title: Dipy, a library for the analysis of diffusion MRI data.
abstract: Diffusion Imaging in Python (Dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. dMRI is an application of MRI that can be used to measure structural features of brain white matter. Many methods have been developed to use dMRI data to model the local configuration of white matter nerve fiber bundles and infer the trajectory of bundles connecting different parts of the brain. Dipy gathers implementations of many different methods in dMRI, including: diffusion signal pre-processing; reconstruction of diffusion distributions in individual voxels; fiber tractography and fiber track post-processing, analysis and visualization. Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface. We have implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography. In addition, cutting edge novel reconstruction techniques are implemented, such as constrained spherical deconvolution and diffusion spectrum imaging (DSI) with deconvolution, as well as methods for probabilistic tracking and original methods for tractography clustering. Many additional utility functions are provided to calculate various statistics, informative visualizations, as well as file-handling routines to assist in the development and use of novel techniques. In contrast to many other scientific software projects, Dipy is not being developed by a single research group. Rather, it is an open project that encourages contributions from any scientist/developer through GitHub and open discussions on the project mailing list. Consequently, Dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing.
authors.affiliation: Computer Science Department, University of Sherbrooke Sherbrooke, QC, Canada ; MRC Cognition and Brain Sciences Unit, University of Cambridge Cambridge, UK.
authors.forename: Eleftherios
authors.initials: E
authors.lastname: Garyfallidis
authors.affiliation: Henry H. Wheeler, Jr. Brain Imaging Center, University of California Berkeley, CA, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Brett
authors.affiliation: Department of Neurology and Graduate Group in Bioengineering, University of California San Francisco, CA, USA.
authors.forename: Bagrat
authors.initials: B
authors.lastname: Amirbekian
authors.affiliation: Department of Psychology, Stanford University Stanford, CA, USA.
authors.forename: Ariel
authors.initials: A
authors.lastname: Rokem
authors.affiliation: Department of Mathematical Sciences, Division of Applied Mathematics, Stellenbosch University Stellenbosch, South Africa.
authors.forename: Stefan
authors.initials: S
authors.lastname: van der Walt
authors.affiliation: MRC Cognition and Brain Sciences Unit, University of Cambridge Cambridge, UK.
authors.forename: Maxime
authors.initials: M
authors.lastname: Descoteaux
authors.affiliation: MRC Cognition and Brain Sciences Unit, University of Cambridge Cambridge, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Nimmo-Smith
keywords: DSI; DTI; HARDI; Python; dMRI; diffusion MRI; free open source software; tractography