quantitative MR: Pulse sequence format

Currently coreMRI is based on .mat files (MATLAB files). All the coordinates are given in the Device Coordinate System (DCS). The .mat file should include the following variables:

dt: is the temporal step of the MR simulation experiment (in sec)

N_pulse: it holds the number of the total timesteps of the pulse sequence

pulse_sequence: it is an [8xN_pulse] matrix. The first row (pulse_sequence(1,:)) holds the time sequence of the magnitude of the RF events (B1), the second row (pulse_sequence(2,:)) holds the time sequence of the phase of the RF events (RFP), the third row (pulse_sequence(3,:)) holds the time sequence of the frequency of the RF events (RFfreq), the fourth row (pulse_sequence(4,:)) holds the time sequence of the gradients on the x axis, the fifth row (pulse_sequence(5,:)) holds the time sequence of the gradients on the y axis and the sixth row (pulse_sequence(6,:)) holds the time sequence of the gradients on the z axis. The last two rows are identical and each one is an array with increasing number from 1 to N_pulse (pulse_sequence(7,:) = 1:N_pulse and pulse_sequence(8,:) = 1:N_pulse). The last two rows are being used by an algorithm that allows for compression of the pulse sequence in order to accelerate the MR simulations (read more here CODE\fast-algorithm).

B1 is given in T (Tesla), RFP is given in radians, RFfreq is given in Hz and gradients are given in T/m (Tesla per meter).

times_fitting_single_point: it is an array of the timepoints for which the MR signal will be recorded in the database/dictionary of the simulated signals (for example the times_fitting_single_point = [1000, 2000, 3000, 4000, 5000] will record the simulated MR signal for timepoints 1000, 2000, 3000, 4000 and 5000. For a dt=0.000001 sec (1μsec), the simulated MR signal will be recorded for t = 1msec, 2msec, 3msec, 4msec and 5msec.)

soft_crushers: it is an array of 0s or 1s and of size [1xN_pulse]. This array is pointing out when a nullification of the transverse components of the magnetization should be induced. It is being used to avoid the introduction of strong gradients in the pulse sequence.

Extra parameters:

gamma: the gyromagnetic ratio in Hz/T. For example, the gyromagnetic ratio for the hydrogen nucleus is 42560000 Hz/T.

coordCenterSlice_mm: it is a [1x3] array that holds the center of the slice in millimeters.

normalVectorSlice: it is a [1x3] array that holds the normal vector of the slice. For example, a transversal slice would have a normalVectorCenterSlice equal to [0,0,1] in the DCS.