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 *************************/
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 *************************/
double freqEx[MAXNSLICE], freqIR[MAXNSLICE];
double pe_steps,pespoil_amp;
double perTime, seqtime, tau1, tauIR=0, te_delay, tr_delay, ti_delay=0;
int table, shapeEx, shapeIR=0;
char spoilflag[MAXSTR],per_name[MAXSTR];
/* 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 vper_mult = v7; // PE rewinder multiplier; turn off rewinder when 0
int vssc = v8; // Compressed steady-states
int vacquire = v9; // Argument for setacqvar, to skip steady state acquires
int vrfspoil_ctr = v10; // RF spoil counter
int vrfspoil = v11; // RF spoil multiplier
int vtrimage = v12; // Counts down from nt, trimage delay when 0
/* Initialize paramaters **********************************/
get_parameters();
get_ovsparameters();
getstr("spoilflag",spoilflag);
/* Check for external PE table ***************************/
table = 0;
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
/* Set Rcvr/Xmtr phase increments for RF Spoiling ********/
/* Ref: Zur, Y., Magn. Res. Med., 21, 251, (1991) *******/
if (rfspoil[0] == 'y') {
rcvrstepsize(rfphase);
obsstepsize(rfphase);
}
/* Initialize gradient structures *************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2 ); // excitation pulse
init_slice(&ss_grad,"ss",thk); // slice select gradient
init_slice_refocus(&ssr_grad,"ssr"); // slice refocus gradient
init_readout(&ro_grad,"ro",lro,np,sw); // readout gradient
init_readout_refocus(&ror_grad,"ror"); // dephase gradient
init_phase(&pe_grad,"pe",lpe,nv); // phase encode gradient
init_phase(&per_grad,"per",lpe,nv); // phase encode gradient
init_generic(&spoil_grad,"spoil",gspoil,tspoil); // spoiler gradient
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice_refocus(&ssr_grad, &ss_grad, NOWRITE,"gssr");
calc_readout(&ro_grad, WRITE, "gro","sw","at");
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,tpemin, WRITE);
/* Calculate phase-rewind & spoiler gradients *************/
pespoil_amp = 0.0;
perTime = 0.0;
if ((perewind[0] == 'y') && (spoilflag[0] == 'n')) { // Rewinder, no spoiler
calc_phase(&per_grad,WRITE,"","");
strcpy(per_name,per_grad.name);
perTime = per_grad.duration;
spoil_grad.amp = 0.0;
}
else if ((perewind[0] == 'n') && (spoilflag[0] == 'y')) { // Spoiler, no rewinder
calc_generic(&spoil_grad,WRITE,"","");
strcpy(per_name,spoil_grad.name);
perTime = spoil_grad.duration;
pespoil_amp = spoil_grad.amp; // Apply spoiler on PE axis if no rewinder
}
else if ((perewind[0] == 'y') && (spoilflag[0] == 'y')) { // Rewinder and spoiler
calc_phase(&per_grad,NOWRITE,"","");
calc_generic(&spoil_grad,NOWRITE,"","");
calc_sim_gradient(&per_grad,&spoil_grad,&null_grad,0.0,WRITE);
strcpy(per_name,per_grad.name);
perTime = per_grad.duration;
}
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ovs[0] == 'y') {
/* Must set up a few voxel specific parameters for create_ovsbands() to function */
vox1_grad.thickness = vox1;
vox2_grad.thickness = vox2;
vox3_grad.thickness = vox3;
vox1_grad.rfBandwidth = vox2_grad.rfBandwidth = vox3_grad.rfBandwidth = p1_rf.bandwidth;
create_ovsbands();
}
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,gcrush,tcrush);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
tauIR = ss_grad.duration - ss_grad.rfCenterBack; // Duration of ss_grad before RF center
ti_delay = ti - (ssi_grad.rfCenterFront + tauIR);
if (ti_delay < 0) {
abort_message("TI too short, Minimum TI = %.2fms\n",(ti-ti_delay)*1000);
}
irTime = 4e-6 + ti + ssi_grad.duration - ssi_grad.rfCenterBack; // Time to add to TR
}
/* Check that all Gradient calculations are ok ************/
sgl_error_check(sglerror);
/* Min TE ******************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + alfa + ro_grad.timeToEcho;
temin = tau1 + 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 - tau1;
/* Min TR ******************************************/
seqtime = ss_grad.duration + te_delay + pe_grad.duration
+ ro_grad.duration + perTime + tep + alfa;
/* Increase TR if any options are selected ****************/
if (sat[0] == 'y') seqtime += satTime;
if (fsat[0] == 'y') seqtime += fsatTime;
if (mt[0] == 'y') seqtime += mtTime;
