pulsesequence() {
/* Internal variable declarations *************************/
int shapelist90,shapelist180,shapelistIR;
double nseg;
double seqtime,tau1,tau2,tau3,
te1_delay,te2_delay,te3_delay,
iti_delay, ti_delay,
tr_delay;
double kzero;
double freq90[MAXNSLICE], freq180[MAXNSLICE], freqIR[MAXNSLICE];
/* Real-time variables used in this sequence **************/
int vpe_ctr = v2; // PE loop counter
int vpe_mult = v3; // PE multiplier, ranges from -PE/2 to PE/2
int vms_slices = v4; // Number of slices
int vms_ctr = v5; // Slice loop counter
int vseg = v6; // Number of ETL segments
int vseg_ctr = v7; // Segment counter
int vetl = v8; // Echo train length
int vetl_ctr = v9; // Echo train loop counter
int vssc = v10; // Compressed steady-states
int vtrimage = v11; // Counts down from nt, trimage delay when 0
int vacquire = v12; // Argument for setacqvar, to skip steady state acquires
int vphase180 = v13; // phase of 180 degree refocusing pulse
/* Initialize paramaters **********************************/
init_mri();
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
} else {
abort_message("petable undefined");
}
seqtime = 0.0;
espmin = 0.0;
kzero = getval("kzero");
/* RF Power & Bandwidth Calculations **********************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Initialize gradient structures *************************/
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_slice(&ss_grad,"ss",thk); /* NOTE assume same band widths for p1 and p2 */
init_slice_butterfly(&ss2_grad,"ss2",thk,gcrush,tcrush);
init_slice_refocus(&ssr_grad,"ssr");
/* Gradient calculations **********************************/
calc_readout(&ro_grad,WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,WRITE,"gpe","tpe");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p1_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad,&null_grad,&ssr_grad,0.0,WRITE);
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof1,rof2);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrushir,tcrushir);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
}
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp, 0,freq90, ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
offsetlist(pss,ssi_grad.ssamp,0,freqIR, ns,seqcon[1]);
shapelist90 = shapelist(p1pat,ss_grad.rfDuration, freq90, ns,0,seqcon[1]);
shapelist180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
shapelistIR = shapelist(pipat,ssi_grad.rfDuration,freqIR, ns,0,seqcon[1]);
/* same slice selection gradient and RF pattern used */
if (ss_grad.rfFraction != 0.5)
abort_message("ERROR %s: RF pulse must be symmetric (RF fraction = %.2f)",
seqfil,ss_grad.rfFraction);
if (ro_grad.echoFraction != 1)
abort_message("ERROR %s: Echo Fraction must be 1",seqfil);
/* Find sum of all events in each half-echo period ********/
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + pe_grad.duration + ro_grad.timeToEcho;
tau3 = ro_grad.timeFromEcho + pe_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(MAX(tau1,tau2),tau3); // Minimum echo spacing
if (minesp[0] == 'y') {
esp = espmin + 8e-6; // ensure at least 4us delays in both TE periods
putvalue("esp",esp);
}
else if (((espmin+8e-6)-esp) > 12.5e-9) {
abort_message("ERROR %s: Echo spacing too small, minimum is %.2fms\n",seqfil,(espmin+8e-6)*1000);
}
te1_delay = esp/2.0 - tau1; // Intra-esp delays
te2_delay = esp/2.0 - tau2;
te3_delay = esp/2.0 - tau3;
te = kzero*esp; // Return effective TE
putvalue("te",te);
/* Minimum TR **************************************/
/* seqtime is total time per slice */
seqtime = 2*4e-6 + ss_grad.rfCenterFront + etl*esp + ro_grad.timeFromEcho + pe_grad.duration + te3_delay;
/* Increase TR if any options are selected****************/
if (sat[0] == 'y') seqtime += ns*satTime;
if (fsat[0] == 'y') seqtime += ns*fsatTime;
if (mt[0] == 'y') seqtime += ns*mtTime;
if (ir[0] == 'y') {
/* Inter-IR delay */
if (ns > 1)
iti_delay = seqtime - ssi_grad.duration;
/* it is probably safe to assume that seqtime is always > the pulse widths */
else
iti_delay = 0;
/* Inversion Recovery */
timin = ssi_grad.rfCenterBack + ss_grad.rfCenterFront;
timin += 8e-6; // from sp1on/off and after 90 pulse power setting
timin += seqtime*(ns-1) + iti_delay;
if (ti < timin + 4e-6) // ensure at least a 4us delay
abort_message("%s: ti too short, minimum is %.2fms",seqfil,timin*1000);
/* Delay after the last IR pulse */
ti_delay = ti - timin;
/* force all slices to be acquired back-to-back, with a single TR delay at end */
trtype = 1;
}
else {
iti_delay = ti_delay = 0;
}
trmin = ns*(seqtime + 4e-6);
if (ir[0] == 'y') {
trmin += (4e-6 + ssi_grad.rfCenterFront + ti);
}
if (mintr[0] == 'y'){
tr = trmin;
putvalue("tr",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000);
}
tr_delay = (tr - trmin)/ns;
/* Set number of segments for profile or full image **********/
nseg = prep_profile(profile[0],nv/etl,&pe_grad,&per_grad);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Calculate total acquisition time */
g_setExpTime(tr*(nt*nseg*getval("arraydim") + ssc) + trimage*getval("arraydim"));
/* Return parameters to VnmrJ */
putvalue("rgss",ss_grad.tramp); //90 slice ramp
if (ss2_grad.enableButterfly) { //180 slice ramps
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgss2",ss2_grad.tramp);
}
if (ro_grad.enableButterfly) {
putvalue("rgro",ro_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgro",ro_grad.tramp); //RO ramp
}
putvalue("tror",ror_grad.duration); //ROR duration
putvalue("rgror",ror_grad.tramp); //ROR ramp
putvalue("gpe",pe_grad.peamp); //PE max amp
putvalue("gss",ss_grad.ssamp);
putvalue("gro",ro_grad.roamp);
/* PULSE SEQUENCE *************************************/
initval(fabs(ssc),vssc); // Compressed steady-state counter
assign(one,vacquire); // real-time acquire flag
/* Phase cycle: Alternate 180 phase to cancel residual FID */
mod2(ct,vphase180); // 0101
dbl(vphase180,vphase180); // 0202
add(vphase180,one,vphase180); // 1313 Phase difference from 90
add(vphase180,oph,vphase180);
obsoffset(resto);
delay(4e-6);
initval(nseg,vseg);
loop(vseg,vseg_ctr);
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vseg_ctr,vssc,vseg_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
ifzero(vseg_ctr);
assign(zero,vacquire); // Start acquiring when vseg_ctr reaches zero
endif(vseg_ctr);
setacqvar(vacquire); // Turn on acquire when vacquire is zero
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
if(ir[0] == 'y') { /* IR for all slices prior to data acquisition */
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(4e-6);
msloop(seqcon[1],ns,vms_slices,vms_ctr);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0,0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayFront);
shapedpulselist(shapelistIR,ssi_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(iti_delay);
endmsloop(seqcon[1],vms_ctr);
delay(ti_delay);
}
msloop(seqcon[1],ns,vms_slices,vms_ctr);
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* 90 degree pulse ************************************/
rotate();
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapelist90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Read dephase and Slice refocus *********************/
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,ror_grad.amp,0.0,-ssr_grad.amp,WAIT);
/* First half-TE delay ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(te1_delay);
peloop(seqcon[2],etl,vetl,vetl_ctr);
mult(vseg_ctr,vetl,vpe_ctr);
add(vpe_ctr,vetl_ctr,vpe_ctr);
getelem(t1,vpe_ctr,vpe_mult);
/* 180 degree pulse *******************************/
/* Note, ss2_grad.amp is max gradient for butterfly shape; flat top = _.ssamp */
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shapelist180,ss2_grad.rfDuration,vphase180,rof1,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
/* Phase-encode gradient ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,-pe_grad.increment,vpe_mult,WAIT);
/* Second half-TE period ******************************/
delay(te2_delay);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquire data ****************************************/
startacq(alfa);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ********************/
/* Phase encode, refocus, and dephase gradient ******************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT);
/* Second half-TE delay *******************************/
delay(te3_delay);
endpeloop(seqcon[2],vetl_ctr);
/* Relaxation delay ***********************************/
if (!trtype)
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
if (trtype)
delay(ns*tr_delay);
endloop(vseg_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence()
{
/* Internal variable declarations *************************/
/*timing*/
double tr_delay;
double te_d1,te_d2,te_d3; /* delays */
double tau1,tau2,tau3;
/*voxel crusher multipliers */
double fx,fy,fz;
/*localization parameters*/
double freq1,freq2,freq3;
double vox1_cr,vox2_cr, vox3_cr;
int nDim;
double rprof,pprof,sprof;
char profile_vox[MAXSTR],profile_ovs[MAXSTR];
double restol, resto_local, csd_ppm;
/*phase cycle****/
int counter,noph;
char autoph[MAXSTR], pcflag[MAXSTR];
int rf1_phase[64] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3};
int rf2_phase[64] = {0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,
0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3};
int rf3_phase[64] = {0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,
0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3};
/* Initialize paramaters **********************************/
init_mri(); //this gets all the parameters that are defined in acqparms.h, etc
get_wsparameters();
get_ovsparameters();
rprof = getval("rprof");
pprof = getval("pprof");
sprof = getval("sprof");
//read the crusher factors that are designed to create grad on the same axis without refoc
fx=getval("fx");
fy=getval("fy");
fz=getval("fz");
getstr("profile_vox",profile_vox);
getstr("profile_ovs",profile_ovs);
/*set voxel sizes for butterfly crushers to 10^6 to set the slice portion to zero ***/
vox1_cr=1000000;
vox2_cr=1000000;
vox3_cr=1000000;
/***** RF power initialize *****/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
/***** Initialize gradient structs *****/
trampfixed=trise; //rise time =trise
tcrush=granularity(tcrush,GRADIENT_RES); //this is to avoid the granularity errors
//if trampfixed is used, rise time needs to be checked
if (trise*2>tcrush){
abort_message("tcrush too short. Minimum tcrush = %fms \n",1000*trise*2);
}
if (gcrush>gmax){
abort_message("gcrush too large. Max gcrush = %f \n",gmax*0.95);
}
init_slice_butterfly(&vox1_grad,"vox1",vox1,gcrush,tcrush);
init_slice_butterfly(&vox2_grad,"vox2",vox2,gcrush,tcrush);
init_slice_butterfly(&vox3_grad,"vox3",vox3,gcrush,tcrush);
init_slice_butterfly(&vox1_crush,"vox1_crush",vox1_cr,gcrush,tcrush);
init_slice_butterfly(&vox2_crush,"vox2_crush",vox2_cr,gcrush,tcrush);
init_slice_butterfly(&vox3_crush,"vox3_crush",vox3_cr,gcrush,tcrush);
if (profile_vox[0] == 'y') {
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
}
/***** RF and Gradient calculations *****/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
calc_slice(&vox1_grad,&p2_rf,WRITE,"gvox1");
calc_slice(&vox2_grad,&p2_rf,WRITE,"gvox2");
calc_slice(&vox3_grad,&p2_rf,WRITE,"gvox3");
calc_slice(&vox1_crush,&p2_rf,WRITE,"vox1_crush");
calc_slice(&vox2_crush,&p2_rf,WRITE,"vox2_crush");
calc_slice(&vox3_crush,&p2_rf,WRITE,"vox3_crush");
if (profile_vox[0] == 'y') {
calc_readout(&ro_grad,WRITE,"gro","sw","at");
putvalue("gro",ro_grad.roamp); // RO grad
calc_readout_refocus(&ror_grad,&ro_grad,WRITE,"gror");
putvalue("tror",ror_grad.duration); // ROR duration
}
//set all gradients along a particular direction to zero if profile is needed
if (profile_ovs[0]=='y'){
if (rprof==1) {
vox1_grad.amp=0; //set slice selection in read direction to none
vox3_crush.amp=0; // set corresponding crusher gradients to none
}
else if(pprof==1) {
vox2_grad.amp=0;
vox1_crush.amp=0;
}
else if(sprof==1) {
vox3_grad.amp=0;
vox2_crush.amp=0;
}
}
/* Optional OVS and Water Suppression */
if (ovs[0] == 'y') create_ovsbands();
if (sat[0] == 'y') create_satbands();
if (ws[0] == 'y') create_watersuppress();
//Read in parameters not defined in acqparms.h and sglHelper
nDim=getval("nDim");
restol=getval("restol"); //local frequency offset
roff=getval("roff"); //receiver offset
csd_ppm=getval("csd_ppm"); //chemical shift displacement factor
noph=getval("noph");
getstr("autoph",autoph);
getstr("pcflag",pcflag);
settable(t3,noph,rf1_phase);
settable(t2,noph,rf2_phase);
settable(t1,noph,rf3_phase);
/* tau1, tau2 and tau3 are sums of all events in TE*/
tau1 = vox1_grad.rfCenterFront+GDELAY+rof2;
tau2 = vox1_grad.rfCenterBack + vox1_grad.rfCenterFront+2*(GDELAY+rof2);
tau3 = vox3_grad.rfCenterBack+GDELAY+rof2;
temin = tau1+5.0*tau2+tau3;
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (te < temin) {
abort_message("te too short. Minimum te = %.2f ms\n",temin*1000);
}
/***** Calculate TE delays *****/
te_d1 = te/12.0 - tau1+GDELAY;
te_d2 = te/6.0 - tau2+2*(GDELAY+rof2);
te_d3 = te/12.0 - tau3+GDELAY+rof2;
//Calculate delta from resto to include local frequency line+ chemical shift offset
resto_local=resto-restol;
/***** Min TR *****/
trmin = GDELAY + p1 + te + at+rof1+rof2;
if (ws[0] == 'y') trmin += wsTime;
if (ovs[0] == 'y') trmin += ovsTime;
if (sat[0] == 'y') trmin += satTime;
if (profile_vox[0] == 'y') trmin += ror_grad.duration + ro_grad.duration - at;
if (mintr[0] == 'y') {
tr = trmin; // ensure at least 4us between gradient events
putvalue("tr",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000);
}
/***** Calculate TR delay *****/
tr_delay = tr - trmin;
/* Frequency offsets */
freq1 = poffset(pos1,vox1_grad.ssamp); // First RF pulse
freq2 = poffset(pos2,vox2_grad.ssamp); // Second RF pulse
freq3 = poffset(pos3,vox3_grad.ssamp); // Third RF pulse
freq1=freq1-csd_ppm*sfrq;
freq2=freq2-csd_ppm*sfrq;
freq3=freq3-csd_ppm*sfrq;
/* Frequency offsets */
if (profile_vox[0] == 'y') {
/* Shift DDR for pro ************************************/
roff = -poffset(pro,ro_grad.roamp);
}
/* Put gradient information back into VnmrJ parameters */
putvalue("gvox1",vox1_grad.ssamp);
putvalue("gvox2",vox2_grad.ssamp);
putvalue("gvox3",vox3_grad.ssamp);
putvalue("rgvox1",vox1_grad.tramp);
putvalue("rgvox2",vox2_grad.tramp);
putvalue("rgvox3",vox3_grad.tramp);
sgl_error_check(sglerror);
if (ss<0) g_setExpTime(tr*(nt-ss)*arraydim);
else g_setExpTime(tr*(nt*arraydim+ss));
/**[2.7] PHASE CYCLING ******************************************************/
assign(zero, oph);
counter=(double)nt*(ix-1);
if (autoph[0] == 'n') counter=0.0; //only goes through nt, if 'y' goes through nt*array
initval(counter,v1);
initval(noph,v3);
add(v1,ct,v2);
modn(v2,v3,v2);
/* Full phase cycling requires 64 steps*/
if (pcflag[0] == 'n') {
assign(zero,v2);
getelem(t1,v2,v10);
getelem(t2,v2,v11);
getelem(t3,v2,v12);
}
else
{
getelem(t1,v2,v10);
getelem(t2,v2,v11);
getelem(t3,v2,v12);
}
/*Start of the sequence*/
obsoffset(resto_local); // need it here for water suppression to work
delay(GDELAY);
rot_angle(vpsi,vphi,vtheta);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
