SPM standalone (mcr) version as a default

[René Küttner]

Hi,

first of all, thanks for the your great work on Nipype!

We have a lot of pipelines and parallel processes but a limited set of Matlab licenses. That is why we want to use the standalone version of SPM (MCR) everwhere. This requires setting matlab_cmd and the use_mcr flag as suggested in doc/users/spmmcr.rst for every single pipeline. In order to handle this easier, we have modified our local copy of nipype to allow for two additional environment variables:

  SPMMCRCMD=<spm standalon command>
  FORCE_SPMMCR (boolean, sets the use_mcr flag)

This works quite well but comes with a drawback: It makes us dependant on the modified nipype code.

Is there an elegant way of having all pipelines using SPM MCR without setting the Matlab path and the use_mcr flag for every pipeline again?

Thanks!

  -- René

[Satrajit Ghosh]

hi rene,

thanks for the encouragement. as you may have seen we just released 0.9.

one way to control this would be via modifying the nipype config system. could you send us a pointer to your modified code so we can see what changes you've made.

cheers,

satra

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[René]

Hi satra,

Thanks for your quick reply.

On Friday, 20 December 2013 23:10:56 UTC+1, satra wrote:

one way to control this would be via modifying the nipype config system. could you send us a pointer to your modified code so we can see what changes you've made.

Modifying Nipype's config system for spm/mcr configuration sounds interesting. I will have a look at it.

Regarding a pointer to my modifications: You are welcome to have a look at my (very small) changes at [1].

  [1]: https://github.com/rku/nipype/commit/99c07f5

  -- René

[Satrajit Ghosh]

hi rene,

can you send a pull request? also could you add to the spm mcr docs that this is how one can control the behavior globally? 

we will merge this in for now - it looks reasonable for this use case.

cheers,

satra

--

[René]

Hi satra,

I created the pull request at: https://github.com/nipy/nipype/pull/759

cheers,

    René