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ggseg - Plotting Tool for Brain Atlases

Provides a 'ggplot2' geom and position for visualizing brain region data on cortical, subcortical, and white matter tract atlases. Brain atlas geometries are stored as polygon data, enabling seamless integration with the 'ggplot2' ecosystem including faceting, custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

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12.23 score 274 stars 1 dependents 834 scripts 1.2k downloads

ggseg.formats - Brain Atlas Data Structures for the 'ggsegverse' Ecosystem

Provides the 'ggseg_atlas' S3 class used across the 'ggsegverse' ecosystem for 2D and 3D brain visualisation. Ships four bundled atlases ('Desikan-Killiany', 'FreeSurfer' 'aseg', 'TRACULA', 'SUIT') and functions for querying, subsetting, renaming, and enriching atlas objects. Also includes readers for 'FreeSurfer' statistics files.

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9.20 score 22 dependents 90 scripts 1.1k downloads

ggseg3d - Interactive 3D Brain Atlas Visualization

Plot brain atlases as interactive 3D meshes using 'Three.js' via 'htmlwidgets', or render publication-quality static images through 'rgl' and 'rayshader'. A pipe-friendly API lets you map data onto brain regions, control camera angles, toggle region edges, overlay glass brains, and snapshot or ray-trace the result. Additional atlases are available through the 'ggsegverse' r-universe. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

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8.84 score 45 stars 1 dependents 181 scripts 719 downloads

ggseg.extra - Create Brain Atlases for the 'ggsegverse' Plotting Ecosystem

Create brain atlas data sets compatible with the 'ggsegverse' plotting packages. Provides pipelines for building cortical, subcortical, white-matter tract, and cerebellar atlases from 'FreeSurfer' annotation files, 'GIFTI' and 'CIFTI' surface formats, 'neuromaps', cerebellar flatmaps, and volumetric 'NIfTI' images.

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8.65 score 66 stars 90 scripts

freesurfer - Wrapper Functions for 'FreeSurfer'

Wrapper functions that interface with 'Freesurfer' <https://surfer.nmr.mgh.harvard.edu/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.

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8.22 score 10 stars 83 scripts 461 downloads

neuromapr - Spatial Null Models and Transforms for Brain Map Comparison

Implements spatial null models and coordinate-space transformations for statistical comparison of brain maps, following the framework described in Markello et al. (2022) <doi:10.1038/s41592-022-01625-w>. Provides variogram-matching surrogates (Burt et al. 2020), Moran spectral randomization (Wagner & Dray 2015), and spin-based permutation tests (Alexander-Bloch et al. 2018). Includes an R interface to the 'neuromaps' annotation registry for browsing, downloading, and comparing brain map annotations from the Open Science Framework ('OSF'). Integrates with 'ciftiTools' for coordinate-space transforms.

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5.78 score 6 stars 8 scripts 419 downloads

ggseg.meshes - Additional Brain Surface Meshes for the 'ggsegverse' Ecosystem

Provides additional brain surface meshes for cortical and cerebellar visualisation in the 'ggsegverse' ecosystem. Cortical surfaces include pial, white, midthickness, semi-inflated, sphere, smoothwm, and orig at fsaverage5 resolution. Cerebellar surfaces include the Spatially Unbiased Infratentorial Template (SUIT) flatmap. All meshes follow the same vertices/faces data frame format used by 'ggseg.formats' and 'ggseg3d'.

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5.35 score 4 scripts 373 downloads

ggsegSchaefer - Schaefer Atlas for the 'ggsegverse' Ecosystem

Schaefer cortical atlas for the 'ggseg' ecosystem. Provides unified 'ggseg_atlas' objects with both 2D polygon geometry and 3D vertex indices, for use with 'ggseg' and 'ggseg3d'. Includes 7-network and 17-network parcellations at resolutions from 100 to 1000 parcels.

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4.75 score 18 stars 104 scripts

ggsegGlasser - Glasser Atlas for the 'ggsegverse' Ecosystem

Glasser multi-modal cortical parcellation (HCP) atlas for the 'ggseg' ecosystem. Provides a unified 'ggseg_atlas' object with 2D polygon geometry for use with 'ggseg'.

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4.55 score 9 stars 132 scripts

ggsegYeo2011 - Yeo 2011 Atlas for the 'ggsegverse' Ecosystem

Yeo 2011 resting-state network atlases for the 'ggseg' ecosystem. Provides 'ggseg_atlas' objects with 2D polygon geometry for use with 'ggseg'. Includes both 7-network and 17-network parcellations.

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3.94 score 12 stars 24 scripts

ggsegGordon - Gordon Atlas for the 'ggseg' Ecosystem

Gordon resting-state cortical parcellation atlas for the 'ggseg' ecosystem. Provides a unified 'ggseg_atlas' object with 2D polygon geometry for use with 'ggseg'.

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3.57 score 5 stars 25 scripts

ggsegBrainnetome - Brainnetome Atlas for the 'ggsegverse' Ecosystem

Brainnetome atlas for the 'ggseg' ecosystem. Provides cortical and subcortical 'ggseg_atlas' objects with 2D polygon geometry and 3D vertex indices for use with 'ggseg' and 'ggseg3d'.

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3.18 score 5 stars 7 scripts

wbcmd - Wrapper Functions for 'Connectome Workbench' Commands

Provides R wrapper functions for the 'Connectome Workbench' command-line tool ('wb_command'). Includes a central dispatcher for executing workbench commands, environment detection, and convenience wrappers for common operations on Connectivity Informatics Technology Initiative (CIFTI), Geometry Informatics Technology Initiative (GIFTI), and surface files.

