[Neuroimaging] Inventory of wrapped commands in nipype?

Satrajit Ghosh satra at mit.edu
Fri Aug 14 17:36:07 CEST 2015

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.,



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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