[nipype] Use SPM standalone (MCR)

[Daniel Geisler]

Hi guys,

first of all, thanks for your amazing project. I currently installed Nipype 0.7 on a cluster with LSF job management. Since only a few Matlab licenses are available (for running in parallel), it would be very helpful to use the SPM standalone version (MCR) in Nipype. I noticed that Nipype supports MCR somehow. But I didnt manage to get it work. Could you please give me a hint? I did the following steps:

I installed SPM standalone according to the instructions on the SPM website. And SPM standalone runs smoothly by entering:

./run_spm8.sh /home/dgeisler/env/opt/MATLAB/MATLAB_Compiler_Runtime/v713/ fmri

Afterwards I run the following python code:

import nipype.interfaces.spm as spm

r = spm.Realign()

r.inputs.in_files = "foo.nii"

r.inputs.use_mcr = True # enable SPM standalone?

r.run()

But it fails with:

IOError: Input "uses_mcr" is mutually exclusive with input "nodesktop", which is already set

I guess that additional setting are required to make it work. Could you please give me a hint?

Thanks for your help,

Daniel

[Satrajit Ghosh]

hi daniel,

i haven't looked into that in a long while. here is an attempt to fix it:

you can download at try this branch:

https://github.com/satra/nipype/tree/fix/mcr

the pull request is open here:

https://github.com/nipy/nipype/pull/516

please keep us posted on how it works - and if you could help us make sure that option works well that would be great.

cheers,

satra

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[Daniel Geisler]

Hi Satra!

Thanks so much for your attempt to fix the MCR thing. I added some more lines of code to get it work. I am sure that there is a much more elegant way to do it. (in particular in the Info class of interfaces/spm/base.py I hardcoded SPM-version and path temporary due to no time - sorry). But anyway, Nipype is now able to run SPM-nodes without Matlab.

I would be happy to share my code changes for further improvements. I am still a bit unfamiliar with git: what would be the best way to send my changes? (Patch file or pull request on your fix/mcr branch?)

best,
Daniel

[Satrajit Ghosh]

hi daniel,

Thanks so much for your attempt to fix the MCR thing. I added some more lines of code to get it work. I am sure that there is a much more elegant way to do it. (in particular in the Info class of interfaces/spm/base.py I hardcoded SPM-version and path temporary due to no time - sorry). But anyway, Nipype is now able to run SPM-nodes without Matlab.

wonderful. if you can figure out how we might get the version from the mcr script that will be great.

 

I would be happy to share my code changes for further improvements. I am still a bit unfamiliar with git: what would be the best way to send my changes? (Patch file or pull request on your fix/mcr branch?)

the best is to do a pull-request - then we can review it.

gitref.org is a good source for git.

cheers,

satra