Name | mri2mesh JSON |
Version |
0.1.1
JSON |
| download |
home_page | None |
Summary | Tool for converting labeled MRI data to a mesh |
upload_time | 2025-08-06 09:56:28 |
maintainer | None |
docs_url | None |
author | None |
requires_python | None |
license | MIT |
keywords |
mri
fem
brain
meshing
|
VCS |
 |
bugtrack_url |
|
requirements |
No requirements were recorded.
|
Travis-CI |
No Travis.
|
coveralls test coverage |
No coveralls.
|
# 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
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