MRI-Toolkit

MRI-toolkit provides a set of features dedicated to MRI data post-processing and analysis.

The implementation is inspired by gMRI2FEM, and some of the code is taken from that project. However, MRI-toolkit is designed to be more modular and extensible, with a focus on providing a user-friendly command-line interface (CLI) for common MRI processing tasks.

Installation

pip install mritk

Documentation

The documentation is available at https://scientificcomputing.github.io/mri-toolkit/. It includes detailed usage instructions, API references, and examples.

Quick Start

To get started with mri-toolkit, you can use the command-line interface (CLI) to inspect and analyze your MRI data.

Features

• File Inspection: detailed NIfTI header analysis (affine, voxel size, shape).

• $T_1$ Mapping: Estimate $T_1$ relaxation times using Look-Locker or Mixed sequences, and seamlessly merge them into comprehensive Hybrid $T_1$ maps.

• $R_1$ Relaxation Rates: Convert $T_1$ maps into $R_1$ relaxation rate maps for linear scaling with tracer concentrations.

• Concentration Mapping: Calculate the spatial distribution of contrast agents (e.g., gadobutrol) utilizing pre- and post-contrast $T_1$ or $R_1$ maps.

• Statistics: Compute comprehensive statistics (volume, mean, median, std, percentiles) for MRI regions based on segmentation maps.

• Visualization:

  • Terminal: View orthogonal slices (Sagittal, Coronal, Axial) directly in your console.

  • Napari: Launch the Napari viewer for interactive 3D inspection.

• Data Management: Utilities to download datasets.

Contributing

Contributions to MRI-toolkit are welcome! If you have an idea for a new feature, improvement, or bug fix, please open an issue or submit a pull request on GitHub. For more details on how to contribute, please see the Contributing Guide.

License

MRI-toolkit is licensed under the MIT License. See the LICENSE file for more information.