Package: ggsegExtra 1.5.33.004

Athanasia Mo Mowinckel

ggsegExtra: Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

Contains functions to create new data sets compatible with the 'ggseg' and 'ggseg3d' packages for plotting brain segmentations through R. Requires several external software to be installed on the system for atlas creations to work, and most of these are not available for windows. But atlas creation tools exist for 2d simple features data, and also 3d tri-surface mesh plots. Also has a list of compatible data sets and functions for easy installation of these.

Authors:Athanasia Mo Mowinckel [aut, cre], Didac Vidal-Piñeiro [aut], John Muschelli [ctb]

ggsegExtra_1.5.33.004.tar.gz

ggsegExtra_1.5.33.004.tgz(r-4.4-any)
ggsegExtra_1.5.33.004.tar.gz(r-4.5-noble)ggsegExtra_1.5.33.004.tar.gz(r-4.4-noble)
ggsegExtra_1.5.33.004.tgz(r-4.4-emscripten)
ggsegExtra.pdf |ggsegExtra.html✨
ggsegExtra/json (API)
NEWS

# Install 'ggsegExtra' in R:

install.packages('ggsegExtra', repos = c('https://ggseg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ggseg/ggsegextra/issues

On CRAN:

4.58 score 54 stars 70 scripts 27 exports 129 dependencies

Last updated 3 years agofrom:c1513ba10d. Checks:1 ERROR, 2 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Feb 21 2025
R-4.5-linux	WARNING	Feb 21 2025
R-4.4-mac	WARNING	Feb 21 2025

Exports:aparc_2_mesh atlas_lab2ctab atlas_vol2label atlas_vol2surf curv2ply fs_curvatures fs_nofixcurv fs_surfaces get_mesh ggseg_atlas_repos install_ggseg_atlas install_ggseg_atlas_all is_ctab make_aparc_2_3datlas make_ggseg3d_2_ggseg make_palette_ggseg make_volumetric_2_3datlas make_volumetric_ggseg mri_annotation2label mri_surf2surf_rereg mri_vol2label mris_ca_label mris_label2annot read_ctab subject_2_ascii surf2ply write_ctab

Dependencies:abind ape askpass base64enc bit bit64 bitops bslib cachem class classInt cli clipr colorspace cpp11 crayon crosstalk curl data.table DBI digest dplyr e1071 evaluate fansi farver fastmap fontawesome freesurfer fs generics geojsonsf geometries geomorph ggplot2 ggseg ggseg3d glue gtable highr hms htmltools htmlwidgets httr isoband janitor jpeg jquerylib jsonify jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle lubridate magick magrittr MASS Matrix matrixStats memoise mgcv mime munsell neurobase nlme openssl oro.nifti pbmcapply pillar pkgconfig plotly plyr prettyunits progress promises proxy purrr R.methodsS3 R.oo R.utils R6 rapidjsonr rappdirs raster RColorBrewer Rcpp readr reshape2 rgdal rgl rlang rmapshaper rmarkdown RNifti RRPP s2 sass scales sf sfheaders smoothr snakecase sp stars stringi stringr sys terra tibble tidyr tidyselect timechange tinytex tzdb units utf8 V8 vctrs viridisLite vroom withr wk xfun xml2 yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Converts annotations to atlas	aparc_2_mesh
Label to ctab	atlas_lab2ctab
Volume to label	atlas_vol2label
Nifti volume to surface	atlas_vol2surf
Change meshes to new system	change_meshes
Check if FS can be run	check_fs
Convert Freesurfer curvature file to ply	curv2ply
Available Freesurfer curvatures	fs_curvatures
Available Freesurfer no fix curvatures	fs_nofixcurv
Available Freesurfer surfaces	fs_surfaces
Extract mesh data from ply	get_mesh
List all online repositories with ggseg-atlases	ggseg_atlas_repos
Install ggseg-atlas from repo	install_ggseg_atlas
Install all ggseg-atlases registeres	install_ggseg_atlas_all
Check if object is colourtable	is_ctab
Convert LCBC surface file to other subjects	lcbc_surf2surf
Create cortical ggseg3d-atlas from annot-file	make_aparc_2_3datlas
Turn ggseg3d-atlas to ggseg	make_ggseg3d_2_ggseg
Create ggseg palette from ggseg3d-atlas	make_palette_ggseg
Volumetric segmentation to 3d-atlas	make_volumetric_2_3datlas
Make ggseg atlas from volumetric template	make_volumetric_ggseg
Convert annotation to label	mri_annotation2label
Re-register an annotation file	mri_surf2surf_rereg
Convert volume to label	mri_vol2label
MRI ca label	mris_ca_label
Convert Label to Annotation	mris_label2annot
Read colourtab	read_ctab
Change old atlas setup to new	restruct_old_3datlas
Turn smooth file to ascii	smooth2srf
Convert subject surface files to ascii	subject_2_ascii
Convert Freesurfer surface file into ply	surf2ply
Split surface file into separate plys	surfsplit
Write colourtab	write_ctab

Package: ggsegExtra 1.5.33.004

ggsegExtra: Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

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