title: The connectome mapper: an open-source processing pipeline to map connectomes with MRI.
abstract: Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.
authors.affiliation: Signal Processing Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. alessandro.daducci@epfl.ch
authors.forename: Alessandro
authors.initials: A
authors.lastname: Daducci
authors.forename: Stephan
authors.initials: S
authors.lastname: Gerhard
authors.forename: Alessandra
authors.initials: A
authors.lastname: Griffa
authors.forename: Alia
authors.initials: A
authors.lastname: Lemkaddem
authors.forename: Leila
authors.initials: L
authors.lastname: Cammoun
authors.forename: Xavier
authors.initials: X
authors.lastname: Gigandet
authors.forename: Reto
authors.initials: R
authors.lastname: Meuli
authors.forename: Patric
authors.initials: P
authors.lastname: Hagmann
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Thiran
mesh_terms: D000465:Algorithms; D001921:Brain / Q000502:physiology; D001931:Brain Mapping / Q000379:methods; D003196:Computer Graphics; D003201:Computers; D063132:Connectome; D003627:Data Interpretation, Statistical; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D020407:Internet; D008279:Magnetic Resonance Imaging / Q000379:methods*; D015233:Models, Statistical; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface