This repository contains a pipeline to generate surfaces from voxelized data using scikit-image and pyvista. It also contains tools for visualization using pyvista.
To install the required packages, run:
python3 -m pip install git+https://github.com/scientificcomputing/mri2mesh.gitThe basic using is through the command line using the command mri2mesh. To see all the options, run:
mri2mesh --helpVisualization is achieved through the subcommand viz. To see all options you can do
mri2mesh viz --helpFor example to visualize a nifty file called T1_synthseg.nii.gz, run:
mri2mesh viz volume-clip -i T1_synthseg.nii.gzwhich will open up the volume with a clipping plane. To see all the options, run:
mri2mesh viz volume-clip --helpTo generate the parenchyma surface from a nifty file, run:
mri2mesh surface parenchyma -i T1_synthseg.nii.gzThe pipeline is developed by Marius Causemann and Henrik Finsberg.
MIT