All ENIGMA protocols are now linked on the ENIGMA GitHub page page. Please check here for the latest amendments and updates!

Anyone is welcome to use these protocols for their projects! If you use the protocols on this site for projects outside of ENIGMA, please include a reference to the ENIGMA main page ( so that your readers and reviewers know about it, as well.


HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data, including preprocessing, single-subject, and group analysis. It provides state-of-the-art preprocessing using fmriprep, but removes the necessity to convert data to the BIDS format. Common resting-state and task-based fMRI features can then be calculated on the fly using FSL and nipype for statistics.

HALFpipe is distributed as a container, meaning that all required software comes bundled in a monolithic file, the container. This allows for easy installation on new systems, and makes data analysis more reproducible, because software versions are guaranteed to be the same for all users.
For full documentation and to download the container, visit the HALFpipe GitHub page:

For questions or support, please submit an issue or contact the development team via e-mail:

Developement Team
Lea Waller, Developer
Ilya Veer, Project manager
Susanne Erk, Project manager
If you use HALFpipe in your project, please also reference the following preprint:


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