Mrd2nii

Overview

Mrd2nii converts ISMRMRD data into NIfTI images with BIDS metadata.

Features

• Convert spatial images
• Convert raw data (currently not supported)
• Convert waveforms (currently only respiratory data is supported)

Getting started

• Clone this repository and navigate to the project directory.

git clone https://github.com/shimming-toolbox/mrd2nii.git
cd mrd2nii

• Create a virtual environment or use an existing one.

python -m venv mrd2nii_venv
source mrd2nii_venv/bin/activate  # On Windows: mrd2nii_venv\Scripts\activate

• Install mrd2nii in the virtual environment.

pip install .

Usage

On the command line, run the following command to display the full list of options

mrd2nii -h

> Usage: mrd2nii [OPTIONS]
> 
> Options:
>   -i, --input PATH   Input path to MRD folder/file  [required]
>   -o, --output PATH  Path to output folder  [required]
>   -h, --help         Show this message and exit.

If you run into any issues, please report them in the GitHub Issues

Development

Download the full suite of tests:

TODO

Run tests and checks from the project root.

pytest