Installation guide
Python
Requirements
subcortex-visualization requires Python ≥ 3.11 and the following packages, which are installed automatically:
| Package | Version | Source |
|---|---|---|
| matplotlib | 3.10.1 | PyPI |
| numpy | 2.2.5 | PyPI |
| pandas | 2.2.3 | PyPI |
| setuptools | 75.8.0 | PyPI |
| svgpath2mpl | 1.0.0 | PyPI |
Direct installation from PyPI
This package can be installed directly with pip from the PyPI repository:
pip install subcortex-visualization
Cloning with GitHub
Alternatively, you can clone this repository from GitHub and then install from your local version:
git clone https://github.com/anniegbryant/subcortex_visualization.git
cd subcortex_visualization
pip install .
This option is good if you want to make any modifications, including adding your own atlas.
R
Requirements
subcortexVisualizationR requires R ≥ 4.1 (tested on R 4.5.2) and the following packages:
| Package | Version | Source |
|---|---|---|
| tidyverse | 2.0.0 | CRAN |
| xml2 | 1.5.2 | CRAN |
| patchwork | 1.3.2 | CRAN |
| RNifti | 1.9.0 | CRAN |
| scales | 1.4.0 | CRAN |
| svgparser | 0.1.2 | GitHub (coolbutuseless/svgparser) |
| ANTsR | 0.6.6 | GitHub (ANTsX/ANTsR) |
| extrantsr | 3.10.0 | GitHub (muschellij2/extrantsr) |
GitHub-sourced packages
svgparser, ANTsR, and extrantsr are not available on CRAN and must be installed from GitHub. These are installed automatically when you run remotes::install_github() below — no additional steps required.
Installing from GitHub
To install the R version of this package (subcortexVisualizationR), run the following in R (either in the terminal or in RStudio):
# if not already installed
install.packages("remotes")
# then install subcortexVisualizationR
remotes::install_github("anniegbryant/subcortex_visualization", subdir = "subcortexVisualizationR")
Dependencies and reproducibility
Both the Python and R packages pin the exact version of every dependency so you can recreate the same environment in the future, even if packages have been updated or removed.
Python
A requirements.txt file in the repository records the exact version of every Python dependency. To recreate the environment used to produce the package:
pip install -r requirements.txt
R
The subcortexVisualizationR project uses renv to manage R package dependencies.
The renv.lock file committed to the repository records the exact version of every R dependency, including the GitHub commit SHA for GitHub-sourced packages (svgparser, ANTsR, extrantsr).
To restore the identical R environment at any point in the future, open R in the subcortexVisualizationR project directory and run:
renv::restore()
This installs exactly the versions recorded in renv.lock, regardless of what package versions are current at that time.