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https://github.com/childmindresearch/niftyone

Large-scale neuroimaging visualization using FiftyOne
https://github.com/childmindresearch/niftyone

Last synced: 12 days ago
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Large-scale neuroimaging visualization using FiftyOne

Host: GitHub
URL: https://github.com/childmindresearch/niftyone
Owner: childmindresearch
License: mit
Created: 2023-07-20T18:37:53.000Z (over 1 year ago)
Default Branch: main
Last Pushed: 2024-07-29T16:10:37.000Z (4 months ago)
Last Synced: 2024-07-29T21:35:30.992Z (4 months ago)
Language: Python
Size: 1.61 MB
Stars: 2
Watchers: 6
Forks: 2
Open Issues: 5
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

        


 NiftyOne 


![Python3](https://img.shields.io/badge/python->=3.10-blue.svg)

[![codecov](https://codecov.io/gh/childmindresearch/niftyone/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/niftyone)

[![stability-alpha](https://img.shields.io/badge/stability-alpha-f4d03f.svg)](https://github.com/mkenney/software-guides/blob/master/STABILITY-BADGES.md#alpha)

[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)

[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/childmindresearch/niftyone/blob/main/LICENSE)

![NiftyOne Mosaic](.github/static/niftyone_mosaic_view.png)



NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets,

leveraging features of [FiftyOne] with popular neuroimaging python packages.

## Installation

> [!TIP]

> For stability, NiftyOne should be installed in its own environment. For example, to

> install NiftyOne using `conda`:

>

> ```sh

> conda create -y -n niftyone python=3.10

> conda activate niftyone

> ```

NiftyOne can be installed using pip:

```sh

pip install -U pip

pip install git+https://github.com/childmindresearch/niftyone.git

```

> [!IMPORTANT]

> [FFmpeg] is a non-Python dependency required for NiftyOne.

> Please refer to their documentation for installation instructions.

## Usage

To get started, try using the boilerplate command:

```sh

niftyone   

```

> [!TIP]

> To see all arguments, run:

>

> ```sh

> niftyone --help

> ```

### Quick-start

1. Generate figures for each participant

    ```sh

    niftyone   participant

    ```

2. Collect participant figures into a compatible dataset

    ```sh

    niftyone   group

    ```

3. Launch FiftyOne app

    ```sh

    niftyone   launch

    ```

## Contributing

Contributions to NiftyOne are welcome! Please refer to the

[Contributions] page for information on how to contribute, report issues, or submit

pull requests.

## License

NiftyOne is distributed under the [MIT license].

## Support

If you encounter any issues or have questions, please open an issue on the

[issue tracker].

[FiftyOne]: https://docs.voxel51.com/

[FFmpeg]: https://ffmpeg.org/

[Contributions]: https://github.com/childmindresearch/niftyone/blob/main/CONTRIBUTING.md

[MIT license]: https://github.com/childmindresearch/niftyone/blob/main/LICENSE

[issue tracker]: https://github.com/childmindresearch/niftyone/issues