Tractography analysis with the scilpy toolbox

Aperture Neuro 2026 Book chapter Open access

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Authors: Emmanuelle Renauld, Arnaud Boré, Charles Poirier, Alex Valcourt-Caron, Philippe Karan, Antoine Théberge, Guillaume Theaud, Manon Edde, Philippe Poulin, Gabriel Girard, Jean-Christophe Houde, Anthony Gagnon
+13 more 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, Maxime Descôteaux
DOI: 10.52294/001c.154022
Cited by: 10
References: 43

Abstract

We present scilpy, an open-source Python library for diffusion magnetic resonance imaging (dMRI) and tractography. It provides a large collection of well-documented, user-friendly scripts that support nearly every stage of the dMRI processing pipeline, from preprocessing (such as denoising, registration, and local fiber reconstruction) to tractography and post-processing of tractograms, including connectivity and bundle analyses. Scilpy leverages the strength of DIPY, is well-tested through modern continuous integration practices, and is actively maintained.

Fields of Study & Subjects

Advanced Neuroimaging Techniques and Applications Functional Brain Connectivity Studies Fetal and Pediatric Neurological Disorders

Publication details

Journal / source
Aperture Neuro
Publisher
Organization for Human Brain Mapping
Volume
6
Publication date
8 January 2026
Language
EN
Document type
Book chapter