[Neuroimaging] Looking for advice regarding releasing some analysis software

Frederick, Blaise B. bbfrederick at mclean.harvard.edu
Thu Jun 16 09:44:04 EDT 2016

Hi all,

For the last few years my lab has been doing time delay analysis on fMRI and concurrent fMRI/NIRS data, and I’ve written a number of python tools for performing the analysis, and they’ve been refined for several years at this point, and I think they could be generally useful to people, so I’m looking to release the software.  I’m fairly new at this, and I’ve found a bunch of recommendations on how to do this, some of which are contradictory.  I’d appreciate any help I could get on this.

What I’ve done so far:
1) Chosen a license (Apache 2, based on a lot of reading and some conversations)
2) Put the core programs up on github (https://github.com/bbfrederick/delaytools)
3) Tried to put together rudimentary documentation and installation directions.

As things exist now, if you install the prerequisites, download the code, and add the main directory to your path, you should be able to run the tools, which is a fine start, but there seems to be a lot more to installation than that (automatically installing dependancies and all that) that I’m unable to figure out. I’d appreciate any feedback on this.  I’m a little mystified by the vagaries of constructing a setup.py file, and what constitutes a ‘package’ and a ‘module’.

Some of the questions I have:
1) In addition to the main program, I have scads of command line utilities that make preparing and interpreting the data easier - do I just put them all in the top level directory, or in a bin directory?
2) The dependancies for the majority of the tools are very simple (numpy, scipy, scikits-learn, matplotlib, nibabel), but there’s a kind of useful gui tool that requires pyqt4 and pyqtgraph - pyqt does not seem to be installable with pip, so I’m not sure how to handle that (installing it all with anaconda is easy though). How should I handle this?
3) What’s the best way to publicize this?  This won’t be useful if nobody can find it.


Blaise Frederick
Associate Professor of Psychiatry/Biophysicist
Harvard Medical School/McLean Hospital
bbfrederick at mclean.harvard.edu<mailto:bbfrederick at mclean.harvard.edu>

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