Package: fiber 0.1.2

Aymeric Stamm

fiber: S7 Data Structures for Diffusion MRI Tractography

Provides three S7 classes — streamline, bundle, and bundle_set — for representing diffusion MRI tractography data in R, together with a concise set of methods for computing shape descriptors (arc-length, curvature, torsion, sinuosity), the Hausdorff distance between streamlines, arc-length reparametrization of streamlines and bundles onto uniform grids, combination of streamlines or bundles into a single bundle, combination of bundles from multiple subjects or sessions into a bundle_set, and coercion to and from the dwiFiber S4 class of the 'dti' package. See Dell'Acqua, F., Descoteaux, M. and Leemans, A. (2024) "Handbook of Diffusion MR Tractography" <doi:10.1016/C2018-0-02520-7> for more about the mathematical and computational underpinnings of diffusion MRI tractography.

Authors:Aymeric Stamm [aut, cre]

fiber_0.1.2.tar.gz
fiber_0.1.2.zip(r-4.7)fiber_0.1.2.zip(r-4.6)fiber_0.1.2.zip(r-4.5)
fiber_0.1.2.tgz(r-4.6-x86_64)fiber_0.1.2.tgz(r-4.6-arm64)fiber_0.1.2.tgz(r-4.5-x86_64)fiber_0.1.2.tgz(r-4.5-arm64)
fiber_0.1.2.tar.gz(r-4.7-arm64)fiber_0.1.2.tar.gz(r-4.7-x86_64)fiber_0.1.2.tar.gz(r-4.6-arm64)fiber_0.1.2.tar.gz(r-4.6-x86_64)
fiber_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
fiber/json (API)
NEWS

# Install 'fiber' in R:
install.packages('fiber', repos = c('https://tractoverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tractoverse/fiber/issues

Pkgdown/docs site:https://tractoverse.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.18 score 1 stars 20 exports 3 dependencies

Last updated from:afd0a17df1. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK118
linux-devel-x86_64OK140
source / vignettesOK159
linux-release-arm64OK126
linux-release-x86_64OK112
macos-release-arm64OK115
macos-release-x86_64OK180
macos-oldrel-arm64OK92
macos-oldrel-x86_64OK231
windows-develOK90
windows-releaseOK88
windows-oldrelOK100
wasm-releaseOK103

Exports:add_shape_descriptorsas_bundleas_bundle_setas_dwifiberas_streamlinebind_bundle_setsbind_bundlesbundlebundle_setcompute_hausdorff_distanceget_curvatureget_curvilinear_lengthget_euclidean_lengthget_sinuosityget_torsionis_bundleis_bundle_setis_streamlinereparametrizestreamline

Dependencies:clicpp11S7

Readme and manuals

Help Manual

Help pageTopics
Adds shape descriptors to a streamline or bundleadd_shape_descriptors
'add_shape_descriptors()' method for 'bundle' objectsadd_shape_descriptors,fiber::bundle-method add_shape_descriptors-fiber-bundle-method
'add_shape_descriptors()' method for 'streamline' objectsadd_shape_descriptors,fiber::streamline-method add_shape_descriptors-fiber-streamline-method
Coerce an object to a bundleas_bundle
Coerce an object to a bundle_setas_bundle_set
'as_bundle()' method for 'bundle' objectsas_bundle,fiber::bundle-method as_bundle-fiber-bundle-method
'as_bundle()' method for 'streamline' objectsas_bundle,fiber::streamline-method as_bundle-fiber-streamline-method
Coerce a streamline or bundle to a 'dwiFiber' objectas_dwifiber
'as_dwifiber()' method for 'bundle' objectsas_dwifiber,fiber::bundle-method as_dwifiber-fiber-bundle-method
'as_dwifiber()' method for 'streamline' objectsas_dwifiber,fiber::streamline-method as_dwifiber-fiber-streamline-method
Coerce an object to a streamlineas_streamline
'as_streamline()' method for 'bundle' objectsas_streamline,fiber::bundle-method as_streamline-fiber-bundle-method
'as_streamline()' method for 'streamline' objectsas_streamline,fiber::streamline-method as_streamline-fiber-streamline-method
Combine bundles and/or bundle_sets into a single bundle_setbind_bundle_sets
Combine streamlines and/or bundles into a single bundlebind_bundles
Bundle S7 classbundle
Bundle set S7 classbundle_set
Computes the Hausdorff distance between streamlinescompute_hausdorff_distance
'compute_hausdorff_distance()' method for 'bundle' objectscompute_hausdorff_distance,fiber::bundle-method compute_hausdorff_distance-fiber-bundle-method
'compute_hausdorff_distance()' method for two 'streamline' objectscompute_hausdorff_distance,fiber::streamline-method compute_hausdorff_distance-fiber-streamline-method
'compute_hausdorff_distance()' catch-all methodcompute_hausdorff_distance,any-method
Curvature of a streamlineget_curvature
Curvilinear length of a streamlineget_curvilinear_length
Euclidean length of a streamlineget_euclidean_length
Sinuosity of a streamlineget_sinuosity
Torsion of a streamlineget_torsion
Test whether an object is a bundleis_bundle
Test whether an object is a bundle_setis_bundle_set
Test whether an object is a streamlineis_streamline
Reparametrize a streamline or bundle onto a uniform arc-length gridreparametrize
'reparametrize()' method for 'bundle' objectsreparametrize,fiber::bundle-method reparametrize-fiber-bundle-method
'reparametrize()' method for 'streamline' objectsreparametrize,fiber::streamline-method reparametrize-fiber-streamline-method
Streamline S7 classstreamline