/* TTL scope trigger **********************************/
//sp1on(); delay(4e-6); sp1off();
/* Saturation bands ***********************************/
if (ovs[0] == 'y') ovsbands();
if (sat[0] == 'y') satbands();
/* Water suppression **********************************/
if (ws[0] == 'y') watersuppress();
/* Slice selective 90 degree RF pulse *****/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GDELAY);
shaped_pulse(p1pat,p1,zero,rof1,rof2);
/* start localization */
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
if (nDim > 2.5) {
delay(te_d1); //this is at least GDELAY == 4 us
obl_shaped3gradient(vox1_grad.name,vox1_crush.name,"",vox1_grad.duration,vox1_grad.amp,fy*vox1_crush.amp,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
shapedpulseoffset(p2_rf.pulseName,vox1_grad.rfDuration,v12,rof1,rof2,freq1);
delay(vox1_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient (vox1_grad.name,vox1_crush.name,"",vox1_grad.duration,vox1_grad.amp,fy*0.777*vox1_crush.amp,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
shapedpulseoffset(p2_rf.pulseName,vox1_grad.rfDuration,v12,rof1,rof2,freq1);
delay(vox1_grad.rfDelayBack);
delay(te_d2);
}
if (nDim > 1.5) { //this is 2nd slice selection
obl_shaped3gradient("",vox2_grad.name,vox2_crush.name,vox2_grad.duration,0,vox2_grad.amp,fz*vox2_crush.amp,NOWAIT);
delay(vox2_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
shapedpulseoffset(p2_rf.pulseName,vox2_grad.rfDuration,v11,rof1,rof2,freq2);
delay(vox2_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient("",vox2_grad.name,vox2_crush.name,vox2_grad.duration,0,vox2_grad.amp,fz*0.777*vox2_crush.amp,NOWAIT);
delay(vox2_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
shapedpulseoffset(p2_rf.pulseName,vox2_grad.rfDuration,v11,rof1,rof2,freq2);
delay(vox2_grad.rfDelayBack);
delay(te_d2);
}
if (nDim > 0.5){ //this is 3rd slice selection
obl_shaped3gradient(vox3_crush.name,"",vox3_grad.name,vox3_grad.duration,fx*vox3_crush.amp,0,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
shapedpulseoffset(p2_rf.pulseName,vox3_grad.rfDuration,v10,rof1,rof2,freq3);
delay(vox3_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient(vox3_crush.name,"",vox3_grad.name,vox3_grad.duration,fx*vox3_crush.amp,0,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
shapedpulseoffset(p2_rf.pulseName,vox3_grad.rfDuration,v10,rof1,rof2,freq3);
delay(vox3_grad.rfDelayBack);
delay(te_d3);
}
if (profile_vox[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,
-rprof*ror_grad.amp,-pprof*ror_grad.amp,-sprof*ror_grad.amp,WAIT);
delay(GDELAY);
obl_shapedgradient(ro_grad.name,ro_grad.duration,
rprof*ro_grad.amp,pprof*ro_grad.amp,sprof*ro_grad.amp,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
} else {
startacq(alfa);
acquire(np,1.0/sw);
endacq();
}
delay(tr_delay);
pulsesequence()
{
/* Internal variable declarations *********************/
double freq90[MAXNSLICE],freq180[MAXNSLICE];
double te_delay1,te_delay2,tr_delay,tau1,tau2,thk2fact,te_delay3=0.0,te_delay4=0.0,navTime=0.0;
double crushm0,pem0,gcrushr,gcrushp,gcrushs,pecrush;
double refsign=1,crushsign=1,navsign=1;
int shape90,shape180,table=0,sepRefocus;
char slprofile[MAXSTR];
/* sequence dependent diffusion variables */
double Gro,Gss; // "gdiff" for readout/readout refocus and slice/slice refocus
double dgro,dgss; // "delta" for readout/readout refocus and slice/slice refocus
double Dgro,Dgss; // "DELTA" for readout/readout refocus and slice/slice refocus
double dcrush,dgss2; // "delta" for crusher and gss2 gradients
double Dcrush,Dgss2; // "DELTA" for crusher and gss2 gradients
int i;
/* Real-time variables used in this sequence **********/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vpe_offset = v5; // PE/2 for non-table offset
int vpe_mult = v6; // PE multiplier, ranges from -PE/2 to PE/2
int vph180 = v7; // Phase of 180 pulse
int vph2 = v8; // alternate phase of 180 on odd transients
int vssc = v9; // Compressed steady-states
int vtrimage = v10; // Counts down from nt, trimage delay when 0
int vacquire = v11; // Argument for setacqvar, to skip steady state acquires
int vtrigblock = v12; // Number of slices per trigger block
/* Initialize paramaters *****************************/
init_mri();
thk2fact=getval("thk2fact");
pecrush=getval("pecrush");
sepRefocus=getvalnwarn("sepRefocus");
getstrnwarn("slprofile",slprofile);
/* Check for external PE table ***********************/
init_tablepar("pelist"); // Initialize pelist parameter
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
writetabletopar(t1,"pelist"); // Write t1 table to pelist parameter
table = 1;
}
/* RF Power & Bandwidth Calculations ******************/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Initialize gradient structures *********************/
init_slice(&ss_grad,"ss",thk);
init_slice(&ss2_grad,"ss2",thk*thk2fact);
init_dephase(&crush_grad,"crush");
init_slice_refocus(&ssr_grad,"ssr");
if (FP_LT(tcrushro,alfa)) tcrushro=alfa;
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_generic(&spoil_grad,"spoil",gspoil,tspoil);
/* Gradient calculations ******************************/
calc_readout(&ro_grad, WRITE,"gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
calc_generic(&spoil_grad,WRITE,"","");
/* Make sure crushing in PE dimension does not refocus signal from 180 */
crushm0=fabs(gcrush*tcrush);
pem0=0.0; gcrushp=0.0;
if (pecrush) pem0=pe_grad.m0;
calc_dephase(&crush_grad,WRITE,crushm0+pem0,"","");
gcrushr = crush_grad.amp*crushm0/crush_grad.m0;
if (pecrush) gcrushp = crush_grad.amp;
gcrushs = crush_grad.amp*crushm0/crush_grad.m0;
/* Allow phase encode and read dephase to be separated from slice refocus */
if (sepRefocus) {
/* Equalize read dephase and PE gradient durations */
calc_sim_gradient(&ror_grad,&pe_grad,&null_grad,0,WRITE);
crushsign=-1;
} else {
if (slprofile[0] == 'y') {
/* Combined slice refocusing and read dephasing,
reverse gradient sign if ror > ssr integral */
refsign = (ss_grad.m0ref > ro_grad.m0ref) ? 1.0 : -1.0;
ss_grad.m0ref -= ro_grad.m0ref;
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
}
/* Equalize both refocus and PE gradient durations */
calc_sim_gradient(&ror_grad,&pe_grad,&ssr_grad,0,WRITE);
}
/* Create optional prepulse events ********************/
if (fsat[0] == 'y') create_fatsat();
if (sat[0] == 'y') create_satbands();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') create_inversion_recovery();
if (diff[0] == 'y') init_diffusion(&diffusion,&diff_grad,"diff",gdiff,tdelta);
sgl_error_check(sglerror);
/* Min TE *********************************************/
te = granularity(te,2*GRADIENT_RES);
/* tau1, tau2 are the sum of events in each half echo period */
/* tau1, tau2 include a GRADIENT_RES as this is minimum delay time */
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront + 2*GRADIENT_RES;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho + GRADIENT_RES;
if (sepRefocus) tau2 += ror_grad.duration;
temin = 2*MAX(tau1,tau2);
/* Diffusion ******************************************/
if (diff[0] == 'y') {
/* granulate tDELTA */
tDELTA = granularity(tDELTA,GRADIENT_RES);
/* taudiff is the duration of events between diffusion gradients */
taudiff = ss2_grad.duration + 2*crush_grad.duration + GRADIENT_RES;
/* set minimum diffusion structure requirements for gradient echo: taudiff, tDELTA, te and minte[0] */
set_diffusion(&diffusion,taudiff,tDELTA,te,minte[0]);
/* set additional diffusion structure requirements for spin echo: tau1 and tau2 */
set_diffusion_se(&diffusion,tau1,tau2);
/* calculate the diffusion structure delays.
