Static B1+ shimming

Warning

This tutorial only covers static B1+ shimming applications performed on Siemens scanners. Shimming-Toolbox currently only handles B1+ maps acquired using Siemens' standard TurboFLASH B1+ mapping sequence. This is the tfl_rfmap sequence, which can be found under Siemens/Service Sequences in the Protocols. Not to be confused with the tfl_b1map sequence, which will not create the channel-specific B1+ maps necessary for the shim process.

Download test data

From your terminal, "cd" to any folder and run:

st_download_data data_b1_shimming

This will download the example B1+ maps dataset in the folder from which you typed this command.

Start the GUI of Shimming Toolbox

In your terminal, run:

shimming-toolbox

The plugin should open as a new panel in FSLeyes.

Convert DICOM to NIfTI

In FSLeyes, click on the dicom_to_nifti tab.

Note

If you don't see the tab, drag the right edge of the Shimming Toolbox panel to make all the tabs appear.

  • Click on Input Folder to select the downloaded data_b1_shimming/dicoms path as an input.

  • Enter a subject name (e.g. "test").

  • Modify the output folder path a new folder called "niftis" in the previously downloaded "data_b1_shimming" folder: <your-local-path>/data_b1_shimming/niftis.

  • Click Run.

  • A B1+ map should automatically load in the overlay.

Create a Mask

In an actual experiment, a mask would probably be created from an anatomical image using a segmentation tool. However, in this tutorial, we will create a simple box mask from the B1+ acquisition. Since the B1+ acquisition has complex 4D B1+ data, we first convert it to a magnitude image and compute the average over the last dimension so that it can be used by the masking pipeline. We are then ready to create a box mask from that 3D image.

In your terminal where you downloaded the b1 dataset, run:

st_maths mag --complex data_b1_shimming/niftis/sub-test/rfmap/sub-test_TB1map_uncombined.nii.gz --output data_b1_shimming/niftis/derivatives/sub-test_TB1map_uncombined_mag.nii.gz
st_maths mean --input data_b1_shimming/niftis/derivatives/sub-test_TB1map_uncombined_mag.nii.gz --output data_b1_shimming/niftis/derivatives/sub-test_TB1map_uncombined_mean.nii.gz

  • Load the data_b1_shimming/niftis/derivatives/sub-test_TB1map_uncombined_mean.nii.gz image in FSLeyes (drag and drop).

  • Select the Mask Tab.

  • Select Box from the dropdown.

  • Select the sub-test_TB1map_uncombined_mean image from the overlay, click the button Input.

  • Input voxel indexes for center (suggestion: 48, 48, 19) and size (suggestion: 35, 50, 12). Look at the Location panel of FSLeyes to locate the center of the ROI.

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

  • Click Run.

  • The output mask should load automatically in the Overlay list.

Static B1+ shimming: CV reduction

(Optional) The SarDataUser.mat is a hard requirement for the "SAR efficiency" shim option, and an optional requirement for CV reduction. To ensure that the SarDataUser.mat on the scanner contains the VOPs of the coil currently being used, create a copy of the anatomical scan used to create the mask, and start the scan. The scan can be stopped once data acquisition starts. In the Exam Card, under System/pTx Volumes, set the B1 shim mode to "Patient Specific". See the figure below for the location of the switch

B1 shim option location

Copy the SarDataUser.mat file from C:/Medcom/MriProduct/PhysConfig/ to the laptop on which Shimming Tooolbox is run

  • Navigate to the B1+ Shim Tab.

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

  • Select the uncombined B1+ maps from the overlay, click the button Input B1+ map.

  • Select the mask, click the button Input Mask.

  • (Optional) If you have a SarDataUser.mat VOP file, you can locate it after clicking on input VOP file. You can then adjust the SAR factor to indicate by how much your optimized shim weights might exceed the max local SAR of a phase only shimming.

  • Click Run.

  • The output text file containing the shim weights should be in the Output Folder.

  • Manually input these shim weights on the scanner console. On Siemens scanners, input them in the Options > Adjustments > B1 Shim window. Make sure to also set System > pTx Volumes > B1 Shim mode to "Patient-specific" in the sequence parameters to ensure that the shim-weights will be applied during the acquisition.