About

HALFpipe is an open-source software developed by the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) consortium.

For more information about the project, please see the ENGIMA functional image processing protocol webpage

Contributors

Core developer

Lea Waller

HALFpipe developer team

Manual documentation

We aknowledge that the manuals were adapted from the MDD ENIGMA resting-state fMRI manual and the OCD ENIGMA task-based fMRI manual.

Website developer team

PI and project supervision

Clara Moreau
Ilya Veer
Lune Bellec
Hao Ting Wang
Paul M Thompson

Contact

Please address questions and comments to [email protected]. You can also join the HALFpipe Mattermost (similar to Slack) using this link.

How to cite

HALFpipe

Waller, L., Erk, S., Pozzi, E., Toenders, Y. J., Haswell, C. C., Büttner, M., Thompson, P. M., Schmaal, L., Morey, R. A., Walter, H., & Veer, I. M. (2022). ENIGMA HALFpipe: Interactive, reproducible, and efficient analysis for resting-state and task-based fMRI data. Human brain mapping, 43(9), 2727–2742. https://doi.org/10.1002/hbm.25829

Software

HALFpipe relies on tools from well-established neuroimaging software packages, we strongly urge users to acknowledge these tools when publishing results obtained with HALFpipe:

Seed Atlas

Pozzi, E., & Toenders, Y. (2024, November 8). ENIGMA HALFpipe ROIs for seed-based connectivity. Retrieved from osf.io/u786p

Atlases

Buckner, R. L., Krienen, F. M., Castellanos, A., Diaz, J. C., & Yeo, B. T. (2011). The organization of the human cerebellum estimated by intrinsic functional connectivity. Journal of neurophysiology, 106(5), 2322–2345. https://doi.org/10.1152/jn.00339.2011

Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., van der Kouwe, A., Killiany, R., Kennedy, D., Klaveness, S., Montillo, A., Makris, N., Rosen, B., & Dale, A. M. (2002). Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341–355. https://doi.org/10.1016/s0896-6273(02)00569-x

Schaefer, A., Kong, R., Gordon, E. M., Laumann, T. O., Zuo, X. N., Holmes, A. J., Eickhoff, S. B., & Yeo, B. T. T. (2018). Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI. Cerebral cortex (New York, N.Y. : 1991), 28(9), 3095–3114. https://doi.org/10.1093/cercor/bhx179