NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets, leveraging features of FiftyOne with popular neuroimaging python packages.
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 niftyoneNiftyOne can be installed using pip:
pip install -U pip
pip install git+https://github.com/childmindresearch/niftyone.gitImportant
FFmpeg is a non-Python dependency required for NiftyOne. Please refer to their documentation for installation instructions.
To get started, try using the boilerplate command:
niftyone <bids_directory> <output_directory> <analysis_level>Tip
To see all arguments, run:
niftyone --help-
Generate figures for each participant
niftyone <bids_directory> <output_directory> participant
-
Collect participant figures into a compatible dataset
niftyone <bids_directory> <output_directory> group
-
Launch FiftyOne app
niftyone <bids_directory> <output_directory> launch
Contributions to NiftyOne are welcome! Please refer to the Contributions page for information on how to contribute, report issues, or submit pull requests.
NiftyOne is distributed under the MIT license.
If you encounter any issues or have questions, please open an issue on the issue tracker.