In this tutorial, we will learn the following:
- Launch
Shimming-Toolbox
's GUI - Create a fieldmap
- Create a mask
- Perform dynamic shimming
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
Then, open Shimming Toolbox
plugin:
Settings --> OrthoView --> 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 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.
- 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.
- 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.
- 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.