[Neuroimaging] Inventory of wrapped commands in nipype?

Satrajit Ghosh satra at mit.edu
Fri Aug 14 17:17:43 CEST 2015

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

$ 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.


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