Multidimensional RF Pulse Design with Consideration of Concomitant Field Effects

Code for generating simulation results for the original and proposed methods in this paper: Ziwei Zhao, Nam G. Lee, Krishna S. Nayak. "Multidimensional RF Pulse Design with Consideration of Concomitant Field Effects". Submitted to Mag. Reson. Med. 2024

Set up

Initialization

set up the path

• Please modify line 3 of ./sim/setup_path.m to declare the root path where the main folder multi_RF is located.

compile .c files

• Please compile bloch.c and bloch_maxwell.c scripts under ./third_party/Bloch_simulator by using mex command in the MATLAB commanding window.

Code Structure

Figures:

• To reproduce Figure 2, please run ./figures/sim_results/Fig2_validation/mrm_figure2.m.
  • To generate the excitation profiles (.mat files), please use MATLAB script ./sim/sim_concomitantfield_approx.m
• To reproduce Figure 3, please run ./figures/sim_results/Fig3_distance/mrm_figure3_distance.m.
  • To generate the excitation profiles (.mat files), please use MATLAB script ./figures/sim_results/Fig3_distance/generate_matfiles_scripts_fig3.m
• To reproduce Figure 4, please run ./figures/sim_results/Fig4_field_strength/mrm_figure4_fieldstrength.m.
  • To generate the related excitation profiles (.mat files), please use MATLAB script ./figures/sim_results/Fig4_field_strength/generate_matfiles_scripts_fig4.m
• To reproduce Figure 5 (A), please run ./figures/sim_results/Fig5_phantom_055T/mrm_figure5A_tailored_b0b1.m.
  • To generate the related excitation profiles (.mat files), please use MATLAB script ./figures/sim_results/Fig5_phantom_055T/generate_matfiles_script_fig5.m
• Supporting Figure S1 was generated inside the function ./sim/sim_concomitantfields_8channel.m with the setting display_figure = true.
• Supporting Figure S2 was generated using ./figures/sim_results/FigS2_duration/mrm_sup_figure2_duration.m.
  • To generate the related excitation profiles (.mat files), please use MATLAB script ./figures/sim_results/FigS2_duration/generate_matfiles_scripts_sup_fig2.m

Main simulation functions:

• sim_concomitantfield_approx.m generates concomitant field accuracy results (Figure 2).
• sim_concomitantfields_8channel.m computes the excitation profiles using original and proposed methods at different isocenter, different main field strengths, different T2 values, and different undersampling foctor of the designed RF pulses using 8 channel setups. The resulting excitation profiles are saved as .mat format.
• sim_concomitantfields_1channel.m computes the excitation profiles using original and proposed methods at different isocenter using 1 channel setups. The resulting excitation profiles are saved as .mat format.

B0, B1+ and GIRF measurement datasets:

• GIRF measurements at 0.55T are provided in ./b0b1_map_055T/GIRF_20200221_Duyn_method_coil2.mat
• B0, B1+ maps with masks at 0.55T with different isocenter (0, 5, 10, 15cm) are provided in ./b0b1_map_055T folder.
• ./b0b1_map_055T/gene_b0_map_flash3d.mat is used to estimate a B0 map from flash_2d images using linear fitting method.

2D Spin echo sequence:

• ./seq/demo_pulseq_Pauly_1989_JMR_modified.mat generates the 2D single slice spin echo sequence in Pulseq .seq file with the excitation RF replaced with the designed RF pulse.

Other functions:

• ./sim/funcs/STA_maxwell_system_matrix_con.m calculates a small-tip-angle system matrix with the consideration of concomitant fields during the iterative RF design (proposed method).
• ./sim/funcs/STA_maxwell_system_matrix.m calculates a small-tip-angle system matrix without the consideration of concomitant fields during the iterative RF design (original method).
• ./sim/funcs/figure_out_transformation_matrix.m and ./sim/funcs/geometry folder outputs the coordination transformation matrix that is used in the application of GIRF at 0.55T.
• ./sim/funcs/apply_GIRF_tx.m calculates the GIRF-corrected trajectory.
• ./sim/funcs/calcgradinfo.m calculates the kspace trajectory from the input gradient waveforms.
• ./seq/input_pulseq_cartesian_spin_echo_multi_RF.m saves sequence parameters that is used in the pulseq file.
• ./seq/calculate_cartesian_spin_echo_imaging_parameters.m calculates basic sequence parameters and define gradient performance at 0.55T that are used in the pulseq file.

Dependencies

reVERSE_GIRF by Shaihan Malik, July 2015.

Phase_relaxed_CPMG_excitation by Shaihan Malik, July 2015.

lsqrSOL for solving a linear non-square matrix problem.

Bloch_simulation by Brian Hargreaves.

pulseq by University Medical Center Freiburg.

MATLAB Dependencies

To make sure the code is able to run, the following toolboxes need to be installed: MATLAB Optimization Toolbox Signal Processing Toolbox Image Processing Toolbox MATLAB Coder

Citing

Zhao Z, Lee NG, Nayak KS. Multidimensional RF Pulse Design with Consideration of Concomitant Field Effects. Magn Reson Med. xxx

License

The Multi_RF packaged code is licensed under a 3-Clause BSD License.

Contact

If you have any questions, please contact [email protected]

Ziwei Zhao, University of Southern California, MREL (Magnetic Resonance Engineering Laboratory, PI: Krishna S. Nayak, https://mrel.usc.edu/) May 2024.