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FSLeyes Plugin for Shimming Toolbox

This plugin allows users to integrate NeuroPoly's shimming-toolbox application with the FSLeyes GUI. You can read the Shimming Toolbox Documentation for more information, or view the Shimming Toolbox GitHub Repo to see the source code.


In the fsleyes-plugin-shimming-toolbox folder, run:

make install


Now, you can open the FSLeyes GUI from any environment by running:


The FSLeyes GUI should open. Once it is open, select from the toolbar:

Settings --> OrthoView --> Shimming Toolbox

The ShimmingToolbox plugin should open as a panel.

Developer Section

Testing with Docker

We can use Docker to spin up a Linux instance and test our install procedure in a clean environment. You will need to install Docker on your computer first:

To create our testing container, we will first build an image called fpst:latest:

docker build --tag fpst:latest .

Once our image is built, we want to remove any running instances of the container:

docker rm --force fpst

Then, we can create a container from our fpst:latest image:

docker run --name fpst -dit fpst:latest

To test our package, we can use the bash function of the container:

docker exec -it fpst bash

Once inside the container terminal, we can find our plugin package and test it:

cd src/fsleyes-plugin-shimming-toolbox
make install


docker rm --force fpst
docker build --tag fpst:latest .
docker run --name fpst -dit fpst:latest
docker exec -it fpst bash

If you want to test the plugin on arm and you are using an M1/M2 mac, use the following commands:

docker rm --force fpst
docker build --platform linux/amd64 --tag fpst:latest .
docker run --name fpst -dit fpst:latest
docker exec -it fpst bash

Testing with VirtualBox

To test on different operating systems, you will need to use a virtual machine. You will need to install VirtualBox: You will also need to install the Oracle VM VirtualBox Extension Pack in order to test MacOSX.

Vagrant is a tool that interfaces with VirtualBox and streamlines the process:

We have 3 different folders with Vagrantfiles for testing each OS:

| testing
| -- vagrant_linux/
| -- vagrant_mac/
| -- vagrant_windows/

To create the virtual box, run:

cd testing/vagrant_{OS}
vagrant up

Next, ssh into the shell and run the fsleyes-plugin-shimming-toolbox installer:

cd src/fsleyes-plugin/shimming-toolbox/
sudo make install
source /Users/vagrant/.bashrc

To convert the install to an editable developer install:

source /Users/vagrant/shimming_toolbox/python/etc/profile.d/
sudo pip3 install -e .

GUI in VirtualBox

Currently this is only functional for the Mac VirtualBox. When you run vagrant up, a GUI should open. When you see the login screen, enter:

user: vagrant
password: vagrant

You can open a terminal from this GUI, and run FSLeyes by:

cd src/fsleyes-plugin/shimming-toolbox/

Vagrant Tips

To stop the box from running (but not remove it):

vagrant suspend

To resume the box:

vagrant resume

To remove the box completely:

vagrant destroy

If you update your Vagrantfile and you want to reload the box:

vagrant reload


Fsleyes plugin for Shimming-Toolbox







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