semi-LASER Slice Map – SpinEvolution | NMR Simulation Software

semi-LASER Pulse Sequence
semi-LASER Slice Map

See Notes in the PRESS example for explanations on a similar simulation.

slaser2D (main input file)

******************************************************************************************                                                                              
** E2000A/GOIA-W(16,4) semi-LASER slice map in N-acetylaspartate (NAA)
** The spin system: one NH proton and one CH3 proton                
** Reference:  Kaiser et al. Neuronal 1H MRS thermometry in vivo.
****** The System ************************************************************************
spectrometer(MHz)  125
spinning_freq(kHz) *
channels           H1
nuclei             H1 H1
atomic_coords      *
cs_isotropic       7.84 2 ppm
csa_parameters     *
j_coupling         *
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 0) (<4>) 0 (0) (<4>) 0 (0) (<4>) 0
power(kHz)    e2000A.pwr 0  0   goia.pwr 0  0 0    *   0  0    *   0  0    *   0
phase(deg)           90  0  0        0   0  0 0    *   0  0    *   0  0    *   0
freq_offs(kHz)       0   0  0   goia.frq 0  0 0    *   0  0    *   0  0    *   0
CHN G
timing(usec)   (t128.tm) 0 (0) (t256.tm) 0 (0 0) (<4>) 0 (0) (<4>) 0 (0) (<4>) 0
grad_offs(kHz)       0   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 the location of the spectrum center (zero frequecy in kHz) in ppm
ppm_center_1=4.9

** 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 10 13]=T180/256
pulse_2_[4 7 10 13]=T180/256
psf_1_[4 7 10 13]=10000/T180
fsf_1_[4 7 10 13]=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 8 11]=[-1  1 -1  1]

** Localization **
** G1, G2, G3 are offsets, kHz, generated by PFGs along X, Y, and Z
G3 = 0.5
scan_par1d G2/-14:0.2:14/
scan_par2d G1/-4.5:0.1:4.5/
grad_offs_1=G1
g=load("goia.pfg")
grad_offs_[4 7 10 13]=g*G[2 2 3 3]

** Refocus the linear phase generated by the selective excitation pulse
pulse_[1 2]_6_1=T90*r90
grad_offs_6_1=G1

** Additional interpulse delays (due to crusher gradients etc.)
t1=1000
t2=1000
pulse_[1 2]_3=t1
pulse_[1 2]_6_2=t1+t2
pulse_[1 2]_9=t1+t2
pulse_[1 2]_12=t1+t2
pulse_[1 2]_14=t2

** Take absolute value of the signal
pdata_re=abs(complex(pdata_re,pdata_im))

x_label="ref, 180° (Offset, kHz)"
y_label="exc, 90° (Offset, kHz)"
fig_options = "--contn 256 --cmap gray"
fig_title = f"Localization map of a E2000A/GOIA-W(16,4) semi-LASER slice [nl] in a two-spin system with signals at 2.0 and 7.8 ppm"

******* Options **************************************************************************
rho0               0.5*F1z
observables        F1p
EulerAngles        *
n_gamma            *
line_broaden(Hz)   *
zerofill           *
FFT_dimensions     *
options            -re -py -contf
******************************************************************************************

Files referenced from the main input file:

mio-inositol.cs

mio-inositol.j

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

t128.tm

t256.tm