The Quantitative Neuroimaging Environment & Toolbox (QuNex) integrates several packages that support a flexible and extensible framework for data organization, preprocessing, quality assurance, and various analyses across neuroimaging modalities. The QuNex suite is flexible and can be updated by adding specific functions and units of code to support new command calls developed around its component tools.

QuNex suite is developed and maintained by the:


QuNex is free and open source, to get access to it visit Official QuNex Registration page.

Forum and issue reporting#

You can find our official QuNex forum at https://forum.qunex.yale.edu/. Feel free to open up a discussion about anything QuNex related there. The forum is also the official QuNex issue reporting platform. If you are struggling with running a command and cannot find the help in the documentation open a post on the forum. To maintain an effective issue resolving workflow and make sure your problems will be solved in a timely manner we prepared simple guide.

QuNex quick start#

Quick start on deploying the QuNex suite starting from raw data to launching HCP pipelines.

General overview#

QuNex overview describes general functionality and specifications.

User guides#

User guides provides in-depth description of QuNex usage, detailing specific functions, workflows and use cases.

Executing QuNex commands#

Onboarding data into QuNex#

Preparing mapping and batch files#

Running HCP pipelines and performing QC#

BOLD preprocessing & analyses#

DWI preprocessing & analyses#

Data visualization & output mapping#

Non human primate (NHP) pipelines#

QuNex deployment in XNAT#

Overview of interacting with the XNAT environment and executing QuNex container using the XNAT container service.

QuNex development#

To support development of QuNex, we have prepared QuNex SDK, a separate set of tools provided as a Git repository created to support the development and acceptance testing procedures for core QuNex developers as well as others who wish to contribute to the QuNex codebase.

For documentation related to development, please use the QuNex SDK Wiki.