Installation

Shimming Toolbox is written in Python. It can be used either from the Terminal or from a graphical user interface (GUI) as a plugin for FSLeyes.

Overview

Dependencies

Shimming Toolbox works on macOs and Linux operating systems. There is a plan to support Windows in the future.

Optional dependencies:

  • If you would like to use prelude for phase unwrapping and/or bet for brain extraction, you need to install FSL.

  • If you would like to use sct_deepseg_sc for spinal cord segmentation, you need to install SCT.

Installation

The installer will automatically install:

  • FSLeyes

  • Shimming Toolbox

  • dcm2niix

Note

The installer will install FSLeyes and dcm2niix into isolated environments. They will be used by Shimming Toolbox and will not interfere if you already have FSLeyes or dcm2niix installed. If you have previously installed FSLeyes, it will not support the GUI.

Open a Terminal and run the following commands.

First, download the FSLeyes plugin:

git clone https://github.com/shimming-toolbox/fsleyes-plugin-shimming-toolbox.git

Next, run the installer:

cd fsleyes-plugin-shimming-toolbox
make install

You will be prompted to source your .*shrc file. For example:

source ~/.bashrc

Note

You can restart your terminal or open a new tab to source your .*shrc file automatically.

The shimming-toolbox command launches FSLeyes with GUI support.

shimming-toolbox

To launch our plugin, go to:

Settings --> OrthoView --> Shimming Toolbox
Overview

The plugin should open as a panel.

Overview

Test the Installation

This step is optional but it's a good measure to ensure Shimming Toolbox is properly installed on your system.

Comprehensive Test

To run the entire testing suite, run pytest from the cloned shimming-toolbox directory:

cd ~/shimming-toolbox/shimming-toolbox
source $HOME/shimming-toolbox/python/etc/profile.d/conda.sh
conda activate ~/shimming-toolbox/python/
pytest

See https://docs.pytest.org/ for more options.

If all tests pass, Shimming Toolbox is properly installed.

Testing subsets of soft dependencies

prelude is a soft dependencies, so you may wish to run the parts of the testing suite that do not depend on it.

To test shimming-toolbox without prelude:

cd ~/shimming-toolbox/shimming-toolbox
source $HOME/shimming-toolbox/python/etc/profile.d/conda.sh
conda activate ~/shimming-toolbox/python/
pytest -m "not prelude"

To test only the parts of shimming-toolbox dependent on prelude, the corresponding -m argument is "prelude"

For Developers

The installation files can be found in the installer folder, and are called by the Makefile.

When you run make install, we first check if the ST_DIR exists, or if a clean install has been requested. The ST_DIR is where the shimming-toolbox package and also the fsleyes-plugin-shimming-toolbox are installed. By choosing clean, you delete the entire install directory, and consequently any prior installs of shimming-toolbox or fsleyes-plugin-shimming-toolbox. Note that this is set to CLEAN==false by default.

We next check if conda has been installed into the ST_DIR. If not, we run the conda installer.

Next, we create a virtual environment for fsleyes-plugin-shimming-toolbox and install the package into it.

Finally, we create a virtual environment for shimming-toolbox and install the package into it.

Note

You can track the Github version of shimming-toolbox if you are a developer. This will remove any previous install of shimming-toolbox, and replace it with the version you have cloned. Note that this may break the plugin since you are using a version that has not been tested on the plugin. You can install shimming-toolbox development version with the following steps:

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

You will be prompted to source your .*shrc file. For example:

source ~/.bashrc

You can then activate the shimming-toolbox environment and start coding!

source $HOME/shimming-toolbox/python/etc/profile.d/conda.sh
conda activate ~/shimming-toolbox/python/