Overlaying plots and transparent
thresholding | Transparent thresholding | Running a vertex-wise linear model | Plotting significant and subthreshold outcome | Overlaying plots together | Overlaying HippUnfold hippocampal plots | Overlaying SubCortexMesh subcortical plots | References:
Package: VertexWiseR 1.5.4
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:
VertexWiseR_1.5.4.tar.gz
VertexWiseR_1.5.4.zip(r-4.7-any)VertexWiseR_1.5.4.zip(r-4.6-any)VertexWiseR_1.5.4.zip(r-4.5-any)
VertexWiseR_1.5.4.tgz(r-4.6-any)VertexWiseR_1.5.4.tgz(r-4.5-any)
VertexWiseR_1.5.4.tar.gz(r-4.7-any)VertexWiseR_1.5.4.tar.gz(r-4.6-any)
VertexWiseR_1.5.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VertexWiseR/json (API)
| # 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:
- edgelist_hip - List of edges for the hippocampal template
- fs6_to_fs5_map - Fsaverage6 template object for nearest neighbor conversion in fs6_to_fs5
- fslr_to_fs5_map - Fslr template object for nearest neighbor conversion in fslr_to_fs5
- hip_points_cells - Points and cells data required to build the hippocampus surface template
- ROImap_fs5 - Atlas parcellations of fsaverage5
- ROImap_fs6 - Atlas parcellations of fsaverage6
- ROImap_fslr32k - Atlas parcellations of FS_LR32k
- ROImap_hip - Atlas parcellations of the hippocampus
Last updated from:1aa254975f. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 199 | ||
| source / vignettes | OK | 407 | ||
| linux-release | NOTE | 168 | ||
| macos-release | NOTE | 121 | ||
| macos-oldrel | NOTE | 150 | ||
| windows-devel | NOTE | 131 | ||
| windows-release | NOTE | 124 | ||
| windows-oldrel | NOTE | 145 | ||
| wasm-release | OK | 148 |
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.tabledigestdoParalleldoSNOWdplyrevaluatefarverfastmapfontawesomeforeachfreesurferformatsfsgenericsggplot2giftigluegtableherehighrhtmltoolshtmlwidgetshttrigraphisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeopensslotelpillarpkgconfigpkgfilecacheplotlypngpromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrmarkdownrprojrootS7sassscalessnowstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml
Overlaying plots and transparent thresholding
Last update: 2026-03-11
Started: 2026-03-11
Example analyses with VertexWiseR - Example 3
Example analyses with VertexWiseR - Example
3 | Requirements | Extracting ASeg subcortical surfaces | Example analysis on the thalamus and caudate nuclei | Analysing all subcortices together | References:
Last update: 2026-03-11
Started: 2026-03-11
Python troubleshooting
1. How to make VWRfirstrun() ignore the system’s Python environment
when starting a fresh installation | 2. How to make VWRfirstrun() use a specific Python installation | 3. VWRfirstrun() shows the message “Clearing reticulate’s uv
cache…” | 4. About the message: “Would you like to create a default Python
environment for the reticulate package? (Yes/no/cancel)” (reticulate
< 1.41.0) | References:
Last update: 2024-12-12
Started: 2024-12-12
Example analyses with VertexWiseR - Example 1
Example analyses with VertexWiseR - Example
1 | Installing VertexWiseR and checking for requirements | Example analysis 1: linear model of age and cortical thickness, and
meta-analytic decoding | References:
Last update: 2024-09-04
Started: 2024-09-04
Example analyses with VertexWiseR - Example 2
Example analyses with VertexWiseR - Example
2 | Example 2: Mixed effect model of intervention-related changes on
hippocampal thickness | Example 2 follow-up: plotting and post-hoc analyses of hippocampal
clusters across regression models | References:
Last update: 2024-09-04
Started: 2024-09-04
Extracting surface data in VertexWiseR
Summary | Extracting cortical surface data: from FreeSurfer | Extracting cortical surface data: from HCP processing, sMRIprep,
fMRIprep, ASLprep or XCP-D | Extracting cortical surface data: from CAT12 | Extracting hippocampal surface data: from HippUnfold | Extracting subcortical surface data: from SubCortexMesh | References:
Last update: 2024-09-04
Started: 2024-09-04
