NiftyOne

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:

conda create -y -n niftyone python=3.10
conda activate niftyone

NiftyOne can be installed using pip:

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:

niftyone <bids_directory> <output_directory> <analysis_level>

Tip

To see all arguments, run:

niftyone --help

Quick-start

1. Generate figures for each participant

   niftyone <bids_directory> <output_directory> participant

2. Collect participant figures into a compatible dataset

   niftyone <bids_directory> <output_directory> group

3. Launch FiftyOne app

   niftyone <bids_directory> <output_directory> 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.