address &temin is required in order to update temin accordingly */
calc_diffTime(&diffusion,&temin);
}
/* TE delays ******************************************/
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (FP_LT(te,temin)) {
abort_message("TE too short, minimum TE = %.3f ms\n",temin*1000);
}
te_delay1 = te/2 - tau1 + GRADIENT_RES;
te_delay2 = te/2 - tau2 + GRADIENT_RES;
if (navigator[0] == 'y') {
/* tau1, tau2 are the sum of events in each half echo period */
tau1 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho;
if (FP_GT(tau1,tau2)) {
te_delay3 = GRADIENT_RES;
te_delay4 = tau1-tau2+GRADIENT_RES;
} else {
te_delay3 = tau2-tau1+GRADIENT_RES;
te_delay4 = GRADIENT_RES;
}
navTime = te_delay3 + ss2_grad.duration + 2*crush_grad.duration + ro_grad.duration + te_delay4 + 2*GRADIENT_RES;
}
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Min TR *********************************************/
trmin = ss_grad.rfCenterFront + te + ro_grad.timeFromEcho + pe_grad.duration + 2*GRADIENT_RES;
/* Increase TR if any options are selected ************/
if (spoilflag[0] == 'y') trmin += spoil_grad.duration;
if (navigator[0] == 'y') trmin += navTime;
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (ticks > 0) trmin += GRADIENT_RES;
/* Adjust for all slices ******************************/
trmin *= ns;
/* Inversion recovery *********************************/
if (ir[0] == 'y') {
/* tauti is the additional time beyond IR component to be included in ti */
/* satTime, fsatTime and mtTime all included as those modules will be after IR */
tauti = satTime + fsatTime + mtTime + GRADIENT_RES + ss_grad.rfCenterFront;
/* calc_irTime checks ti and returns the time of all IR components */
trmin += calc_irTime(tauti,trmin,mintr[0],tr,&trtype);
}
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("TR too short, minimum TR = %.3f ms\n",trmin*1000);
}
/* TR delay *******************************************/
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Calculate B values *********************************/
if (ix == 1) {
/* Calculate bvalues according to main diffusion gradients */
calc_bvalues(&diffusion,"dro","dpe","dsl");
/* Add components from additional diffusion encoding imaging gradients peculiar to this sequence */
/* Initialize variables */
dgro = 0.5*(ror_grad.duration+ro_grad.timeToEcho);
Gro = ro_grad.m0ref/dgro; Dgro = dgro;
if (!sepRefocus) Dgro = te-ss_grad.rfCenterBack-ro_grad.timeToEcho;
dgss = 0.5*(ss_grad.rfCenterBack+ssr_grad.duration);
Gss = ss_grad.m0ref/dgss; Dgss = dgss;
dgss2 = ss2_grad.duration/2; Dgss2 = dgss2;
dcrush = crush_grad.duration-crush_grad.tramp; Dcrush = crush_grad.duration+ss2_grad.duration;
for (i = 0; i < diffusion.nbval; i++) {
/* set droval, dpeval and dslval */
set_dvalues(&diffusion,&droval,&dpeval,&dslval,i);
/* Readout */
diffusion.bro[i] += bval(Gro,dgro,Dgro);
diffusion.bro[i] += bval(crushsign*gcrushr,dcrush,Dcrush);
diffusion.bro[i] += bval_nested(gdiff*droval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
if (!sepRefocus) {
diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,gdiff*droval,tdelta,tDELTA);
diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,crushsign*gcrushr,dcrush,Dcrush);
}
/* Phase */
if (pecrush) {
diffusion.bpe[i] += bval(gcrushp,dcrush,Dcrush);
diffusion.bpe[i] += bval_nested(gdiff*dpeval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
}
/* Slice */
diffusion.bsl[i] += bval(Gss,dgss,Dgss);
diffusion.bsl[i] += bval(gcrushs,dcrush,Dcrush);
diffusion.bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
diffusion.bsl[i] += bval_nested(gcrushs,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
if (pecrush) diffusion.brp[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
if (!sepRefocus) {
diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gdiff*dpeval,tdelta,tDELTA);
if (pecrush) diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gcrushp,dcrush,Dcrush);
}
/* Readout/Slice Cross-terms */
diffusion.brs[i] += bval2(crushsign*gcrushr,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
if (!sepRefocus) {
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gdiff*dslval,tdelta,tDELTA);
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Slice/Phase Cross-terms */
diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
if (pecrush) {
diffusion.bsp[i] += bval2(gcrushs,gcrushp,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gcrushp,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
}
} /* End for-all-directions */
/* Write the values */
write_bvalues(&diffusion,"bval","bvalue","max_bval");
}
/* Generate phase-ramped pulses ***********************/
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]);
shape180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]);
/* Set pe_steps for profile or full image *************/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
F_initval(pe_steps/2.0,vpe_offset);
/* Shift DDR for pro **********************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *******************/
if (ssc<0) {
if (seqcon[2] == 'c') g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*pe_steps*arraydim));
}
else g_setExpTime(trmean*ntmean*pe_steps*arraydim + tr*ssc);
/* Slice profile **************************************/
if (slprofile[0] == 'y' && !sepRefocus) ror_grad.amp = 0;
/* Set phase cycle table ******************************/
if (sepRefocus) settable(t2,1,ph180); // Phase encode is just before readout
else settable(t2,2,ph180);
/* PULSE SEQUENCE *************************************/
status(A); // Set status A
rotate(); // Set gradient rotation according to psi, phi and theta
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto); // Set spectrometer frequency
delay(GRADIENT_RES); // Delay for frequency setting
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
if (trtype) delay(ns*tr_delay); // relaxation delay
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vpe_ctr,vssc,vpe_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
if (seqcon[2] == 's')
assign(zero,vacquire); // Always acquire for non-compressed loop
else {
ifzero(vpe_ctr);
assign(zero,vacquire); // Start acquiring when vpe_ctr reaches zero
endif(vpe_ctr);
}
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_mult);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_mult);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states
endif(vacquire);
}
/* Phase cycle ****************************************/
getelem(t2,vpe_ctr,vph180); // For phase encoding with slice rephase
add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver
mod2(ct,vph2);
dbl(vph2,vph2);
add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (!trtype) delay(tr_delay); // Relaxation delay
if (ticks > 0) {
modn(vms_ctr,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(GRADIENT_RES);
elsenz(vtest);
delay(GRADIENT_RES);
endif(vtest);
}
sp1on(); delay(GRADIENT_RES); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (ir[0] == 'y') inversion_recovery();
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus gradient *****************************/
if (sepRefocus)
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
else
/* Include phase encode and readout dephase gradient if refocus gradients not separated */
pe_shapedgradient(pe_grad.name,pe_grad.duration,ror_grad.amp,0,-ssr_grad.amp*refsign,pe_grad.increment,vpe_mult,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d1);
diffusion_dephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d2);
}
else
delay(te_delay1);
