Dynamic Shimming

In this tutorial, we will learn the following:

  • Launch Shimming-Toolbox's GUI

  • Create a fieldmap

  • Create a mask

  • Perform dynamic shimming

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

Launch the plugin

In your terminal, run the command:

shimming-toolbox

Then, open Shimming Toolbox plugin:

Settings --> OrthoView --> Shimming Toolbox

The plugin should open as a new panel in FSLeyes.

Create a Fieldmap

  • 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 from the overlay and click the Input Phase 1 button.

  • Select the first magnitude image in the overlay and click the Input Magnitude.

  • (Optional) Change the output file and folder by clicking on Output File.

  • Click Run.

  • The output fieldmap should load automatically.

Create a Mask

  • Load the target anatomical 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 from the overlay, 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 140, 124, 6 and a size of 30, 15, 12 could work.

  • (Optional) Change the output file and folder by clicking on Output File.

  • Click Run.

  • The output mask should load automatically.

Dynamic shimming

  • Navigate to the B0 Shim Tab.

  • Select Dynamic in the dropdown menu (it should already be selected by default).

  • Select the fieldmap from the overlay, click the button Input Fieldmap.

  • Select the target anatomical image, click the button Input Anat.

  • Select the mask, click the button Input Mask.

  • Select a Slice Ordering of Sequential (should be the default).

  • 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.