Bibliography#

[1]

Brian B Avants, Nicholas J Tustison, Michael Stauffer, Gang Song, Baohua Wu, and James C Gee. The insight ToolKit image registration framework. Front. Neuroinform., 8:44, April 2014. doi:https://doi.org/10.3389/fninf.2014.00044.

[2]

Dogu Baran Aydogan and Yonggang Shi. Parallel transport tractography. IEEE Trans. Med. Imaging, 40(2):635–647, February 2021. doi:https://doi.org/10.1109/tmi.2020.3034038.

[3]

Matthew Cieslak, Philip A Cook, Xiaosong He, Fang-Cheng Yeh, Thijs Dhollander, Azeez Adebimpe, Geoffrey K Aguirre, Danielle S Bassett, Richard F Betzel, Josiane Bourque, Laura M Cabral, Christos Davatzikos, John A Detre, Eric Earl, Mark A Elliott, Shreyas Fadnavis, Damien A Fair, Will Foran, Panagiotis Fotiadis, Eleftherios Garyfallidis, Barry Giesbrecht, Ruben C Gur, Raquel E Gur, Max B Kelz, Anisha Keshavan, Bart S Larsen, Beatriz Luna, Allyson P Mackey, Michael P Milham, Desmond J Oathes, Anders Perrone, Adam R Pines, David R Roalf, Adam Richie-Halford, Ariel Rokem, Valerie J Sydnor, Tinashe M Tapera, Ursula A Tooley, Jean M Vettel, Jason D Yeatman, Scott T Grafton, and Theodore D Satterthwaite. QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data. Nat. Methods, pages 1–4, June 2021. doi:https://doi.org/10.1038/s41592-021-01185-5.

[4]

Alessandro Daducci, Alessandro Dal Palù, Alia Lemkaddem, and Jean-Philippe Thiran. COMMIT: convex optimization modeling for microstructure informed tractography. IEEE Trans. Med. Imaging, 34(1):246–257, January 2015. doi:10.1109/TMI.2014.2352414.

[5]

Maxime Descoteaux, Kurt G Schilling, Dogu Baran Aydogan, Christian Beaulieu, Elena Borra, Maxime Chamberland, Alessandro Daducci, Alberto De Luca, Flavio Dell'Acqua, Jessica Dubois, Tim B Dyrby, Shawna Farquharson, Stephanie Forkel, Martijn Froeling, Alessandra Griffa, Mareike Grotheer, Pamela Guevara, Suzanne N Haber, Vinod Kumar Jangir, Alexander Leemans, Joël Lefebvre, Ching-Po Lin, Graham Little, Chun-Yi Zac Lo, Chiara Maffei, Helen S Mayberg, Jennifer A McNab, Pratik Mukherjee, Lauren J O'Donnell, Martin Parent, Carlo Pierpaoli, Francois Rheault, Kathleen S Rockland, Alard Roebroeck, Ariel Rokem, R Jarrett Rushmore, Silvio Sarubbo, Simona Schiavi, Stamatios N Sotiropoulos, Diego Szczupak, Michel Thiebaut de Schotten, J-Donald Tournier, Francesco Vergani, Joseph Yuan-Mou Yang, Fan Zhang, Derek Jones, and Laurent Petit. Millennium pathways for tractography: 40 grand challenges to shape the future of tractography. ArXiv, September 2025.

[6]

Eleftherios Garyfallidis, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stefan van der Walt, Maxime Descoteaux, Ian Nimmo-Smith, and Dipy Contributors. Dipy, a library for the analysis of diffusion MRI data. Front. Neuroinform., 8:8, February 2014. doi:https://doi.org/10.3389/fninf.2014.00008.

[7]

Krzysztof J Gorgolewski, Tibor Auer, Vince D Calhoun, R Cameron Craddock, Samir Das, Eugene P Duff, Guillaume Flandin, Satrajit S Ghosh, Tristan Glatard, Yaroslav O Halchenko, Daniel A Handwerker, Michael Hanke, David Keator, Xiangrui Li, Zachary Michael, Camille Maumet, B Nolan Nichols, Thomas E Nichols, John Pellman, Jean-Baptiste Poline, Ariel Rokem, Gunnar Schaefer, Vanessa Sochat, William Triplett, Jessica A Turner, Gaël Varoquaux, and Russell A Poldrack. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific data, 3(1):1–9, June 2016.