/* Refocusing RF pulse ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d3);
diffusion_rephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d4);
}
else
delay(te_delay2);
/* Readout dephase, phase encode & readout gradients **/
roff = -poffset(pro,ro_grad.roamp); // incase inverted navigator is acquired
if (slprofile[0] == 'y') {
/* Readout gradient only if refocus gradients not separated */
if (sepRefocus)
obl_shapedgradient(ror_grad.name,ror_grad.duration,0,0,-ror_grad.amp,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,0,0,ro_grad.amp,NOWAIT);
} else {
/* Readout gradient only if refocus gradients not separated */
if (sepRefocus)
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,-pe_grad.increment,vpe_mult,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
}
/* Acquisition ****************************************/
delay(ro_grad.atDelayFront-alfa);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind Phase encoding ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT);
/* Navigator acquisition ******************************/
if (navigator[0] == 'y') {
delay(te_delay3);
obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT);
delay(te_delay4);
obl_shapedgradient(ro_grad.name,ro_grad.duration,navsign*ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
}
if (spoilflag[0] == 'y') {
obl_shapedgradient(spoil_grad.name,spoil_grad.duration,navsign*spoil_grad.amp,0,spoil_grad.amp,WAIT);
}
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
/* Duty cycle *****************************************/
calc_grad_duty(tr);
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE];
int shape90=0, shape180=0, shapeIR=0;
double te_delay1, te_delay2, tr_delay, ti_delay = 0;
double del1=0, del2=0, del3=0, del4=0;
double tau1=0, tau2=0, difftime=0, tetime=0;
int table=0;
/* Diffusion parameters */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl,
i;
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* and the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* Real-time variables ************************************/
int vpe_steps = v1;
int vpe_ctr = v2;
int vms_slices = v3;
int vms_ctr = v4;
int vpe_offset = v5;
int vpe_index = v6;
int vph180 = v7; // Phase of 180 pulse
int vph2 = v8; // alternate phase of 180 on odd transients
/* Initialize paramaters *********************************/
init_mri();
/* Check for external PE table ***************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
if ((diff[0] == 'y') && (gcrush < 4))
warn_message("Advisory: set gcrush to higher value to avoid image artifacts");
/* Initialize gradient structures *************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof2,rof2);
init_slice(&ss_grad,"ss",thk);
init_slice_butterfly(&ss2_grad,"ss2",thk*1.1,gcrush,tcrush);
init_slice_refocus(&ssr_grad,"ssr");
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
if (p2_rf.header.rfFraction != 0.5)
abort_message("RF pulse for refocusing (%s) must be symmetric",p2pat);
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
calc_slice_refocus(&ssr_grad, &ss_grad, NOWRITE,"gssr");
calc_readout(&ro_grad, WRITE, "gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad, &ro_grad, NOWRITE, "gror");
calc_phase(&pe_grad, NOWRITE, "gpe","tpe");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad, &pe_grad, &ssr_grad,0,WRITE);
/* Set up diffusion gradient */
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
calc_generic(&diff_grad,NOWRITE,"","");
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if (ix == 1) diff_grad.duration += diff_grad.tramp;
calc_generic(&diff_grad,WRITE,"","");
}
/* Min TE *************************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + 4e-6 + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + ror_grad.duration + ro_grad.timeToEcho + alfa;
temin = 2*(MAX(tau1,tau2) + 2*4e-6); /* have at least 4us between gradient events */
/* Calculate te_delays with the current TE, then later see how diffusion fits */
if ((minte[0] == 'y') || (te < temin)) {
te_delay1 = temin/2 - tau1;
te_delay2 = temin/2 - tau2;
}
else {
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
}
if (diff[0] =='y') {
/* Is tDELTA long enough for RF refocusing gradient? */
if (tDELTA < diff_grad.duration + ss2_grad.duration)
abort_message("DELTA too short, increase to %.2fms",
(diff_grad.duration + ss2_grad.duration)*1000+0.005);
/* Is tDELTA too long for TE dead time? */
difftime = tDELTA + diff_grad.duration; // tDELTA + front & back half diff_grad
tetime = ss2_grad.duration + te_delay1 + te_delay2;
if (difftime > tetime) {
temin += (difftime - tetime);
}
}
/* We now know the minimum TE incl. diffusion */
if (minte[0] == 'y') {
te = temin;
putvalue("te",ceil(te*1e6)*1e-6); /* round up to nearest us */
}
if (te < temin) {
if (diff[0] == 'n') {
abort_message("TE too short. Minimum TE = %.2fms\n",temin*1000);
}
else {
abort_message("TE too short, increase to %.2fms or reduce DELTA to %.2fms",
temin*1000,(tetime-diff_grad.duration)*1000);
}
}
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
/* Set up delays around diffusion gradients */
/* RF1 - del1 - diff - del2 - RF2 - del3 - diff - del4 - ACQ */
if (diff[0] == 'y') {
del1 = (tetime - difftime)/2;
del4 = del1;
del2 = te_delay1 - diff_grad.duration;
del3 = te_delay2 - diff_grad.duration;
if (del3 < 0.0) { // shift diff block to right
del1 += del3;
del2 -= del3;
del4 -= del3;
del3 = 0;
} else if (del2 < 0.0) { // shift diff block to left
del1 -= del2;
del3 -= del2;
del4 += del2;
del2 = 0;
}
}
else { /* No diffusion */
del1 = 0;
del3 = 0;
del2 = te_delay1;
del4 = te_delay2;
}
/* Min TR *************************************************/
trmin = (ss_grad.duration - ss_grad.rfCenterBack) + te + ro_grad.timeFromEcho;
if (navigator[0] == 'y')
trmin += (pe_grad.duration + ro_grad.duration);
/* Optional prepulse calculations *************************/
if (sat[0] == 'y') {
create_satbands();
trmin += satTime;
}
if (fsat[0] == 'y') {
create_fatsat();
trmin += fsatTime;
}
if (mt[0] == 'y') {
create_mtc();
trmin += mtTime;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof2,rof2);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrushir,tcrushir);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
tau1 = ss_grad.duration - ss_grad.rfCenterBack; /* duration of ss_grad before RF center */
ti_delay = ti - (ssi_grad.rfCenterBack + tau1);
if (ti_delay < 0) {
abort_message("TI too short, Minimum TI = %.2fms\n",(ti-ti_delay)*1000);
}
irTime = ti + ssi_grad.duration - ssi_grad.rfCenterBack; /* time to add to TR */
trmin += irTime;
trmin -= tau1; /* but subtract out ss_grad which was already included in TR */
}
trmin *= ns;
if (mintr[0] == 'y'){
tr = trmin + ns*4e-6;
putvalue("tr",tr);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000);
}
tr_delay = (tr - trmin)/ns > 4e-6 ? (tr - trmin)/ns : 4e-6;
/***************************************************/
/* CALCULATE B VALUES ******************************/
if (diff[0] == 'y') {
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
/* Readout */
Dro = ror_grad.duration;
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
bro[i] += bval(ro_grad.amp,ro_grad.timeToEcho,Dro);
/* Slice */
dgss2 = Dgss2 = ss_grad.rfCenterFront;
dcrush = tcrush; //"delta" for crusher part of butterfly
Dcrush = dcrush + ss_grad.rfDuration; //"DELTA" for crusher
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*slarr[i],gdiff*pearr[i],tdelta,tDELTA);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Generate phase-ramped pulses: 90, 180, and IR */
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
