Tractography analysis with the scilpy toolbox

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, Maxime Descoteaux

Aperture Neuro

https://doi.org/10.52294/001c.154022

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.