Scripts for convenient visualization of 3D meshes and associated per-vertex values from the command line based on pyvista. Basic image visualization can also be done. It can deal with FreeSurfer file types, .plys, and numpy arrays in arbitrary combinations.
Download this repository
git clone git@github.com:fabibo3/visgeom.git
Install conda environment and activate
cd visgeom
conda env create -f requirements.yml
conda activate visgeom
Note: If you are running MacOS on an Apple Silicon device, use requirements_arm.yml.
Install the visgeom package in editable mode
pip install -e .
Visualize meshes, e.g., for a brain with cortical thickness
visgeom --meshes /path/to/lh.inflated --meshvalues /path/to/lh.thickness.npy --clim 1 4
When given multiple meshes or meshvalues, they are visualized sequentially.
Plotting cortical overlays from all views at a time is now also possible with
plot-cortex --subject_dir <SUBJECT_DIR> --output_dir <OUTPUT_DIR>