if (ir[0] == 'y') {
offsetlist(pss,ssi_grad.ssamp,0,freqIR,ns,seqcon[1]);
shapeIR = shapelist(pipat,ssi_grad.rfDuration,freqIR,ns,0,seqcon[1]);
}
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
initval(pe_steps/2.0,vpe_offset);
sgl_error_check(sglerror);
/* Return parameters to VnmrJ */
putvalue("rgss",ss_grad.tramp); //90 slice ramp
if (ss2_grad.enableButterfly) { //180 slice ramps
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgss2",ss2_grad.tramp);
}
if (ro_grad.enableButterfly) {
putvalue("rgro",ro_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgro",ro_grad.tramp); //RO ramp
}
putvalue("tror",ror_grad.duration); //ROR duration
putvalue("rgror",ror_grad.tramp); //ROR ramp
putvalue("gpe",pe_grad.peamp); //PE max amp
putvalue("gss",ss_grad.ssamp);
putvalue("gro",ro_grad.roamp);
g_setExpTime(tr*(nt*pe_steps*arraydim + ssc));
/* PULSE SEQUENCE *************************************/
rotate();
obsoffset(resto);
roff = -poffset(pro,ro_grad.roamp);
delay(4e-6);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_index);
else
sub(vpe_ctr,vpe_offset,vpe_index);
settable(t2,2,ph180); // initialize phase tables and variables
getelem(t2,vpe_ctr,vph180);
add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver
mod2(ct,vph2);
dbl(vph2,vph2);
add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
}
/* TTL scope trigger **********************************/
sp1on(); delay(5e-6); sp1off();
/* Prepulses ******************************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Optional IR pulse **********************************/
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0,0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayFront);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,-ssr_grad.amp,
pe_grad.increment,vpe_index,WAIT);
delay(del1); // delay to start of first diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del2); // delay from end of diffusion to slice refocusing
/* Refocusing RF pulse ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
delay(del3); // delay from slice refocusing to second diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del4); // delay from end of diffusion gradient to readout event
/* Readout gradient and acquisition ********************/
roff = -poffset(pro,ro_grad.roamp);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind Phase encoding ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
pe_grad.increment,vpe_index,WAIT);
if (navigator[0] == 'y') {
roff = -poffset(pro,-ro_grad.roamp);
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
}
/* Relaxation delay ***********************************/
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freqEx[MAXNSLICE];
double pespoil_amp,spoilMoment,maxgradtime,pe2_offsetamp=0.0,nvblock;
double tetime,te_delay,tr_delay,perTime;
int table=0,shapeEx=0,sepSliceRephase=0,image,blocknvs;
char spoilflag[MAXSTR],perName[MAXSTR],slab[MAXSTR];
/* Real-time variables used in this sequence **************/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vpe_offset = v3; // PE/2 for non-table offset
int vpe_mult = v4; // PE multiplier, ranges from -PE/2 to PE/2
int vper_mult = v5; // PE rewinder multiplier; turn off rewinder when 0
int vpe2_steps = v6; // Number of PE2 steps
int vpe2_ctr = v7; // PE2 loop counter
int vpe2_mult = v8; // PE2 multiplier
int vpe2_offset = v9; // PE2/2 for non-table offset
int vpe2r_mult = v10; // PE2 rewinder multiplier
int vtrigblock = v11; // Number of PE steps per trigger block
int vpe = v12; // Current PE step out of total PE*PE2 steps
/* Initialize paramaters *********************************/
init_mri();
getstr("spoilflag",spoilflag);
getstr("slab",slab);
image = getval("image");
blocknvs = (int)getval("blocknvs");
nvblock = getval("nvblock");
if (!blocknvs) nvblock=1; // If blocked PEs for trigger not selected nvblock=1
trmin = 0.0;
temin = 0.0;
/* Check for external PE table ***************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
if (ns > 1) abort_message("No of slices must be set to one");
/* RF Calculations ****************************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2); /* hard pulse */
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2); /* soft pulse */
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Gradient calculations **********************************/
if (slab[0] == 'y') {
init_slice(&ss_grad,"ss",thk);
init_slice_refocus(&ssr_grad,"ssr");
calc_slice(&ss_grad,&p2_rf,WRITE,"gss");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
}
if (FP_GT(tcrushro,0.0))
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
else
init_readout(&ro_grad,"ro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
calc_readout(&ro_grad,WRITE,"gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
init_phase(&pe_grad,"pe",lpe,nv);
init_phase(&pe2_grad,"pe2",lpe2,nv2);
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
if (!blocknvs) nvblock=1;
calc_phase(&pe2_grad,NOWRITE,"gpe2","");
if (spoilflag[0] == 'y') { // Calculate spoil grad if spoiling is turned on
init_dephase(&spoil_grad,"spoil"); // Optimized spoiler
spoilMoment = ro_grad.acqTime*ro_grad.roamp; // Optimal spoiling is at*gro for 2pi per pixel
spoilMoment -= ro_grad.m0def; // Subtract partial spoiling from back half of readout
calc_dephase(&spoil_grad,WRITE,spoilMoment,"gspoil","tspoil");
}
/* Is TE long enough for separate slab refocus? ***********/
maxgradtime = MAX(ror_grad.duration,MAX(pe_grad.duration,pe2_grad.duration));
if (spoilflag[0] == 'y')
maxgradtime = MAX(maxgradtime,spoil_grad.duration);
tetime = maxgradtime + alfa + ro_grad.timeToEcho + 4e-6;
if (slab[0] == 'y') {
tetime += ss_grad.rfCenterBack + ssr_grad.duration;
if ((te >= tetime) && (minte[0] != 'y')) {
sepSliceRephase = 1; // Set flag for separate slice rephase
} else {
pe2_grad.areaOffset = ss_grad.m0ref; // Add slab refocus on pe2 axis
calc_phase(&pe2_grad,NOWRITE,"gpe2",""); // Recalculate pe2 to include slab refocus
}
}
/* Equalize refocus and PE gradient durations *************/
pespoil_amp = 0.0;
perTime = 0.0;
if ((perewind[0] == 'y') && (spoilflag[0] == 'y')) { // All four must be single shape
if (ror_grad.duration > spoil_grad.duration) { // calc_sim first with ror
calc_sim_gradient(&pe_grad,&pe2_grad,&ror_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
} else { // calc_sim first with spoil
calc_sim_gradient(&pe_grad,&pe2_grad,&spoil_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
}
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
putvalue("tspoil",perTime);
putvalue("gspoil",spoil_grad.amp);
} else { // post-acquire shape will be either pe or spoil, but not both
calc_sim_gradient(&ror_grad,&pe_grad,&pe2_grad,tpemin,WRITE);
if ((perewind[0] == 'y') && (spoilflag[0] == 'n')) { // Rewinder, no spoiler
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
spoil_grad.amp = 0.0;
putvalue("tpe",perTime);
} else if ((perewind[0] == 'n') && (spoilflag[0] == 'y')) { // Spoiler, no rewinder
strcpy(perName,spoil_grad.name);
perTime = spoil_grad.duration;
pespoil_amp = spoil_grad.amp; // Apply spoiler on PE & PE2 axis if no rewinder
}
}
if (slab[0] == 'y') pe2_offsetamp = sepSliceRephase ? 0.0 : pe2_grad.offsetamp; // pe2 slab refocus
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
sgl_error_check(sglerror); // Check for any SGL errors
/* Min TE ******************************************/
tetime = pe_grad.duration + alfa + ro_grad.timeToEcho;
if (slab[0] == 'y') {
tetime += ss_grad.rfCenterBack;
tetime += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
