Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum

Recent years have seen an expanding repertoire of code-based tools for visualizing neuroimaging data, promoting reproducibility and interpretability of brain-mapping findings. However, most open-source visualization packages for the human brain are geared toward the cerebral cortex, and the comparatively fewer options for the subcortex and cerebellum are limited in scope (i.e., atlas support) and flexibility. We address this critical gap by introducing subcortex_visualization, an open-source package offered in both Python and R, that provides a unified and accessible framework for programmatically visualizing non-cortical data across many popular atlases for the subcortex (including thalamic nuclei and the brainstem) and cerebellum. These two-dimensional vector-based visuals are inspired by the ggseg R package for cortical data, which implements standardized rendering conventions to facilitate comparison across atlases in a vectorized two-dimensional format. In addition to the vectorized versions of twelve atlases—to our knowledge, the largest collection of non-cortical atlases in a single vector-based brain visualization toolbox—we also provide a step-by-step tutorial for users to generate custom vector-based visualizations from any given brain segmentation, enabling flexible extension to new atlases and structures. Collectively, subcortex_visualization and the accompanying documentation support reproducible and interpretable visualization of region-level data below the cortical mantle.