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.
Important
Indexes generated with v0.1.x are incompatible with v0.2.x+, as well as latest
development versions.
The following tools are used throughout the workflows.
| Tool | Version |
|---|---|
| Python | 3.11+ |
| 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
- Neuroimaging tools (e.g. ANTs) only need to be installed if workflows are run without the use of containers
- If you are using Singularity or Apptainer, containers need to first be downloaded
- Mrtrix3Tissue is only required if processing single-shell data.
You can install the latest stable version of nhp-dwiproc using pip:
pip install git+https://github.com/HumanBrainED/nhp-dwiprocTo get started, try the following command:
nhp_dwiproc --helpFor detailed application information, including advanced usage, please visit the documentation page.
Contributions to nhp-dwiproc are welcome! Please refer to Contributions page for
information on how to contribute, report issues, or submit pull requests.
nhp-dwiproc is distributed under the MIT license. See the LICENSE file for details.
If you encounter any issues or have questions, please open an issue on the issue tracker