}
else if (ws[0] == 'y')
tetime += p2/2.0 + rof2; /* soft pulse */
else
tetime += p1/2.0 + rof2; /* hard pulse */
temin = tetime + 4e-6; // Ensure that te_delay is at least 4us
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (te < temin) {
abort_message("TE too short. Minimum TE= %.2fms\n",temin*1000+0.005);
}
te_delay = te - tetime;
/* Min TR ******************************************/
trmin = te_delay + pe_grad.duration + ro_grad.duration + perTime;
if (slab[0] == 'y') {
trmin += ss_grad.duration;
trmin += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
}
else if (ws[0] == 'y')
trmin += p2 +rof1 + rof2; /* soft pulse */
else
trmin += p1 +rof1 + rof2; /* hard pulse */
trmin += 8e-6;
/* Increase TR if any options are selected *********/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (ticks > 0) trmin += 4e-6;
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000+0.005);
}
/* Calculate tr delay */
tr_delay = granularity(tr-trmin,GRADIENT_RES);
if(slab[0] == 'y') {
/* Generate phase-ramped pulses: 90 */
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1pat,ss_grad.rfDuration,freqEx,ns,ss_grad.rfFraction,seqcon[1]);
}
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
F_initval(pe_steps/2.0,vpe_offset);
pe2_steps = prep_profile(profile[1],nv2,&pe2_grad,&null_grad);
F_initval(pe2_steps/2.0,vpe2_offset);
assign(zero,oph);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *******************/
g_setExpTime(tr*(nt*pe_steps*pe2_steps));
/* PULSE SEQUENCE *************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(4e-6);
/* trigger */
if (ticks > 0) F_initval((double)nvblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
delay(tr_delay); // relaxation delay
sub(vpe_ctr,vpe_offset,vpe_mult);
sub(vpe2_ctr,vpe2_offset,vpe2_mult);
mult(vpe2_ctr,vpe_steps,vpe);
add(vpe_ctr,vpe,vpe);
/* PE rewinder follows PE table; zero if turned off ***/
if (perewind[0] == 'y') {
assign(vpe_mult,vper_mult);
assign(vpe2_mult,vpe2r_mult);
}
else {
assign(zero,vper_mult);
assign(zero,vpe2r_mult);
}
if (ticks > 0) {
modn(vpe,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
elsenz(vtest);
delay(4e-6);
endif(vtest);
}
sp1on(); delay(4e-6); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (slab[0] == 'y') {
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapeEx,ss_grad.rfDuration,zero,rof1,rof2,seqcon[1],zero);
delay(ss_grad.rfDelayBack);
if (sepSliceRephase) {
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(te_delay + tau); /* tau is current B0 encoding delay */
}
} else {
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
if (ws[0] == 'y')
shapedpulse(p2pat,p2,zero,rof1,rof2); /* soft CS pulse */
else
shapedpulse(p1pat,p1,zero,rof1,rof2); /* hard pulse */
delay(te_delay + tau); /* tau is current B0 encoding delay */
}
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp*image,0,-pe2_offsetamp,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
if ((slab[0] == 'y') && !sepSliceRephase) delay(te_delay + tau); /* tau is current B0 encoding delay */
/* Readout gradient and acquisition ********************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp*image,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind / spoiler gradient *********************************/
if (perewind[0] == 'y' || (spoilflag[0] == 'y')) {
pe2_shapedgradient(perName,perTime,spoil_grad.amp,pespoil_amp,pespoil_amp,
pe_grad.increment,pe2_grad.increment,vper_mult,vpe2r_mult,WAIT);
}
endpeloop(seqcon[2],vpe_ctr);
endpeloop(seqcon[3],vpe2_ctr);
}
pulsesequence()
{
/***** Internal variable declarations *****/
int shapelist1,shapelist2,shapelist3; /* pulse shapes (lists) */
double freq1,freq2,freq3,ws_delta;
double rprof,pprof,sprof;
double restol, resto_local,csd_ppm;
char profile_ovs[MAXSTR];
char profile_vox[MAXSTR];
int wsfirst; //wsfirst makes ws unit to be exececuted first
int isis;
int counter,noph;
char autoph[MAXSTR],pcflag[MAXSTR];
/* sequence timing variables */
double te_delay1, te_delay2, newdelay,tr_delay, tm_delay;
double tau1=0, tau2=0;
/* Extra crushers */
double gcrushtm,tcrushtm;
double ky;
double vox3_cr, vox3r_cr;
double gcrush_end, tcrush_end;
/*extra ws pulse flag*/
char ws_tm[MAXSTR];
double wsflipftm;
double tmwstpwr,tmwstpwrf;
init_mri();
noph=(int)getval("noph");
isis=(int)getval("isis");
int inv1[32]= {0, 0, 0, 0, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3};//excitation pulse
int inv2[32]= {0, 0, 1, 1, 2, 2, 3, 3, 0, 0, 1, 1, 2, 2, 3, 3, 1, 1, 2, 2, 3, 3, 0, 0, 1, 1, 2, 2, 3, 3, 0, 0}; //refocusing pulse
int inv3[32]= {0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3};//inversion pulse
int phrec[32]= {0, 2, 2, 0, 2, 0, 0, 2, 0, 2, 2, 0, 2, 0, 0, 2, 1, 3, 3, 1, 3, 1, 1, 3, 1, 3, 3, 1, 3, 1, 1, 3};// rec phase
int phrec0[32]= {0, 0, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 0, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1};// rec phase for non-isis
/***** Real-time variables used in this sequence *****/
int vinv1 = v1; // on/off flag first inversion pulse
int vms = v5; // dummy shapedpulselist slice counter (= one)
get_ovsparameters();
get_wsparameters();
rprof = getval("rprof");
pprof = getval("pprof");
sprof = getval("sprof");
ky=getval("ky");
getstr("autoph",autoph);
getstr("pcflag",pcflag);
getstr("profile_ovs",profile_ovs);
getstr("profile_vox",profile_vox);
wsfirst=(int)getval("wsfirst");
restol=getval("restol"); //local frequency offset
roff=getval("roff"); //receiver offset
csd_ppm=getval("csd_ppm"); //chemical shift displacement factor
gcrushtm = getval("gcrushtm");
tcrushtm = getval("tcrushtm");
wsflipftm = getval("wsflipftm");
getstr("ws_tm",ws_tm);
ws_delta=getval("ws_delta");
vox3_cr=1000000;
/***** RF power calculations *****/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
shape_rf(&p3_rf,"p3",p3pat,p3,flip3,rof1,rof2);
shape_rf(&p4_rf,"p4",p4pat,p4,flip4,rof1,rof2);
p4_rf.flipmult=wsflipftm;
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
calc_rf(&p3_rf,"tpwr3","tpwr3f");
calc_rf(&p4_rf,"tpwr4","tpwr4f");
// wsfpwrtm=p4_rf.powerFine*wsflipftm; /* ws fine RF power */
trampfixed=trise; //rise time =trise
tcrush=granularity(tcrush,GRADIENT_RES); //this is to avoid the granularity errors
//if trampfixed is used, rise time needs to be checked
if (trise*2>tcrush){
abort_message("tcrush too short. Minimum tcrush = %fms \n",1000*trise*2);
}
if (gcrush>gmax){
abort_message("gcrush too large. Max gcrush = %f \n",gmax*0.95);
}
init_slice(&vox1_grad,"vox1",vox1);
init_slice(&vox2_grad,"vox2",vox2);
init_slice_butterfly(&vox3_crush,"vox3_crush",vox3_cr,gcrush,tcrush);
init_slice_butterfly(&vox3r_crush,"vox3r_crush",vox3_cr,gcrush,tcrush);
init_slice_butterfly(&vox3_grad,"vox3",vox3,gcrush,tcrush);
init_generic(&tmcrush_grad,"tmcrush",gcrushtm,tcrushtm); //crusher grad during tm
if (profile_vox[0] == 'y') {
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
}
/***** Gradient calculations *****/
calc_slice(&vox1_grad,&p1_rf,WRITE,"vox1_grad");
calc_slice(&vox2_grad,&p2_rf,WRITE,"vox2_grad");
calc_slice(&vox3_grad,&p3_rf,NOWRITE,"");
calc_slice(&vox3_crush,&p3_rf,WRITE,"vox3_crush");
calc_slice(&vox3r_crush,&p3_rf,NOWRITE,"");
vox3r_crush.crusher1Moment0 -= vox2_grad.m0ref; //only now can re-calculate the moment
vox3r_crush.crusher1CalcFlag=AMPLITUDE_FROM_MOMENT_DURATION_RAMP;
calc_slice(&vox3r_crush,&p3_rf,WRITE,"vox3r_crush");
vox3_grad.crusher2Moment0 *= vox3_grad.m0def/vox3_grad.m0ref*ky; //only now can re-calculate the moment
vox3_grad.crusher2CalcFlag=AMPLITUDE_FROM_MOMENT_DURATION_RAMP;
