[Neuroimaging] Inventory of wrapped commands in nipype?

[Ben Cipollini]

https://github.com/nipy/nipype/issues/1186

Feel free to add comments or contribute!

On Fri, Aug 14, 2015 at 8:54 AM, vanessa sochat <vsochat at stanford.edu>
wrote:

> 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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>
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