psutils stopps pipeline

[cni-md]

Hi,
I had the problem, that heudiconv -c dcm2niix was working on my office PC but not on the server. On the server the process dcm2niix was in sleepmode (status S+) and nothing happend.

Changing
convertnode.inputs.terminal_output = 'allatonce' to 'stream' solved this problem.

In addition interfaces.freesurfer.reconall stopped working too with psutils installed. No error message only a frozen output during the smoothing after approx 1h.

newest nipype, psutils 4.3.0

Joerg

[satra]

@cni-md - thanks for the feedback. we will have to look into this.

could you please let us know what OS just so we have a record of this.

[cni-md]

Debian 6.0 64bit AMD Thanks

[satra]

@cni-md - if you uninstall psutils, does it work fine?

[cni-md]

Yes. python-psutils to be more clear. That's what I did.

Am 14. Juli 2016 01:53:37 MESZ, schrieb Satrajit Ghosh notifications@github.com:

@cni-md - if you uninstall psutils, does it work fine?

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#1532 (comment)

[carolFrohlich]

Please tell us what pipeline are you using, then we can debug the problem. Is it a nipype freesurfer pipeline or you own pipeline?

[cni-md]

Back from vacation. I use the nipype interfaces.freesurfer.reconall interface in my pipeline.

recon_all = pe.Node(interface=fs.ReconAll(), name='recon_all')
recon_all.inputs.subjects_dir = os.environ['SUBJECTS_DIR']
recon_all.inputs.use_T2 = True
recon_all.inputs.flags = '-3T -cm -parallel'

It is running fine without the python-psutils installed. With psutils it hangs like heudiconv.

[satra]

@ccraddock and @carolFrohlich - it would be good to get this resolved.

[carolFrohlich]

Thanks! We'll run the pipeline and debug the problem.