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
Note
The installer will install Shimming Toolbox
, FSLeyes
and dcm2niix
into an isolated environment. They will not interfere if you already have FSLeyes
or dcm2niix
installed. If you
have previously installed FSLeyes
, that version 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/