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kaitj / nhp-dwiproc

BIDS app for performing diffusion processing on NHP dataset(s)
MIT License
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NHP Diffusion Processing
(nhp-dwiproc)

![Python3](https://img.shields.io/badge/python->=3.11-blue.svg) [![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) ![stability-stable](https://img.shields.io/badge/stability-experimental-orange.svg) [![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/kaitj/nhp-dwiproc/blob/main/LICENSE) [![Documentation](https://img.shields.io/badge/documentation-8CA1AF?logo=readthedocs&logoColor=fff)](https://kaitj.github.io/nhp-dwiproc)

nhp-dwiproc is an application, leveraging features of NiWrap and Styx to perform processing of non-human primate (NHP) diffusion datasets. The application aims to provide flexible, reproducible workflows for various stages of processing (e.g. preprocessing, tractography, etc) across various acquisition protocols.

Requirements

You will need the following pre-requisites:

Tool Version
Python 3.11+
ANTs 2.5.3
c3d 1.1.0
FSL 6.0.5
Greedy 1.0.1
Mrtrix3 3.0.4
Mrtrix3Tissue 5.2.8

!Note is only required if processing single-shell data.

Installation

You can install nhp-dwiproc using pip:

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

For additional details, please consult the documentation.

Usage

To get started, try using the boilerplate command:

nhp_dwiproc <bids_directory> <output_directory> <processing_stage>

To see all arguments, run:

nhp_dwiproc --help

Documentation

For detailed application information, including advanced usage, please visit our documentation

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