[Neuroimaging] Inventory of wrapped commands in nipype?

[Satrajit Ghosh]

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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