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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.

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