Package: VertexWiseR 1.5.1

Charly Billaud

VertexWiseR: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical Surface

Provides functions to run statistical analyses on surface-based neuroimaging data, computing measures including cortical thickness and surface area of the whole-brain and of the hippocampi. It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed datasets, 'HippUnfold' hippocampal outputs and 'SubCortexMesh' subcortical outputs for a given sample by restructuring the data values into a single file. The single file can then be used by the package for analyses independently from its base dataset and without need for its access.

Authors:Junhong Yu [aut], Charly Billaud [aut, cre]

VertexWiseR_1.5.1.tar.gz
VertexWiseR_1.5.1.zip(r-4.7)VertexWiseR_1.5.1.zip(r-4.6)VertexWiseR_1.5.1.zip(r-4.5)
VertexWiseR_1.5.1.tgz(r-4.6-any)VertexWiseR_1.5.1.tgz(r-4.5-any)
VertexWiseR_1.5.1.tar.gz(r-4.7-any)VertexWiseR_1.5.1.tar.gz(r-4.6-any)
VertexWiseR_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
VertexWiseR/json (API)
NEWS

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

Bug tracker:https://github.com/cogbrainhealthlab/vertexwiser/issues

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

Datasets:

On CRAN:

Conda:

7.28 score 12 stars 19 scripts 570 downloads 25 exports 86 dependencies

Last updated from:3df30242a8. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING184
source / vignettesOK214
linux-release-x86_64WARNING191
macos-release-arm64WARNING182
macos-oldrel-arm64WARNING222
windows-develWARNING120
windows-releaseWARNING153
windows-oldrelWARNING130
wasm-releaseOK127

Exports:atlas_to_surfCAT12vextractdecode_surf_dataDTSERIESvextractfs_statsfs5_to_fs6fs5_to_fslrfs6_to_fs5fslr_to_fs5FSLRvextractgetting_startedHIPvextractplot_overlay_surfplot_surfplot_surf3dRFT_vertex_analysisSCMvextractsmooth_surfsurf_to_atlassurf_to_volSURFvextractTFCE_thresholdTFCE_vertex_analysisTFCE_vertex_analysis_mixedVWRfirstrun

Dependencies:askpassbase64encbslibcachemclicodetoolscpp11crosstalkcurldata.tabledigestdoParalleldoSNOWdownloaderdplyrevaluatefarverfastmapfontawesomeforeachfreesurferformatsfsgenericsggplot2giftigluegtableherehighrhtmltoolshtmlwidgetshttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslotelpillarpkgconfigpkgfilecacheplotlypngpromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrmarkdownrprojrootS7sassscalessnowstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml

Example analyses with VertexWiseR - Example 1

Rendered fromVertexWiseR_Example_1.html.asisusingR.rsp::asison May 22 2026.

Last update: 2024-09-04
Started: 2024-09-04

Example analyses with VertexWiseR - Example 2

Rendered fromVertexWiseR_Example_2.html.asisusingR.rsp::asison May 22 2026.

Last update: 2024-09-04
Started: 2024-09-04

Example analyses with VertexWiseR - Example 3

Rendered fromVertexWiseR_Example_3.html.asisusingR.rsp::asison May 22 2026.

Last update: 2026-03-11
Started: 2026-03-11

Extracting surface data in VertexWiseR

Rendered fromVertexWiseR_surface_extraction.html.asisusingR.rsp::asison May 22 2026.

Last update: 2024-09-04
Started: 2024-09-04

Overlaying plots and transparent thresholding

Rendered fromVertexWiseR_plot_overlay.html.asisusingR.rsp::asison May 22 2026.

Last update: 2026-03-11
Started: 2026-03-11

Python troubleshooting

Rendered fromPython_troubleshooting.html.asisusingR.rsp::asison May 22 2026.

Last update: 2024-12-12
Started: 2024-12-12

Readme and manuals

Help Manual

Help pageTopics
Atlas to surfaceatlas_to_surf
CAT12vextractCAT12vextract
Decode surface datadecode_surf_data
DTSERIESvextractDTSERIESvextract
List of edges for the hippocampal templateedgelist_hip
Edge list objectedgelist-class
fs_stats()fs_stats
fsaverage5 to fsaverage6fs5_to_fs6
fsaverage5 to fslrfs5_to_fslr
fsaverage6 to fsaverage5fs6_to_fs5
fsaverage6 template object for nearest neighbor conversion in fs6_to_fs5()fs6_to_fs5_map
fslr to fsaverage5fslr_to_fs5
FSLRvextractFSLRvextract
Getting started with tutorialsgetting_started
points and cells data required to build the hippocampus surface templatehip_points_cells
HIPvextractHIPvextract
MNI surface map objectMNIsurface-class
Surface overlay plotterplot_overlay_surf
Surface plotterplot_surf
3D Surface plotterplot_surf3d
Vertex-wise analysis with random field theory cluster correctionRFT_vertex_analysis
Atlas parcellations of fsaverage5ROImap_fs5
Atlas parcellations of fsaverage6ROImap_fs6
Atlas parcellations of FS_LR32kROImap_fslr32k
Atlas parcellations of the hippocampus (CITI168)ROImap_hip
Region-of-Interest mapping objectROImap-class
SCMvextractSCMvextract
Smooth surfacesmooth_surf
Surface to atlassurf_to_atlas
Surface to volumesurf_to_vol
SURFvextractSURFvextract
Thresholding TFCE outputTFCE_threshold
Vertex-wise analysis with threshold-free cluster enhancement (fixed effect)TFCE_vertex_analysis
Vertex-wise analysis with threshold-free cluster enhancement (mixed effect)TFCE_vertex_analysis_mixed
VertexWiseR system requirements installationVWRfirstrun