mri2mesh

This repository contains a pipeline to generate surfaces from voxelized data using scikit-image and pyvista. It also contains tools for visualization using pyvista.

Installation

To install the required packages, run:

python3 -m pip install git+https://github.com/scientificcomputing/mri2mesh.git

Usage

The basic using is through the command line using the command mri2mesh. To see all the options, run:

mri2mesh --help

Visualization

Visualization is achieved through the subcommand viz. To see all options you can do

mri2mesh viz --help

For example to visualize a nifty file called T1_synthseg.nii.gz, run:

mri2mesh viz volume-clip -i T1_synthseg.nii.gz

which will open up the volume with a clipping plane. To see all the options, run:

mri2mesh viz volume-clip --help

Surface generation

To generate the parenchyma surface from a nifty file, run:

mri2mesh surface parenchyma -i T1_synthseg.nii.gz

Authors

The pipeline is developed by Marius Causemann and Henrik Finsberg.

License

MIT