# mni2mz3
[](https://crates.io/crates/mni2mz3)
[](https://github.com/FNNDSC/mni2mz3/blob/main/LICENSE)
[](https://github.com/FNNDSC/mni2mz3/actions/workflows/test.yml)
[](https://codecov.io/gh/FNNDSC/mni2mz3)
Converts a file from MNI polygonal surface mesh format (`.obj`\*) or
vertex-wise data (e.g. curvature, cortical thickness, `*.txt`)
to [Surf-Ice MZ3 (`.mz3`)](https://github.com/neurolabusc/surf-ice/tree/master/mz3).
Useful for visualizing surfaces using [Surf-Ice](https://github.com/neurolabusc/surf-ice) or [NiiVue](https://github.com/niivue/niivue).
> [!WARNING]
> \*Not to be confused with Wavefront .obj, which is a different spec but with the same file extension.
## Installation
There are many ways to install and use `mni2mz3`. Linux, Mac, and Windows are supported.
### Using _ChRIS_
The easiest way to run `mni2mz3` is on [_ChRIS_](https://chrisproject.org), no installation needed.
Simply upload your data to a feed in https://app.chrisproject.org, then run `pl-mni2common`.
### Using Apptainer
`pl-mni2common` is a _ChRIS_ plugin wrapper for `mni2mz3`, which means you can
use its container image to run `mni2mz3`.
```shell
apptainer run docker://ghcr.io/fnndsc/pl-mni2common:latest mni2mz3 input.obj output.mz3
```
Call the wrapper script `mni2mz3` instead to do bulk processing on an input directory.
```shell
apptainer run docker://ghcr.io/fnndsc/pl-mni2common:latest mni2mz3 inputdir/ outputdir/
```
### Using [cargo-binstall](https://github.com/cargo-bins/cargo-binstall)
```shell
cargo binstall mni2mz3
```
### Using pip
```shell
pip install mni2mz3
```
### Manual Download
Select and download the right binary for your architecture and OS from GitHub Releases:
https://github.com/FNNDSC/mni2mz3/releases/latest
### Compile From Source
Install [Rust](https://rustup.rs), then run
```shell
cargo install mni2mz3
```
## Usage
```shell
# convert mesh
mni2mz3 surface_81920.obj surface.mz3
# convert data
mni2mz3 thickness.txt thickness.mz3
```
To do bulk conversions, use the [_ChRIS_ plugin wrapper](#using-chris).
## Details
- Output file will be gzip compressed.
- For surfaces, only triangle meshes are supported.
- For data, only 32-bit single-precision "float" is supported.
## Testing
It is recommended to install [cargo-nextest](https://nexte.st/).
```shell
cargo nextest run
```
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"description": "# mni2mz3\n\n[](https://crates.io/crates/mni2mz3)\n[](https://github.com/FNNDSC/mni2mz3/blob/main/LICENSE)\n[](https://github.com/FNNDSC/mni2mz3/actions/workflows/test.yml)\n[](https://codecov.io/gh/FNNDSC/mni2mz3)\n\nConverts a file from MNI polygonal surface mesh format (`.obj`\\*) or\nvertex-wise data (e.g. curvature, cortical thickness, `*.txt`)\nto [Surf-Ice MZ3 (`.mz3`)](https://github.com/neurolabusc/surf-ice/tree/master/mz3).\nUseful for visualizing surfaces using [Surf-Ice](https://github.com/neurolabusc/surf-ice) or [NiiVue](https://github.com/niivue/niivue).\n\n> [!WARNING]\n> \\*Not to be confused with Wavefront .obj, which is a different spec but with the same file extension.\n\n## Installation\n\nThere are many ways to install and use `mni2mz3`. Linux, Mac, and Windows are supported.\n\n### Using _ChRIS_\n\nThe easiest way to run `mni2mz3` is on [_ChRIS_](https://chrisproject.org), no installation needed.\nSimply upload your data to a feed in https://app.chrisproject.org, then run `pl-mni2common`.\n\n### Using Apptainer\n\n`pl-mni2common` is a _ChRIS_ plugin wrapper for `mni2mz3`, which means you can\nuse its container image to run `mni2mz3`.\n\n```shell\napptainer run docker://ghcr.io/fnndsc/pl-mni2common:latest mni2mz3 input.obj output.mz3\n```\n\nCall the wrapper script `mni2mz3` instead to do bulk processing on an input directory.\n\n```shell\napptainer run docker://ghcr.io/fnndsc/pl-mni2common:latest mni2mz3 inputdir/ outputdir/\n```\n\n### Using [cargo-binstall](https://github.com/cargo-bins/cargo-binstall)\n\n```shell\ncargo binstall mni2mz3\n```\n\n### Using pip\n\n```shell\npip install mni2mz3\n```\n\n### Manual Download\n\nSelect and download the right binary for your architecture and OS from GitHub Releases:\nhttps://github.com/FNNDSC/mni2mz3/releases/latest\n\n### Compile From Source\n\nInstall [Rust](https://rustup.rs), then run\n\n```shell\ncargo install mni2mz3\n```\n\n## Usage\n\n```shell\n# convert mesh\nmni2mz3 surface_81920.obj surface.mz3\n\n# convert data\nmni2mz3 thickness.txt thickness.mz3\n```\n\nTo do bulk conversions, use the [_ChRIS_ plugin wrapper](#using-chris).\n\n## Details\n\n- Output file will be gzip compressed.\n- For surfaces, only triangle meshes are supported.\n- For data, only 32-bit single-precision \"float\" is supported.\n\n## Testing\n\nIt is recommended to install [cargo-nextest](https://nexte.st/).\n\n```shell\ncargo nextest run\n```\n\n",
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