Dynamic Shimming Tutorial

In this tutorial, we will learn the following:

Download test data

Open a Terminal and download this small dataset by running the following command:

st_download_data data_dynamic_shimming

Go to the dataset folder:

cd data_dynamic_shimming

In your terminal, run the command:

shimming-toolbox

The plugin should open as a new panel in FSLeyes.

Load the phase echo(es) and the first magnitude NIfTI files in FSLeyes.
- data_dynamic_shimming/sub-spine/fmap/sub-spine_magnitude1.nii.gz
- data_dynamic_shimming/sub-spine/fmap/sub-spine_phase2.nii.gz
Navigate to the Fieldmap Tab. If you don't see the tab, drag the right edge of the Shimming Toolbox panel to make all the tabs appear.
Enter 1 for the Number of Echoes.
Select the phase image in the overlay (sub-spine_phase2) and click the Input Phase 1 button.
Select the first magnitude image in the overlay (sub-spine_magnitude1) and click the Input Magnitude.
Select the unwrapper you wish to use. Select skimage if you do not have prelude installed (External dependency: FSL).
(Optional) Change the output file and folder by clicking on Output File.
Click Run.
The output fieldmap should load automatically.

Load the target image.
- data_dynamic_shimming/sub-spine/anat/sub-spine_unshimmed_e1.nii.gz
Select The Mask Tab.
Select Box from the dropdown.
Select the target image in the overlay (sub-spine_unshimmed_e1), then click the button Input.
Input voxel indexes for center and size. TIP: Look at the Location panel of fsleyes to locate the center of the ROI.
- For the spine, a center of 128, 124, 6 and a size of 30, 15, 12 could work.
- TIP: You can use external tools such as Spinal Cord Toolbox (SCT) to create spinal cord masks automatically.
(Optional) Change the output file and folder by clicking on Output File.
Click Run.
The output mask should load automatically.

Navigate to the B0 Shim Tab.
Select Dynamic in the dropdown menu (it should already be selected by default).
Select the fieldmap in the overlay and click the button Input Fieldmap.
Select the target image in the overlay (sub-spine_unshimmed_e1), then click the button Input target.
Select the mask in the overlay and click the button Input Mask.
Select a Slice Ordering of Ascending.
Select a Slice Factor of 1 (should be the default).
Select a Scanner Order of 1. It means that dynamic shimming will be performed with the linear gradients of the scanner. In typical scanners, order 2 or higher is not compatible with dynamic shimming, due to the high inductance of the shim coils (they cannot be updated as rapidly as the gradient coils).
(Optional) Change the output folder by clicking the Output Folder button.
Click Run.
The output text files and figures should be in the Output Folder. You can then copy the text files onto the MRI console to be read by the pulse sequence.