float, [('input_phase', 'in_file')]),
(img2float, prepphase, [('out_file', 'phase')]),
(inputspec, moco, [('motion_par', 'in_matrix')]),
(prepphase, moco, [('detrended_phase', 'in_file')]),
(inputspec, applyalign, [('run_txfm','in_matrix_file')]),
(moco, applyalign, [('out_file', 'in_file')]),
(applyalign, maskfunc, [('out_file', 'in_file')]),
(inputspec, maskfunc, [('mask_file', 'in_file2')]),
(maskfunc, outputspec,[('out_file', 'proc_phase')])
])
Please put URL to code or code here (if not too long).
Platform details:
{'nibabel_version': '2.1.0', 'sys_executable': '/cfmm/home/ostanle2/.virtualenvs/nipype2/bin/python', 'networkx_version': '1.9.1', 'numpy_version': '1.12.0', 'sys_platform': 'linux2', 'sys_version': '2.7.10 (default, Oct 28 2015, 11:22:11) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-16)]', 'commit_source': u'installation', 'commit_hash': u'4d08138', 'pkg_path': '/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype', 'nipype_version': u'1.0.0-dev', 'traits_version': '4.6.0', 'scipy_version': '0.18.1'}
1.0.0-dev
171005-22:46:15,712 interface INFO:
Closing display (if virtual)
Execution environment
- My python environment outside container