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Installation

Basic Installation

You can install the package directly from pypi using pip:

pip install mritk

Note that it is recommended to use a virtual environment when installing the package, to avoid conflicts with other packages. You can create a virtual environment using venv:

python3 -m venv venv
source venv/bin/activate  # On Windows, use `venv\Scripts\activate`
pip install mritk

Installing extra dependencies

Some features of mritk require additional dependencies. You can install these extra dependencies using pip with the appropriate extras syntax.

  • The show command: To use the show command for visualizing MRI data in the terminal, you need to install the textual-image, pillow and matplotlib packages. You can do this with the following command:
pip install mritk[show]
  • The napari command: To use the napari command for visualizing MRI data in the Napari viewer, you need to install the napari package. You can do this with the following command:
pip install mritk[napari]

Development Installation

If you want to contribute to the development of mritk, you can install the package in editable mode. This allows you to make changes to the source code and have them reflected immediately without needing to reinstall the package (see also the Contributing guide for more info).

git clone https://github.com/scientificcomputing/mri-toolkit.git
cd mri-toolkit
python3 -m venv venv
source venv/bin/activate  # On Windows, use `venv\Scripts\activate`
pip install -e .

It is also possible the package directly from GitHub without cloning the repository:

pip install git+https://github.com/scientificcomputing/mri-toolkit.git

Installation with pipx

If you intend to use the command line interface, you may want to install the package in an isolated environment using pipx. You can do this with the following command:

pipx install mritk