Metadata-Version: 2.4
Name: mri2mesh
Version: 0.2.0
Summary: Tool for converting labeled MRI data to a mesh
Author-email: Henrik Finsberg <henriknf@simula.no>, Marius Causemann <mariusca@simula.no>
License: MIT
Project-URL: Homepage, https://github.com/scientificcomputing/mri2mesh
Keywords: mri,fem,brain,meshing
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pyvista
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: nibabel
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: meshio
Provides-Extra: mesh
Requires-Dist: wildmeshing; extra == "mesh"
Requires-Dist: h5py; extra == "mesh"
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: mri2mesh[mesh]; extra == "test"
Provides-Extra: docs
Requires-Dist: pyvista[jupyter]; extra == "docs"
Requires-Dist: jupyter-book; extra == "docs"
Requires-Dist: mri2mesh[mesh]; extra == "docs"
Dynamic: license-file

# 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
