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Phybers: a package for brain tractography analysis
Indexado
WoS WOS:001190027400001
DOI 10.3389/FNINS.2024.1333243
Año 2024
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



We present a Python library (Phybers) for analyzing brain tractography data. Tractography datasets contain streamlines (also called fibers) composed of 3D points representing the main white matter pathways. Several algorithms have been proposed to analyze this data, including clustering, segmentation, and visualization methods. The manipulation of tractography data is not straightforward due to the geometrical complexity of the streamlines, the file format, and the size of the datasets, which may contain millions of fibers. Hence, we collected and structured state-of-the-art methods for the analysis of tractography and packed them into a Python library, to integrate and share tools for tractography analysis. Due to the high computational requirements, the most demanding modules were implemented in C/C++. Available functions include brain Bundle Segmentation (FiberSeg), Hierarchical Fiber Clustering (HClust), Fast Fiber Clustering (FFClust), normalization to a reference coordinate system, fiber sampling, calculation of intersection between sets of brain fibers, tools for cluster filtering, calculation of measures from clusters, and fiber visualization. The library tools were structured into four principal modules: Segmentation, Clustering, Utils, and Visualization (Fibervis). Phybers is freely available on a GitHub repository under the GNU public license for non-commercial use and open-source development, which provides sample data and extensive documentation. In addition, the library can be easily installed on both Windows and Ubuntu operating systems through the pip library.

Revista



Revista ISSN
Frontiers In Neuroscience 1662-453X

Métricas Externas



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Disciplinas de Investigación



WOS
Neurosciences
Scopus
Sin Disciplinas
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Rodriguez, Lazara Liset Gonzalez Mujer Universidad de Concepción - Chile
2 Osorio, Ignacio Hombre Universidad de Concepción - Chile
3 Cofre, G. Alejandro - Universidad de Concepción - Chile
4 Larzabal, Hernan Hernandez - Universidad de Concepción - Chile
Universidad Adolfo Ibáñez - Chile
5 ROMAN-GODOY, CLAUDIO ESTEBAN Hombre Universidad de Valparaíso - Chile
6 Poupon, C. Hombre Univ Paris Saclay - Francia
7 Mangin, Jean-Francois Hombre Univ Paris Saclay - Francia
8 HERNANDEZ-RIVAS, CECILIA PAOLA Mujer Universidad de Concepción - Chile
Ctr Biotechnol & Bioengn CeBiB - Chile
9 GUEVARA-ALVEZ, PAMELA BEATRIZ Mujer Universidad de Concepción - Chile

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Financiamiento



Fuente
McDonnell Center for Systems Neuroscience at Washington University
NIH Blueprint for Neuroscience Research
NIH Institutes and Centers
Agencia Nacional de Investigacin y Desarrollo10.13039/501100020884

Muestra la fuente de financiamiento declarada en la publicación.

Agradecimientos



Agradecimiento
HCP Data were provided by the Human Connectome Project, WUMinn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657), funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University.

Muestra la fuente de financiamiento declarada en la publicación.