[Neuroimaging] Inventory of wrapped commands in nipype?

Ben Cipollini bcipolli at ucsd.edu
Fri Aug 14 17:27:32 CEST 2015

Would the documentation-generating scripts allow snippets of Python code to
list the wrapped functions/binaries for each project (or indicate that all
are wrapped, if automatic)?

I'm guessing nipype uses Sphinx; I don't know the system, but I guess this
wouldn't be too hard. Seems extremely useful to me.

If possible and not too tough, I'd be happy to open a github issue and look
at contributing it.

On Fri, Aug 14, 2015 at 8:17 AM, Satrajit Ghosh <satra at mit.edu> wrote:

> hi john,
> Out of curiosity, is there a document out there that notes which commands
>> for AFNI,FSL,etc have been wrapped into Nipype and which have not?
> there is no explicit function to list this, but the following example
> command will generate the info if you are in the nipype/nipype source
> directory:
> $ grep -r "_cmd = " interfaces/afni/
>> I know that there are quite a few AFNI commands that can't be used with
>> nipype just yet (e.g., 3dToutcount), and it might be useful to know which
>> ones are and aren't available (and also, if they won't be wrapped and why).
> wrapping has always been a function of user need/contribution. for
> example, freesurfer has over 700 binaries - not all are useful or needed.
> so anytime something is missing we ask that people contribute it if they
> need a wrapper for it. we are also moving towards a system where software
> providers themselves expose the binary using a standard architecture (e.g.,
> slicer, brainstools use XML, cbrain has something called boutiques, and
> then there is recent effort towards a common workflow language
> specification), and then these get automatically wrapped for nipype.
> cheers,
> satra
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