semi-LASER
See Notes in the PRESS example for explanations on a similar simulation.
slaser (main input file)
******************************************************************************************
** semi-LASER localization: 1H spectrum averaged over 3D voxel
** Reference: Kaiser, L. G., Young, K., Matson, G. B. (2008)
** Numerical simulations of localized high field 1H MR spectroscopy.
** Journal of Magnetic Resonance, 195(1), 67–75.
****** The System ************************************************************************
spectrometer(MHz) 125
spinning_freq(kHz) *
channels H1
nuclei *
atomic_coords *
cs_isotropic MOL.cs ppm
csa_parameters *
j_coupling MOL.j
quadrupole *
dip_switchboard *
csa_switchboard *
exchange_nuclei *
bond_len_nuclei *
bond_ang_nuclei *
tors_ang_nuclei *
groups_nuclei *
******* Pulse Sequence *******************************************************************
CHN 1
timing(usec) (t128.tm) 0 (0) (t256.tm 0 0 t256.tm) 0 (0) (<4>) 0 (4000)8k
power(kHz) e2000A.pwr 0 0 goia.pwr 0 0 goia.pwr 0 0 * 0 0
phase(deg) 90 0 0 0 0 0 0 0 0 * 0 0
freq_offs(kHz) 0 0 0 goia.frq 0 0 goia.frq 0 0 * 0 0
CHN G
timing(usec) (t128.tm) 0 (0) (t256.tm 0 0 t256.tm) 0 (0) (<4>) 0 (4000)
grad_offs(kHz) 0 0 0 0 0 0 0 0 0 * 0 0
******* Variables ************************************************************************
** <4> at the timing(usec) line above means "the same as pulse sequence 4"
** e2000A.pwr is the excitation pulse powers, kHz, for a 10 ms pulse
** goia.pwr/frq are the refocusing pulse powers and freqs, kHz, for a 10 ms pulse
** See examples/selective-pulses to investigate how these pulses work
** Specify selective pulses lengths, usec
T90 = 4000
T180 = 2500
** Specify (refocusing time)/(pulse length) ratio for the excitation pulse
** The refocusing time for the excitation pulse is given as a comment in e2000A.pwr
r90 = 0.3069
** Set up the selective excitation pulse
pulse_[1 2]_1=T90/128
psf_1_1=10000/T90
** Print B1max, uT, for the excitation pulse
disp("e2000A B1max = "&str(1000*max(abs(power_1_1*psf_1_1))/42.5773,1)&" uT")
** Set up the selective refocusing pulses
pulse_1_[4 7](1:256 & 259:514)=T180/256
pulse_2_[4 7]=pulse_1_[4 7]
psf_1_[4 7]=10000/T180
fsf_1_[4 7]=10000/T180
** Print B1max, uT, for the refocusing pulse
disp("GOIA B1max = "&str(1000*max(abs(power_1_4*psf_1_4))/42.5773,1)&" uT")
** Coherence pathway selected with the crusher gradinents
select_[2 5]=[-1 -1]
select_[4 7]_256=[1 1]
** Localization **
** G1, G2, G3 are offsets, kHz, generated by PFGs along X, Y, and Z
ave_par1d G1/-4:0.2:4/
ave_par2d G2/-10:0.5:10/
ave_par3d G3/-10:0.5:10/
grad_offs_1 = G1
g = load("goia.pfg")
grad_offs_[4 7](1:256 & 259:514) = (g; g)*G[2 3]
** Refocus the linear phase generated by the selective excitation pulse
pulse_[1 2]_4_257=T90*r90
grad_offs_4_257=G1
** Additional interpulse delays (due to crusher gradients etc.)
t1=1000
t2=1000
pulse_[1 2]_3=t1
pulse_[1 2]_4_258=t1+t2
pulse_[1 2]_6=t1+t2
pulse_[1 2]_7_258=t1+t2
pulse_[1 2]_8=t2
fig_options="--text 0.07,0.90,Myo-inositol"
fig_title="semi-LASER localization: 1H spectrum averaged over 3D voxel"
******* Options **************************************************************************
rho0 F1z
observables F1p
EulerAngles *
n_gamma *
line_broaden(Hz) 1
zerofill *
FFT_dimensions 1 ppm
options -re -macroMOL=myo-inositol -sysh6 -varppm_center_1=3.6 -py
******************************************************************************************
Files referenced from the main input file:
mio-inositol.cs
3.5217 4.0538 3.5217 3.6144 3.2690 3.6144 0.1
mio-inositol.j
1 2 2.889 1 6 9.998 2 3 3.006 3 4 9.997 4 5 9.485 5 6 9.482
e2000A.pwr
0.00099595415 0.0026470772 0.0051755127 ... -0.0052844896 -0.0023038224 -0.00038598437
goia.pwr
7.9844889e-05 0.00071732455 0.0019882247 ... 0.0019882247 0.00071732455 7.9844889e-05
goia.frq
-1.9998643 -1.9987807 -1.996614 ... 1.9966142 1.9987807 1.9998643
t128.tm
78.125 78.125 78.125 ... 78.125 78.125 78.125
t256.tm
39.0625 39.0625 39.0625 ... 39.0625 39.0625 39.0625