fmri_spm.py - No crash file, workflow just seems to stall

[jnecus]

Summary

I am attempting to use the example tutorial workflow :fmri_spm.py

Everything seems to run OK until it reaches rapidart (ra.ArtifactDetect()).

At this point the following warning is provided in the IPython terminal. No crash file is given and all processes just seem to kind of stop. A blank matplotlib figure also pops up.

As an additional note: ArtifactDetect will run to completion (as no crash file is generated);however, in order to allow the workflow to progress I must keep on manually exiting (Ctrl+C) and restarting the workflow until every subject has surpassed this step.

Warning

because the backend has already been chosen;
matplotlib.use() must be called before pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

Platform details:

{'nibabel_version': '2.1.0', 'networkx_version': '1.11', 'numpy_version': '1.11.3', 'sys_platform': 'linux2', 'sys_version': '2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'commit_source': u'archive substitution', 'commit_hash': '%h', 'pkg_path': '/home/joe/anaconda2/lib/python2.7/site-packages/nipype', 'sys_executable': '/home/joe/anaconda2/bin/python', 'traits_version': '4.6.0', 'scipy_version': '0.18.1'}
0.13.0-dev

[djarecka]

can you please point me to the specific tutorial you're using? are you just running fmri_spm.py?

Do you know what is a version of your matplotlib?

[jnecus]

Link to tutorial: http://nipype.readthedocs.io/en/latest/users/examples/fmri_spm.html

Matplotlib version: 1.5.1

Only thing that I have changed from this tutorial (other than imputs and contrasts) is:

Set default path to be SPM8 (didnt seem to work with SPM12): mlab.MatlabCommand.set_default_paths('/software/matlab/spm8')

[djarecka]

I'm having problem with replicating your issue, but matplotlib windows should not pop up. It looks to me that it might be a combination that you have interactive matplotlib settings and that in nipype we're not changing them everywhere. I'll try to suggest a small changes to the nipype code, but you can also try:

• check your settings:

    import matplotlib
    matplotlib.is_interactive() #should be False
    matplotlib.get_backend() #  if it's not Agg and it's not change properly in nipype, that can cause problems 

• run this with Python (instead of IPython)
• there is also a new version 2.0 of matplotlib, updating might help

[oesteban]

@jnecus could you provide more specific details on you settings?. Particularly:

• 1. Running on container or "bare-metal". If container, are them "official" nipype containers?
• 2. Plugin used and settings for the plugin.

[satra]

@jnecus - if the current master resolves this issue, could you please close it?

[jnecus]

Sorry for the delay, I'm setting up a new PC. Planning to retry once set up and will check whether errors still occur. I'll close the issue for now and repost after retesting.