NHP Diffusion Processing (nhp-dwiproc)

nhp-dwiproc is a BIDS application, leveraging NiWrap to perform processing of diffusion MRI data. While primarily built to process non-human primate (NHP), it is a species-agnostic pipeline that can also be used to process other datasets (e.g. human). The application aims to provide robust and reproducible workflows across various processing stages (e.g. preprocessing, tractography, etc.) with compatibility across different acquisition protocols.

Warning

Indexes generated with v0.1.x are incompatible with v0.2.x+, as well as latest development versions.

Tools

The following non-Python neuroimaging tools are used throughout the workflows.

Tool	Version
ANTs	2.5.3
c3d	1.1.0
FSL	6.0.4
Greedy	1.0.1
Mrtrix3	3.0.4
Mrtrix3Tissue	5.2.8

Note

• Mrtrix3Tissue is only required for processing single-shell data.

Installation

You can install the latest stable version of nhp-dwiproc using pip:

pip install git+https://github.com/HumanBrainED/nhp-dwiproc@v0.2.0

Usage

To get started, try the following command:

nhp_dwiproc --help

Documentation

For detailed application information, including advanced usage, please visit the documentation page.

Contributing

Contributions to nhp-dwiproc are welcome! Please refer to Contributions page for information on how to contribute, report issues, or submit pull requests.

License

nhp-dwiproc is distributed under the MIT license. See the LICENSE file for details.

Support

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