The genesis of QuNex
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The genesis of QuNex

QuNex, Qualitative Neuroimaging Environment and Toolbox, started as a set of Matlab scripts that I started developing to enable efficient, robust, and reproducible preprocessing and analysis of fMRI data for task-related and resting state functional connectivity studies while working as a post-doc in Deanna Barch and Todd Braver's Cognitive Control and Psychopathology Laboratory at Washington University in Saint Louis. Besides a number of other studies the tools were soon put to good use for analyses supporting the work of Alan Anticevic, a PhD student of Deanna Barch at the time. To make my Matlab tools easier to use interoperably with other software and run in a server and then cluster environment, I built a python processing engine, niutlities, accessible through gmri command that ran the Matlab scripts and provided additional functionality.

After returning to Ljubljana from my post-doc, the tools became both integral to analytical work in the lab as well as a focus of work on its own. At the same time research collaboration with Alan took off and a number of functionalities were added to specifically support collaborative research needs. The investment into the toolset further increased when Alan set up his own lab at Yale and started contributing code in form of additional bash wrappers and scripts to the toolbox. With increasing functionality and milage of use, realising the value of the toolbox, additional lab members and collaborators both at Ljubljana and Yale started contributing to the code and a decision was made to polish the toolbox and make it available to the neuroimaging community.

The toolbox is now available as open source software in both source and container form at

I'd like to thank all the collaborators and users that have provided feedback, feature request, opinions, advice and contributed code to QuNex as well as all contributors to this blog.

Grega Repovš