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.
Dependencies
Shimming Toolbox works on macOs and Linux operating systems. There is a plan to support
Windows in the future.
Optional dependencies:
Installation
The installer will automatically install:
FSLeyesShimming Toolboxdcm2niix
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
The plugin should open as a panel.
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/