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3.18 score 4 scripts

ggsegJHU - JHU White Matter Atlases for the 'ggseg' Ecosystem

JHU and ICBM white matter atlases for the 'ggseg' ecosystem. Includes the JHU probabilistic tract atlas (Hua et al. 2008), built from its probabilistic maps as a tract atlas with a centerline per tract, and the ICBM-DTI-81 white matter labels (Mori et al. 2005). Both are coregistered to the FreeSurfer 'cvs_avg35_inMNI152' template so 2D slices show cortical reference outlines, and ship as 'ggseg_atlas' objects with 3D geometry for use with 'ggseg3d'.

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3.04 score 5 stars 11 scripts

ggsegAicha - AICHA Atlas for the 'ggseg' Ecosystem

AICHA (Atlas of Intrinsic Connectivity of Homotopic Areas) atlas for the 'ggseg' ecosystem. Provides cortical and subcortical 'ggseg_atlas' objects with 2D polygon geometry and 3D vertex or mesh data, for use with 'ggseg' and 'ggseg3d'.

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3.02 score 3 stars 4 scripts

ggsegAAL - AAL Atlases for the 'ggsegverse' Ecosystem

AAL (Automated Anatomical Labeling) atlases for the 'ggseg' ecosystem. Provides unified 'ggseg_atlas' objects for AAL2 (cortical, Rolls et al. 2015) and AAL3 (cortical, subcortical, cerebellum, Rolls et al. 2020), with both 2D polygon geometry and 3D vertex/mesh data for use with 'ggseg' and 'ggseg3d'.

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3.00 score 4 stars 6 scripts

ggsegHO - Harvard-Oxford Atlas for the 'ggseg' Ecosystem

Harvard-Oxford cortical and subcortical atlases for the 'ggseg' ecosystem. Includes the original Harvard-Oxford atlas (FSL) and the Harvard-Oxford Atlas 2.0 (HOA-2, Rushmore et al. 2022) as 'ggseg_atlas' objects with 2D polygon and 3D mesh geometry.

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2.89 score 2 stars 11 scripts

ggsegChen - Chen datasets for the ggseg-plotting tool

This is a support package for the ggseg, and ggseg3d packages. It contains the Chen atlases to plot using functions from those two packages.

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2.78 score 3 stars 4 scripts

ggsegFreeSurfer - FreeSurfer Brain Atlases for the 'ggseg' Ecosystem

FreeSurfer cortical and subcortical brain atlases for the 'ggseg' ecosystem. Provides unified 'ggseg_atlas' objects with 2D polygon geometry and 3D mesh or vertex data, for use with 'ggseg' and 'ggseg3d'.

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2.70 score 2 stars 4 scripts

ggsegArslan - Arslan Atlas for the 'ggseg' Ecosystem

Arslan multi-level parcellation atlas for the 'ggseg' ecosystem. Provides a unified 'ggseg_atlas' object with both 2D polygon geometry and 3D vertex indices, for use with 'ggseg' and 'ggseg3d'.

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2.54 score 1 stars 4 scripts

ggsegIca - ICA Atlas for the 'ggseg' Ecosystem

Probabilistic independent component analysis (ICA) cortical atlas for the 'ggseg' ecosystem. Provides a unified 'ggseg_atlas' object with 2D polygon geometry for use with 'ggseg'.

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2.48 score 1 stars 4 scripts

ggsegPower - Power Atlas for the 'ggseg' Ecosystem

Power functional network cortical parcellation atlas for the 'ggseg' ecosystem. Provides a unified 'ggseg_atlas' object with 2D polygon geometry for use with 'ggseg'.

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2.48 score 4 scripts

ggsegAtlasTrack - AtlasTrack Fiber Tract Atlas for the 'ggseg' Ecosystem

AtlasTrack probabilistic white matter fiber tract atlas for the 'ggseg' ecosystem. Provides 'ggseg_atlas' objects for DTI fiber tract visualization, commonly used with ABCD study data.

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2.40 score 4 scripts

ggsegHistorical - Historical Brain Atlases for the 'ggseg' Ecosystem

Six historical cortical brain atlases digitally reconstructed by Pijnenburg et al. (2021) <doi:10.1016/j.neuroimage.2021.118274> from the Dutch Connectome Lab. Includes Brodmann (1909), Campbell (1905), Economo & Koskinas (1925), Flechsig (1920), Kleist (1934), and Smith (1907). Each atlas provides a unified 'ggseg_atlas' object with both 2D polygon geometry and 3D vertex indices, for use with 'ggseg' and 'ggseg3d'.

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2.40 score 4 scripts

ggsegCerebellum - Cerebellar Atlases for the 'ggsegverse' Ecosystem

Collection of cerebellar parcellation atlases for the 'ggsegverse' ecosystem. Includes anatomical (Diedrichsen 2009), resting-state network (Buckner 2011, Ji 2019, Xue 2021), task-based (King/MDTB 2019), and hierarchical functional (Nettekoven 2024) parcellations. All atlases derived from the DiedrichsenLab cerebellar atlas collection.

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2.30 score 5 scripts

ggsegMiccai - MICCAI 2012 Multi-Atlas Labeling Brain Atlas for the 'ggseg' Ecosystem

Neuromorphometrics maximum probability tissue labels, derived from the MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling and distributed with SPM12, for the 'ggseg' ecosystem. Provides cortical and subcortical 'ggseg_atlas' objects with both 2D polygon geometry and 3D vertex indices, for use with 'ggseg' and 'ggseg3d'. The label data are released under CC BY-NC; MRI scans originate from the OASIS project and the labeled data are provided by Neuromorphometrics, Inc. under academic subscription.

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1.70 score 4 scripts