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 [email protected]:fabibo3/visgeom.git

Install conda environment and activate

cd visgeom
conda env create -f requirements.yml
conda activate visgeom

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.