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 (https://enigma.ini.usc.edu/) so that your readers and reviewers know about it, as well.
ENIGMA HALFpipe
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 at https://github.com/HALFpipe, and the ENIGMA-rsfMRI Working Group webpage.
- Download HALFpipe
- Step-by-step Quality Control manual
- Full Manual (updated Apr. 2025)
- Command-Line Quick Guide (updated Apr. 2025)
For questions or support, please submit an issue or contact the development team via e-mail at halfpipe@fmri.science and clara.moreau@umontreal.ca.
Development & Support Team
Lea Waller, Developer & ENIGMA rs-fMRI co-chair
Ilya Veer, Project manager & ENIGMA rs-fMRI co-chair
Susanne Erk, Project manager
Clara Moreau, ENIGMA rs-fMRI co-chair
Frank Hillary, ENIGMA rs-fMRI co-chair
If you use HALFpipe in your project, please reference the following manuscript:
