Matthew F. Glasser
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
Authors
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
Abstract
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.
Citation
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, https://doi.org/10.1016/j.neuroimage.2013.04.127
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 | 1095-9572 |
Publisher | Elsevier |
Peer Reviewed | Peer Reviewed |
Volume | 80 |
DOI | https://doi.org/10.1016/j.neuroimage.2013.04.127 |
Public URL | https://nottingham-repository.worktribe.com/output/718719 |
Publisher URL | https://www.sciencedirect.com/science/article/pii/S1053811913005053?via%3Dihub |
Contract Date | Jul 11, 2018 |
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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by-nc-nd/4.0
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