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Preparation Modules

OpenMRF is a modular framework. All magnetization preparation and readout modules are implemented as Matlab structs and follow a similar structure. The following information provides an overview of all magnetization preparations that are currently available in OpenMRF. The source code can be found in include_pulseq_toolbox/src_preparations.

Overview

Module Name Long Name Notes
ADIASL ADIAbatic Spin Lock Defines an adiabatic spin-lock module for T1\(\rho\) preparation
CEST Chemical Exchange Saturation Transfer Work in progress. Currently, you can encode CEST contrast; however, the dictionary calculation needs an update for Bloch-McConnell simulation.
CRUSH CRUSHer Crusher gradients are necessary for all magnetization preparations.
FAT FAT Suppression Fat suppression is used for abdominal and cardiac MRF sequences.
INV INVersion Inversion recovery preparation module.
MLEV Malcolm LEVitt Preparation module based on MLEV phase cycling; can be used as an alternative for robust T2 encoding or for encoding T2\(\rho\) contrast.
SAT SATuration Saturation recovery preparation module.
SL Spin Lock Defines a continuous-wave spin-lock module for T1\(\rho\) preparation.
T2 T2 preparation Conventional T2 preparation module.

The ..._init() function

Before magnetization preparations can be added to a sequence, all preparation modules have to be initialized. The first step is to create the struct (e.g. INV) and choose your parameters (e.g. INV.tExc = 0.01). Second, the respective ..._init() function is called, with the respective struct as the first input argument. You do not have to define all parameters of the module yourself - optional parameters have default values that will be assigned by the ..._init() function unless specified explicitly. When in doubt, just look at the source code of the module in question.

Multiple instances of the same preparation module

If you are planning to add multiple instances of the same magnetization preparation module with different preparation times (as often done in cardiac and abdominal MRF), you can initialize them all at once by making the respective field (e.g. inversion times) an array instead of a single value. See the examples below.

Examples

The inversion recovery module uses, by default, a hyperbolic sechans inversion pulse calculated via sigpy. Optionally, the inversion recovery times can be an array. 

INV.rf_type      = 'HYPSEC_inversion';
INV.tExc         = 10 *1e-3;  % [s]  hypsech pulse duration
INV.beta         = 700;       % [Hz] maximum rf peak amplitude
INV.mu           = 4.9;       % [ ]  determines amplitude of frequency sweep
INV.inv_rec_time = [15 75 150 250] *1e-3;
INV = INV_init(INV, FOV, system);

The saturation recovery preparation uses, by default, a B1-Insensitive-Rotation pulse calculated via sigpy. Optionally, the saturation recovery times can be an array. 

SAT.mode         = 'on';
SAT.rf_type      = 'adiabatic_BIR4';
SAT.bir4_tau     = 10 *1e-3;  % [s]  bir4 pulse duration
SAT.bir4_f1      = 640;       % [Hz] maximum rf peak amplitude
SAT.bir4_beta    = 10;        % [ ]  am waveform parameter
SAT.bir4_kappa   = atan(10);  % [ ]  fm waveform parameter
SAT.bir4_dw0     = 30000;     % [rad/s] fm waveform scaling
SAT.sat_rec_time = [100 200] *1e-3; % [s] saturation times
SAT = SAT_init(SAT, FOV, system);

The T2 preparation uses, by default, two B1-Insensitive-Rotation pulses calculated via sigpy and a two-composite-refocusing-block pulse scheme. Optionally, the T2 preparation times can be an array. 

T2.exc_mode   = 'adiabatic_BIR4';
T2.rfc_dur    = 2 *1e-3;   % [s]  duration of composite refocusing pulses
T2.bir4_tau   = 10 *1e-3;  % [s]  bir4 pulse duration
T2.bir4_f1    = 640;       % [Hz] maximum rf peak amplitude
T2.bir4_beta  = 10;        % [ ]  am waveform parameter
T2.bir4_kappa = atan(10);  % [ ]  fm waveform parameter
T2.bir4_dw0   = 30000;     % [rad/s] fm waveform scaling
T2.prep_times = [40 80] * 1e-3;  % [s] inversion times
T2            = T2_init(T2, FOV, system);

The spin-lock preparation can be used for T1\(\rho\), T2\(\rho\), or T2. By default, the Balanced Spin-Lock preparation is used. The default excitation and refocusing pulses are adiabatic half-passage pulses. Optionally, spin-lock times and amplitudes can be arrays. 

