[Neuroimaging] Inventory of wrapped commands in nipype?

[vanessa sochat]

Keep me in the loop on this! I'm interested in the functions that different
programs have - in case it's useful I created a data structure for FSL
<https://github.com/vsoch/font-brain/blob/master/script/fsl.json>, and am just
starting one for SPM
<https://github.com/vsoch/font-brain/blob/master/script/spm_commands.txt>
(right
now it's just a list). Nipype / nilearn etc are much more dynamic, so it
would good to generate something like this programatically.

On Fri, Aug 14, 2015 at 8:36 AM, Satrajit Ghosh <satra at mit.edu> wrote:

> hi ben,
>
> an issue  + contribution would be much welcome!
>
> it wouldn't be too hard to do this, as we already have scripts that
> traverse all interfaces. in fact it would be nice to even create a reverse
> mapping from underlying command to nipype interface(s) name (in some cases
> there is a many nipype interfaces to single command mapping - e.g.,
> fslmaths).
>
> cheers,
>
> satra
>
> On Fri, Aug 14, 2015 at 11:27 AM, Ben Cipollini <bcipolli at ucsd.edu> wrote:
>
>> 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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>>>
>>
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>
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-- 
Vanessa Villamia Sochat
Stanford University
(603) 321-0676
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