process-3T-MRI-data: the MRIMate library

This is a Python library for processing par/rec MRI data. So far it is specific to the V-10 3T Philips scanner.

Features

• Process par/rec MRI data into spin density and/or phase/velocity images.
• Access experiment parameters, check units/information, etc. I still need to finish updating the definition of the different parameters.
• Data can be exported to hdf5 (still need to test if the h5 was written correctly).
• Processed data can be plotted. For now only 2D or MS experiments.

Quickstart

A Linux distribution is required. For windows users we reccomend following the wiki guide on how to install a Windows Linux Subsystem.

1. Create a Virtual Environment: you can use venv or poetry for example. venv is a bit easier to use in my opinion.

   cd your_project_directory
   python3 -m venv myenv
   source myenv/bin/activate

   Install packages within the virtual environment using pip. Deactivate the environment when finished:

   deactivate

2. Integrate with Jupyter Notebook in VSCode: Install ipykernel and load the environment to the notebook.

   pip install ipykernel
   python -m ipykernel install --user --name=myenv --display-name "Python (myenv)”

3. Install the MRIMate library

   pip install git+https://collaborating.tuhh.de/v-10/private/data-evaluation/MRImate.git
   

4. Check the quick demo notebook to learn how to use it.

Credits

Raquel - [email protected] This package was created with Cookiecutter and the fedejaure/cookiecutter-modern-pypackage project template.