% spin-lock pulses
SL.relax_type = {'T1p'};         % T1p or T2p or T2
SL.seq_type   = {'BSL'};         % BSL or CSL or RESL
SL.tSL        = [40 80] *1e-3;   % [s]  SL time
SL.fSL        = [200 200];       % [Hz] SL amplitude

% excitation pulses
SL.exc_mode  = 'adiabatic_AHP';  % 'adiabatic_AHP', 'sinc', 'sigpy_SLR' or 'bp'
SL.exc_time  = 3.0 *1e-3;        % [s] excitation time
SL.adia_wmax = 600 * 2*pi;       % [rad/s] amplitude of adiabatic pulse

% refocusing pulses
SL.rfc_mode = 'bp';              % 'bp', 'sinc', 'sigpy_SLR' or 'comp'
SL.rfc_time = 1.0 *1e-3;         % [s] refocusing time

SL = SL_init(SL, FOV, system);

The MLEV preparation can be used for T2 or T2\(\rho\) preparation. The original idea of MLEV phase cycling was already published in 1981. The concept of this implementation is explained here. The preparation uses, by default, adiabatic half passages for excitation. Refocusing is done using multiple composite block pulses, which have a symmetric phase-cycling scheme (e.g. + - - +). The number of refocusing pulses is always a multiple of 4. The interpulse delay is the delay between consecutive block pulses and defines the T2 weighting. However, MLEV preparations use many refocusing pulses, and during these pulses the magnetization will experience additional T2\(\rho\) weighting. If the interpulse delay is set to 0, the preparation will encode pure T2\(\rho\) contrast. The final preparation times are stored in MLEV.t2_prep_times and MLEV.t2p_prep_times. These are calculated in the init function and cannot be set directly. Choosing MLEV.n_mlev and MLEV.t_inter defines the final contrast weighting. MLEV.fSL defines the amplitude of the composite refocusing pulses and is equivalent to a spin-lock amplitude (e.g. 250 Hz leads to a 4 ms composite pulse). 

MLEV.n_mlev   = [1 2 4 8];       % number of MLEV4 preps, -> MLEV4 MLEV8 MLEV16 MLEV32
MLEV.fSL      = 250;             % [Hz] eff spin-lock field strength
MLEV.t_inter  = 1 *1e-5;         % [s]  inter pulse delay for T2 preparation
MLEV.exc_mode = 'adiabatic_AHP'; % 'adiabatic_BIR4' or 'adiabatic_AHP'
MLEV = MLEV_init(MLEV, FOV, system);

The adiabatic spin-lock preparation can be used to encode a contrast that is similar to T1\(\rho\); however, the value of the relaxation time will be considerably higher. Adiabatic spin-locking is currently under active research and might be an alternative to the conventional continuous-wave approach, since it improves robustness to field inhomogeneities. We recommend using a multiple of 4, since the preparation uses an MLEV-like phase-cycling pattern. Even numbers will generate magnetization along +z, and odd numbers will generate an inversion to -z. In the dictionary calculation, a constant adiabatic relaxation time is assumed. 

ADIASL.N_HS  = [4 8 12 16]'; % number of inversion pulses
ADIASL.tau   = 0.015;        % [s] duration of inversion pulse
ADIASL.f1max = 500;          % [Hz] peak amplitude of inversion pulse
ADIASL.beta  = 5;            % [ ] shape parameter
ADIASL.dfmax = 200;          % [ ] shape parameter
ADIASL       = ADIASL_init(ADIASL, FOV, system);

The ..._add() function

When building a sequence, instances of a module can be added using the respective ..._add() function. If your sequence features multiple instances of the same magnetization preparation module, a counter is increased automatically to ensure that each instance is added with the correct preparation time.

Tip

Take a closer look at main_sequences/fingerprinting/pulseq_mrf.m and main_sequences/fingerprinting/pulseq_cmrf.m to understand the use of magnetization preparation and readout modules.