[8]

Soichi Hayashi, Bradley A Caron, Anibal Sólon Heinsfeld, Sophia Vinci-Booher, Brent McPherson, Daniel N Bullock, Giulia Bertò, Guiomar Niso, Sandra Hanekamp, Daniel Levitas, Kimberly Ray, Anne MacKenzie, Paolo Avesani, Lindsey Kitchell, Josiah K Leong, Filipi Nascimento-Silva, Serge Koudoro, Hanna Willis, Jasleen K Jolly, Derek Pisner, Taylor R Zuidema, Jan W Kurzawski, Kyriaki Mikellidou, Aurore Bussalb, Maximilien Chaumon, Nathalie George, Christopher Rorden, Conner Victory, Dheeraj Bhatia, Dogu Baran Aydogan, Fang-Cheng F Yeh, Franco Delogu, Javier Guaje, Jelle Veraart, Jeremy Fischer, Joshua Faskowitz, Ricardo Fabrega, David Hunt, Shawn McKee, Shawn T Brown, Stephanie Heyman, Vittorio Iacovella, Amanda F Mejia, Daniele Marinazzo, R Cameron Craddock, Emanuale Olivetti, Jamie L Hanson, Eleftherios Garyfallidis, Dan Stanzione, James Carson, Robert Henschel, David Y Hancock, Craig A Stewart, David Schnyer, Damian O Eke, Russell A Poldrack, Steffen Bollmann, Ashley Stewart, Holly Bridge, Ilaria Sani, Winrich A Freiwald, Aina Puce, Nicholas L Port, and Franco Pestilli. Brainlife.io: a decentralized and open-source cloud platform to support neuroscience research. Nat. Methods, 21(5):809–813, May 2024. doi:https://doi.org/10.1038/s41592-024-02237-2.

[9]

John Kruper, Mckenzie P Hagen, François Rheault, Isaac Crane, Asa Gilmore, Manjari Narayan, Keshav Motwani, Eardi Lila, Chris Rorden, Jason D Yeatman, and Ariel Rokem. Tractometry of the human connectome project: resources and insights. Front. Neurosci., 18:1389680, June 2024.

[10]

Jon Haitz Legarreta, Simona Schiavi, Wei Tang, Garrett Banks, Matthew Cieslak, Kurt Schilling, Alberto De Luca, Jacques-Donald Tournier, John Kruper, Francois Rheault, Stamatios N Sotiropoulos, Franco Pestilli, Jelle Veraart, Joseph Yuan-Mou Yang, Maxime Descoteaux, Sarah Heilbronner, and Ariel Rokem. What needs to be standardized for reliable, reproducible, and robust tractography? Gigascience, 15(giag034):giag034, January 2026.

[11]

Jeremi Levesque, Antoine Théberge, Maxime Descoteaux, and Pierre-Marc Jodoin. Exploring the robustness of TractOracle methods in RL-based tractography. Medical Image Analysis, 106:103743, 2025. doi:10.1016/j.media.2025.103743.

[12]

Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Sonia Pujol, Alex Yarmarkovich, Alexandra J Golby, Gordon Kindlmann, Demian Wassermann, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Ron Kikinis, Hans J Johnson, Carl-Fredrik Westin, and Lauren J O'Donnell. SlicerDMRI: open source diffusion MRI software for brain cancer research. Cancer Res., 77(21):e101–e103, November 2017. doi:https://doi.org/10.1158/0008-5472.CAN-17-0332.

[13]

Emmanuelle Renauld, Arnaud Boré, Charles Poirier, Alex Valcourt-Caron, Philippe Karan, Antoine Théberge, Guillaume Théaud, Manon Edde, Philippe Poulin, Gabriel Girard, Jean-Christophe Houde, Anthony Gagnon, Etienne St-Onge, Graham Little, Jon Haitz Legarreta, Stanislas Thoumyre, Gabrielle Grenier, Zineb El Yamani, Mario Ocampo Pineda, Matteo Battocchio, Vincent Beaudoin, Alexandre Joanisse, Laurent Petit, François Rheault, and Maxime Descoteaux. Tractography analysis with the scilpy toolbox. Aperture Neuro, 2026. doi:10.52294/001c.154022.

[14]

Francois Rheault, Jean-Christophe Houde, and Maxime Descoteaux. Visualization, interaction and tractometry: dealing with millions of streamlines from diffusion MRI tractography. Front. Neuroinform., 11:42, June 2017.

[15]

Christopher Rorden. Surfice: visualizing neuroimaging meshes, tractography streamlines and connectomes. Nat. Methods, 22(8):1615–1616, August 2025. doi:https://doi.org/10.1038/s41592-025-02764-6.

[16]

Etienne St-Onge, Kurt G Schilling, and Francois Rheault. BundleSeg: a versatile, reliable and reproducible approach to white matter bundle segmentation. arXiv preprint arXiv:2308.10958, 2023. doi:10.48550/arXiv.2308.10958.

[17]

J-Donald Tournier, Robert Smith, David Raffelt, Rami Tabbara, Thijs Dhollander, Maximilian Pietsch, Daan Christiaens, Ben Jeurissen, Chun-Hung Yeh, and Alan Connelly. MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation. Neuroimage, 202:116137, November 2019. doi:https://doi.org/10.1016/j.neuroimage.2019.116137.