Shell scripts

A good way to get started is looking at one of the examples scripts.

demo_realtime_shimming.sh

This shell script calls different shimming-toolbox command lines functions to perform a whole shimming scenario. Acquisitions are downloaded from a Github repository and output text files and quality control figures are generated.

This function will generate static and dynamic (due to respiration) Gx, Gy, Gz components based on a field map time series (magnitude and phase images) and respiratory trace information obtained from Siemens bellows. An additional multi-gradient echo (MGRE) magnitude image is used to generate a ROI. The static and real-time components are extracted and decomposed into the optimal Gx, Gy and Gz values for each slice.

B1+ shimming

This shell script calls different command lines functions to perform static B1+ shimming. Text files, scaled B1 maps and result figures are generated in the testing-data folder. In this example, a magnitude least square algorithm is used to target a B1+ value specified by the user. This scenario assumes that the B1 maps have already been converted into NIfTI files.