<div dir="ltr"><a href="https://github.com/nipy/nipype/issues/1186">https://github.com/nipy/nipype/issues/1186</a><br><div><br></div><div>Feel free to add comments or contribute!</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 14, 2015 at 8:54 AM, vanessa sochat <span dir="ltr"><<a href="mailto:vsochat@stanford.edu" target="_blank">vsochat@stanford.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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 <a href="https://github.com/vsoch/font-brain/blob/master/script/fsl.json" target="_blank">data structure for FSL</a>, and am <a href="https://github.com/vsoch/font-brain/blob/master/script/spm_commands.txt" target="_blank">just starting one for SPM</a> (right now it's just a list). Nipype / nilearn etc are much more dynamic, so it would good to generate something like this programatically.</div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">On Fri, Aug 14, 2015 at 8:36 AM, Satrajit Ghosh <span dir="ltr"><<a href="mailto:satra@mit.edu" target="_blank">satra@mit.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>hi ben,</div><div><br></div><div>an issue + contribution would be much welcome!</div><div><br></div>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). <div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">cheers,<br><br>satra<br><br></div></div></div></div></div></div></div><div><div><div class="gmail_quote">On Fri, Aug 14, 2015 at 11:27 AM, Ben Cipollini <span dir="ltr"><<a href="mailto:bcipolli@ucsd.edu" target="_blank">bcipolli@ucsd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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)?<div><br></div><div>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.</div><div><br></div><div>If possible and not too tough, I'd be happy to open a github issue and look at contributing it.</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Fri, Aug 14, 2015 at 8:17 AM, Satrajit Ghosh <span dir="ltr"><<a href="mailto:satra@mit.edu" target="_blank">satra@mit.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">hi john,<div><br></div><div><div class="gmail_extra"><div class="gmail_quote"><span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>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? </div></div></blockquote><div><br></div></span><div>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:</div><div>
<p>
</p><p><span>$ grep -r "_cmd = " interfaces/afni/</span></p></div><span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>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).<br></div></div></blockquote><div><br></div></span><div>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.</div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div dir="ltr"><div dir="ltr">cheers,<br><br></div></div></div></div></div></div><div>satra</div><div><br></div></div></div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><div>Vanessa Villamia Sochat<br>Stanford University<br><div><div><div><a href="tel:%28603%29%20321-0676" value="+16033210676" target="_blank">(603) 321-0676</a></div></div></div></div>
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