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
1 maintainer
Metadata
1 maintainer
Release files for mri2mesh 0.3.0
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| File | Size | Uploaded | |
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| mri2mesh-0.3.0.tar.gz | 18.5 kB | Details |
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|---|---|---|---|---|
| mri2mesh-0.3.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 40.9 kB
Release files / mri2mesh-0.3.0.tar.gz
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