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Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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spm.Coregister() deletes output after computation #2049

Closed gladomat closed 7 years ago

gladomat commented 7 years ago

Summary

When I run spm.Coregister() on a T1w image using a Node() I can see the file being computed in the tmp directory but as soon as it finishes the output is erased. This, however, doesn't happen when I do it with my functional data in a MapNode Interface

Actual behavior

File gets deleted after computation.

Expected behavior

File shouldn't be deleted, instead it should be sent to the DataSink.

How to replicate the behavior

Try coregistering a single image with a Node.

Script/Workflow details

coregister_struc = Node(Coregister(), overwrite=True, name="coregister_struc") preproc_frequency_localizer.connect([ (datasource, coregister_struc, [('struc', 'source')]) ])

Platform details:

Python 2.7 nipype 0.12.1

Execution environment

ipython with python 2.7

Choose one

satra commented 7 years ago

@gladomat - you can set coregister_struc.config['execution']['remove_unnecessary_outputs'] = False (see the config for all options)

mgxd commented 7 years ago

@gladomat did that fix your issue?

gladomat commented 7 years ago

It apparently has fixed the issue. Thanks!

gladomat commented 7 years ago

I looked into it in more detail and came to realize that the issue isn't fixed. The output 'coregistered_files' is left empty. Here's what it looks like:

Node: coregister_struc (spm)
============================

 Hierarchy : preprocFrequencyLoc.coregister_struc
 Exec ID : coregister_struc.a0

Original Inputs
---------------

* apply_to_files : <undefined>
* cost_function : <undefined>
* fwhm : <undefined>
* ignore_exception : False
* jobtype : estimate
* matlab_cmd : <undefined>
* mfile : True
* out_prefix : r
* paths : <undefined>
* separation : <undefined>
* source : ['/data/p_nmc002/TDMGB_FMRI/sub-05/ses-localizer/anat/sub-05_acq-T1w.nii']
* target : /data/pt_nmc002/TDMGB_FMRI_Frequency_Localizer/tmp/preprocFrequencyLoc/_subject_id_sub-05/RealignUnwarp/mapflow/_RealignUnwarp0/meanusub-05_task-localizer_run-01_bold.nii
* tolerance : <undefined>
* use_mcr : <undefined>
* use_v8struct : True
* write_interp : <undefined>
* write_mask : <undefined>
* write_wrap : <undefined>

Execution Inputs
----------------

* apply_to_files : <undefined>
* cost_function : <undefined>
* fwhm : <undefined>
* ignore_exception : False
* jobtype : estimate
* matlab_cmd : <undefined>
* mfile : True
* out_prefix : r
* paths : <undefined>
* separation : <undefined>
* source : ['/data/pt_nmc002/TDMGB_FMRI_Frequency_Localizer/tmp/preprocFrequencyLoc/_subject_id_sub-05/coregister_struc/sub-05_acq-T1w.nii']
* target : /data/pt_nmc002/TDMGB_FMRI_Frequency_Localizer/tmp/preprocFrequencyLoc/_subject_id_sub-05/coregister_struc/meanusub-05_task-localizer_run-01_bold.nii
* tolerance : <undefined>
* use_mcr : <undefined>
* use_v8struct : True
* write_interp : <undefined>
* write_mask : <undefined>
* write_wrap : <undefined>

Execution Outputs
-----------------

* coregistered_files : <undefined>
* coregistered_source : /data/pt_nmc002/TDMGB_FMRI_Frequency_Localizer/tmp/preprocFrequencyLoc/_subject_id_sub-05/coregister_struc/sub-05_acq-T1w.nii

Runtime info
------------

* duration : 60.22063
* hostname : marillion.cbs.mpg.de

Terminal output
~~~~~~~~~~~~~~~

Environment
~~~~~~~~~~~

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Edit: Pasted the wrong report.rst file.

gladomat commented 7 years ago

I just realized my mistake. The souce is the file I am looking for and the coregistered_files are the ones that are coregistered when apply_to_files is set. I apologize!

mgxd commented 7 years ago

@gladomat feel free to open this if you still run into issues