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The minimal preprocessing pipelines for the Human Connectome Project

Glasser, Matthew F.; Sotiropoulos, Stamatios N.; Wilson, J. Anthony; Coalson, Timothy S.; Fischl, Bruce; Andersson, Jesper L.; Xu, Junqian; Jbabdi, Saad; Webster, Matthew; Polimeni, Jonathan R.; Van Essen, David C.; Jenkinson, Mark

The minimal preprocessing pipelines for the Human Connectome Project Thumbnail


Matthew F. Glasser

Stamatios N. Sotiropoulos

J. Anthony Wilson

Timothy S. Coalson

Bruce Fischl

Jesper L. Andersson

Junqian Xu

Saad Jbabdi

Matthew Webster

Jonathan R. Polimeni

David C. Van Essen

Mark Jenkinson


The Human Connectome Project (HCP) faces the challenging task of bringing multiple magnetic resonance imaging (MRI) modalities together in a common automated preprocessing framework across a large cohort of subjects. The MRI data acquired by the HCP differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. These pipelines are specially designed to capitalize on the high quality data offered by the HCP. The final standard space makes use of a recently introduced CIFTI file format and the associated grayordinate spatial coordinate system. This allows for combined cortical surface and subcortical volume analyses while reducing the storage and processing requirements for high spatial and temporal resolution data. Here, we provide the minimum image acquisition requirements for the HCP minimal preprocessing pipelines and additional advice for investigators interested in replicating the HCP's acquisition protocols or using these pipelines. Finally, we discuss some potential future improvements to the pipelines.


Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B., Andersson, J. L., …Jenkinson, M. (2013). The minimal preprocessing pipelines for the Human Connectome Project. NeuroImage, 80,

Journal Article Type Article
Acceptance Date Apr 30, 2013
Online Publication Date May 11, 2013
Publication Date Oct 15, 2013
Deposit Date Jul 11, 2018
Publicly Available Date Jul 11, 2018
Journal NeuroImage
Print ISSN 1053-8119
Electronic ISSN 1053-8119
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 80
Public URL
Publisher URL


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