AFNI Allineate not generating prefix argument

[ostanley]

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

[effigies]

Can you share the text of the error?

[ostanley]

Yes sorry, I don't know how I missed that. Here you go:

	 Saving crash info to /cfmm/data/ostanle2/code/nipype_phase_regression/pipelines/crash-20171005-225337-ostanle2-_moco2-26ac07fa-84d4-4694-8aeb-54d2973a3fad.pklz
Traceback (most recent call last):
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/pipeline/engine/nodes.py", line 407, in run
    self._run_interface()
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/pipeline/engine/nodes.py", line 517, in _run_interface
    self._result = self._run_command(execute)
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/pipeline/engine/nodes.py", line 649, in _run_command
    result = self._interface.run()
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/interfaces/base.py", line 1086, in run
    runtime = self._run_interface(runtime)
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/interfaces/afni/base.py", line 129, in _run_interface
    return super(AFNICommandBase, self)._run_interface(runtime)
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/interfaces/base.py", line 1587, in _run_interface
    self.raise_exception(runtime)
  File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype-1.0.0.dev0+g4d08138-py2.7.egg/nipype/interfaces/base.py", line 1526, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
3dAllineate -source /workspace/ostanle2/SEvsGE2/metaflow/preprocphase/_subject_id_20171004/moco/mapflow/_moco2/20171004GERun3Phase_dtype_detrendphase.nii.gz -1Dmatrix_apply /workspace/ostanle2/SEvsGE2/metaflow/preprocmag/_subject_id_20171004/volreg/mapflow/_volreg2/20171004GERun3Mag_dtype.aff12.1D
Standard output:

Standard error:
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (Sep 13 2012) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as /workspace/ostanle2/SEvsGE2/metaflow/preprocphase/_subject_id_20171004/moco/mapflow/_moco2/20171004GERun3Phase_dtype_detrendphase.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/workspace/ostanle2/SEvsGE2/metaflow/preprocphase/_subject_id_20171004/moco/mapflow/_moco2/20171004GERun3Phase_dtype_detrendphase.nii.gz is 39.500000 degrees from plumb.
++ Source dataset: /workspace/ostanle2/SEvsGE2/metaflow/preprocphase/_subject_id_20171004/moco/mapflow/_moco2/20171004GERun3Phase_dtype_detrendphase.nii.gz
++ Base dataset:   (not given)
** FATAL ERROR: -1D*_apply also needs -prefix :-(
** Program compile date = Sep 13 2012

Return code: 1

[ostanley]

Just an update. After reinstall of version 0.14.0 the issue appears different with no output files although the interface runs correctly with prefix working. This results in the interface which uses these files crashing because the interface did not provide any output.

[effigies]

Oh, I'm sorry. I either didn't see this or forgot to reply. Could you post the new error text? If you resolved the -prefix issue, my suggestions based on this output are going to be out-of-date. If you have the _report/report.rst from your moco working directory, that might be useful, as well.

[ostanley]

The new error only appears for the node subsequent to the moco node and is below. I have also attached a report from the moco node. Thanks for the help!
report.rst.txt

 Node applyalign.a0 failed to run on host hubel2.imaging.robarts.ca.

180123-16:19:53,404 workflow ERROR:
Saving crash info to /cfmm/data/ostanle2/code/nipype_phase_regression/pipelines/crash-20180123-161953-ostanle2-applyalign.a0-217fc979-6d13-41ab-87e5-83694347d616.pklz
Traceback (most recent call last):
File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 238, in _send_procs_to_workers
num_subnodes = self.procs[jobid].num_subnodes()
File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 1271, in num_subnodes
self._check_iterfield()
File "/cfmm/home/ostanle2/.virtualenvs/nipype2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 1296, in _check_iterfield
"in iterfields.") % iterfield)
ValueError: Input in_file was not set but it is listed in iterfields.

[effigies]

It looks like that interface could use some care, but in the short term, if you define out_file in Allineate with some default file name, that should resolve it.

nipype/nipype/interfaces/afni/preprocess.py

Lines 497 to 498 in 045b28e

	if self.inputs.out_file:
	outputs['out_file'] = op.abspath(self.inputs.out_file)

[ostanley]

Thanks! That plus rename is a working work around for now. I was poking around trying to solve this so I could PR it but had no luck. I'll keep an eye on the issues incase it gets solved or I could help in some way.

Thanks again,

Olivia