https://github.com/scientificcomputing/mri2mesh
Brain meshing pipeline from MRI using pyvista, scikit-image and ftetwild
https://github.com/scientificcomputing/mri2mesh
Last synced: 2 months ago
JSON representation
Brain meshing pipeline from MRI using pyvista, scikit-image and ftetwild
- Host: GitHub
- URL: https://github.com/scientificcomputing/mri2mesh
- Owner: scientificcomputing
- License: mit
- Created: 2024-12-13T08:00:42.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-02-26T07:59:03.000Z (4 months ago)
- Last Synced: 2026-02-26T12:57:05.092Z (4 months ago)
- Language: Python
- Homepage: https://scientificcomputing.github.io/mri2mesh/
- Size: 724 KB
- Stars: 3
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# 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:
```bash
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:
```bash
mri2mesh --help
```
### Visualization
Visualization is achieved through the subcommand `viz`. To see all options you can do
```bash
mri2mesh viz --help
```
For example to visualize a nifty file called `T1_synthseg.nii.gz`, run:
```bash
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:
```bash
mri2mesh viz volume-clip --help
```
### Surface generation
To generate the parenchyma surface from a nifty file, run:
```bash
mri2mesh surface parenchyma -i T1_synthseg.nii.gz
```
## Authors
The pipeline is developed by Marius Causemann and Henrik Finsberg.
## License
MIT