calc_slice(&vox3_grad,&p3_rf,WRITE,"vox3_grad");
calc_generic(&tmcrush_grad,WRITE,"","");
if (profile_vox[0] == 'y') {
calc_readout(&ro_grad,WRITE,"gro","sw","at");
putvalue("gro",ro_grad.roamp); // RO grad
calc_readout_refocus(&ror_grad,&ro_grad,WRITE,"gror");
putvalue("tror",ror_grad.duration); // ROR duration
}
if (profile_ovs[0]=='y'){
if (rprof==1) {
vox1_grad.amp=0;
}
else if(pprof==1) {
vox2_grad.amp=0;
}
else if(sprof==1) {
vox3_grad.amp=0;
}
}
/***** Check nt is a multiple of 2 *****/
if (ix == 1) {
if ((int)nt%2 != 0)
text_message("WARNING: SPECIAL requires 2 steps. Set nt as a multiple of 2\n");
}
/* Optional Outer Volume Suppression */
if (ovs[0] == 'y') create_ovsbands();
if (sat[0] == 'y') create_satbands();
/* Optional Water Suppression */
if (ws[0] == 'y') create_watersuppress();
/***** Set up frequency offset pulse shape list *****/
offsetlist(&pos1,vox1_grad.ssamp,0,&freq1,1,'s');
offsetlist(&pos2,vox2_grad.ssamp,0,&freq2,1,'s');
offsetlist(&pos3,vox3_grad.ssamp,0,&freq3,1,'s');
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
freq1=freq1-csd_ppm*sfrq;
freq2=freq2-csd_ppm*sfrq;
freq3=freq3-csd_ppm*sfrq;
shapelist1 = shapelist(p1_rf.pulseName,vox1_grad.rfDuration,&freq1,1,vox1_grad.rfFraction,'s');
shapelist2 = shapelist(p2_rf.pulseName,vox2_grad.rfDuration,&freq2,1,vox2_grad.rfFraction,'s');
shapelist3 = shapelist(p3_rf.pulseName,vox3_grad.rfDuration,&freq3,1,vox3_grad.rfFraction,'s');
/* Calculate delta from resto to include local frequency line + chemical shift offset */
resto_local=resto-restol;
/* Frequency offsets */
if (profile_vox[0] == 'y') {
/* Shift DDR for pro ************************************/
roff = -poffset(pro,ro_grad.roamp);
}
/* Set tables */
/* Real time variables for inversion pulses */
settable(t1,noph,inv1);
settable(t2,noph,inv2);
settable(t3,noph,inv3);
/* Phase cycle for excitation pulse and receiver */
if (isis!=1) settable(t4,noph,phrec0);
else settable(t4,noph,phrec);
/* shapedpulselist variable */
assign(one,vms);
/* Put gradient information back into VnmrJ parameters */
putvalue("gvox1",vox1_grad.ssamp);
putvalue("gvox2",vox2_grad.ssamp);
putvalue("gvox3",vox3_grad.ssamp);
putvalue("rgvox1",vox1_grad.tramp);
putvalue("rgvox2",vox2_grad.tramp);
putvalue("rgvox3",vox3_grad.tramp);
sgl_error_check(sglerror);
if (ss<0) g_setExpTime(trmean*(nt-ss)*arraydim);
else g_setExpTime(tr*(ntmean*arraydim+ss));
/* PULSE SEQUENCE *************************************/
/* Real time variables for inversion pulses */
counter=(double)nt*(ix-1);
if (autoph[0] == 'n') counter=0.0;
initval(counter,v11);
initval(noph,v13); //v13=number of phase cycling steps
add(v11,ctss,v12); //v12=counter
modn(v12,v13,v12); //v12 runs from 1:v13
getelem(t1,v12,v8); /* 90 DEG. SPIN ECHO PULSE */
getelem(t2,v12,v9); /* 180 DEG. SPIN ECHO P. */
getelem(t3,v12,v10); /* ISIS 180 DEG. ADIAB. PULSE */
getelem(t4,v12,oph); /*RCVR PHASE*/
mod2(v12,vinv1); // this controls 1D isis on, off, on, of... up to noph(=32)
/****************************************************/
/* Sequence Timing **********************************/
/****************************************************/
/* Min TE ******************************************/
tau1 = vox2_grad.rfCenterBack + vox3_grad.rfCenterFront;
tau2 = vox3_grad.rfCenterBack+alfa;
temin = 2*(MAX(tau1,tau2) + 4e-6); /* have at least 4us between gradient events */
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
else if (te < temin) {
abort_message("TE too short. Minimum TE = %.2fms\n",temin*1000);
}
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
printf("te delay1 is %f", te_delay1);
printf("te delay2 is %f", te_delay2);
/***************************************************/
/* Min TM ******************************************/
if (ws_tm[0] == 'y') {
tau1 = vox1_grad.rfCenterBack + rof1+rof2+p4_rf.rfDuration+tmcrush_grad.duration + 4e-6 + vox2_grad.rfCenterFront;
}
else tau1 = vox1_grad.rfCenterBack + rof2+tmcrush_grad.duration + 4e-6 + vox2_grad.rfCenterFront;
tmmin = tau1 + 4e-6; /* have at least 4us between gradient events */
if (mintm[0] == 'y') {
tm = tmmin;
putvalue("tm",tm);
}
else if (tm < tmmin) {
abort_message("TM too short. Minimum TM = %.2fms\n",tmmin*1000);
}
tm_delay = (tm - tau1);
/* Relaxation delay ***********************************/
/***** Min TR *****/
trmin = vox1_grad.rfCenterFront + tm + te+alfa + at + 20e-6;
if (profile_vox[0] == 'y') trmin += ror_grad.duration + ro_grad.duration - at;
if (ws[0] == 'y') trmin += wsTime;
if (ovs[0] == 'y') trmin += ovsTime;
if (sat[0] == 'y') trmin += satTime;
if (mintr[0] == 'y') {
tr = trmin;
putCmd("setvalue('tr',%f,'current')\n",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("tr too short. Minimum tr = %.2f ms\n",(trmin)*1000);
}
/***** Calculate TR delay *****/
tr_delay = tr - trmin;
/**Sequence Begin**/
status(A);
obsoffset(resto_local);
delay(4e-6);
set_rotation_matrix(vpsi,vphi,vtheta);
if (ticks > 0) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* Saturation bands ***********************************/
if (ovs[0] == 'y') ovsbands();
if (sat[0] == 'y') satbands();
/* Post OVS water suppression *************************/
if (ws[0] == 'y') watersuppress();
/* First inversion pulse *****/
if (isis >= 1){ /*for the ISIS pulse on,off,on,off... or on,on,on,on... */
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
if (isis == 1) /* for ISIS on,off,on,off,... */{
ifzero(vinv1);
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
shapedpulselist(shapelist1,vox1_grad.rfDuration,v10,rof1,rof2,'s',vms);
delay(vox1_grad.rfDelayBack);
elsenz(vinv1);
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,WAIT);
endif(vinv1);
}
else { /* for ISIS on,on,on,on...*/
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
shapedpulselist(shapelist1,vox1_grad.rfDuration,v10,rof1,rof2,'s',vms);
delay(vox1_grad.rfDelayBack);
}
}
else delay(vox1_grad.duration); //this is for isis off,off,off,off
/* tm delay before excitation pulse *****/
/* Optional TM water suppression ***********************/
if (ws_tm[0] == 'y') {
if (wsrf[0]=='y') {
obspower(p4_rf.powerCoarse);
obspwrf(p4_rf.powerFine);
delay(4e-6);
shapedpulseoffset(p4_rf.pulseName,p4_rf.rfDuration,zero,rof1,rof2,ws_delta);
}
else delay(p4_rf.rfDuration+rof1+rof2);
} //end of ws_tm='y' condition
delay(tm_delay);
/* TM Gradient crusher ********************************/
obl_shapedgradient(tmcrush_grad.name,tmcrush_grad.duration,0,0,tmcrush_grad.amp,WAIT);
/* 90 degree excitation pulse *****/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(vox2_grad.name,vox2_grad.duration,0,vox2_grad.amp,0,NOWAIT);
delay(vox2_grad.rfDelayFront);
shapedpulselist(shapelist2,vox2_grad.rfDuration,v8,rof1,rof2,'s',vms);
delay(vox2_grad.rfDelayBack);
delay(te_delay1);
/* 180 degree pulse ********************************/
obspower(p3_rf.powerCoarse);
obspwrf(p3_rf.powerFine);
delay(4e-6);
obl_shaped3gradient (vox3_crush.name,vox3r_crush.name,vox3_grad.name,vox3_grad.duration,vox3_crush.amp,vox3r_crush.amp,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
shapedpulselist(shapelist3,vox3_grad.rfDuration,v9,rof1,rof2,'s',vms);
delay(vox3_grad.rfDelayBack);
delay(te_delay2);
//acquisition starts
if (profile_vox[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,
-rprof*ror_grad.amp,-pprof*ror_grad.amp,-sprof*ror_grad.amp,WAIT);
delay(4e-6);
obl_shapedgradient(ro_grad.name,ro_grad.duration,
rprof*ro_grad.amp,pprof*ro_grad.amp,sprof*ro_grad.amp,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
} else {
startacq(alfa);
acquire(np,1.0/sw);
endacq();
}
delay(tr_delay);
}