if (ovs[0] == 'y') seqtime += ovsTime;
if (ir[0] == 'y') {
seqtime += irTime;
seqtime -= tauIR; /* subtract out ss_grad which was already included in TR */
}
trmin = seqtime + 4e-6; /* ensure that tr_delay is at least 4us */
trmin *= ns;
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000+0.005);
}
tr_delay = (tr - seqtime*ns)/ns;
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1pat,ss_grad.rfDuration,freqEx,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,&per_grad);
initval(pe_steps/2.0,vpe_offset);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
g_setExpTime(tr*(nt*pe_steps*arraydim + ssc));
/* PULSE SEQUENCE *************************************/
status(A);
rotate();
obsoffset(resto);
delay(4e-6);
initval(fabs(ssc),vssc); // Compressed steady-state counter
assign(zero,vrfspoil_ctr); // RF spoil phase counter
assign(zero,vrfspoil); // RF spoil multiplier
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* Delay all channels except gradient *****************/
sub(ssval,ssctr,v30);
add(v30,ct,v30);
if (ix == 1) { ifzero(v30); grad_advance(tep); endif(v30); }
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
/* 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);
}
/* Set rcvr/xmtr phase for RF spoiling *******************/
if (rfspoil[0] == 'y') {
incr(vrfspoil_ctr); // vrfspoil_ctr = 1 2 3 4 5 6
add(vrfspoil,vrfspoil_ctr,vrfspoil); // vrfspoil = 1 3 6 10 15 21
xmtrphase(vrfspoil);
rcvrphase(vrfspoil);
}
/* 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);
}
/* PE rewinder follows PE table; zero if turned off ***/
if (perewind[0] == 'y')
assign(vpe_mult,vper_mult);
else
assign(zero,vper_mult);
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
triggerSelect(trigger); // Selectable trigger input
delay(4e-6);
if (ticks) {
xgate(ticks);
grad_advance(tep); // Gradient propagation delay
}
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
if (ovs[0] == 'y') {ovsbands(); rotate();}
/* 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,rof2,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(shapeEx,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,-ror_grad.amp,0,-ssr_grad.amp,
-pe_grad.increment,vpe_mult,WAIT);
/* TE delay *******************************************/
delay(te_delay);
/* Readout gradient and acquisition ********************/
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 / spoiler gradient *********************************/
if ((perewind[0] == 'y') || (spoilflag[0] == 'y')) {
pe_shapedgradient(per_name,perTime,spoil_grad.amp,pespoil_amp,spoil_grad.amp,
per_grad.increment,vper_mult,WAIT);
}
/* Relaxation delay ***********************************/
if (!trtype)
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
if (trtype)
delay(ns*tr_delay);
endpeloop(seqcon[2],vpe_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
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 freq90[MAXNSLICE],freq180[MAXNSLICE];
int shape90,shape180;
double minTE, te_delay1, te_delay2, minTR, tr_delay;
double tref, te1, te2;
int tpwr1f, tpwr2f;
/* Real-time variables ****************************/
int vms_slices = v1;
int vms_ctr = v2;
/* Initialize parameters *************************/
init_mri();
tpwr1f = (int) getval("tpwr1f");
tpwr2f = (int) getval("tpwr2f");
if ((nv > 0) && (profile[0] == 'n'))
abort_message("Sorry, this sequence only acquires a profile, check the profile flag");
/* Read RF shape but don't calculate powers *******/
init_rf(&p1_rf,p1pat,p1,-1,rof1,rof2);
calc_rf(&p1_rf,"","");
init_rf(&p2_rf,p2pat,p2,-1,rof1,rof1);
calc_rf(&p2_rf,"","");
/* Gradient Calculations **************************/
init_slice(&ss_grad,"gss",thk);
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
init_slice_refocus(&ssr_grad, "ssr");
calc_slice_refocus(&ssr_grad, &ss_grad, NOWRITE,"gssr");
init_slice_butterfly(&ss2_grad,"gss2",thk,gcrush,tcrush);
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss");
init_readout(&ro_grad,"ro",lro,np,sw);
calc_readout(&ro_grad, WRITE, "gro","sw","at");
init_readout_refocus(&ror_grad,"ror");
calc_readout_refocus(&ror_grad, &ro_grad, NOWRITE, "gror");
/* Equalize Refocus Gradients ********************/
tref = calc_sim_gradient(&ror_grad, &ssr_grad, &null_grad, 0, WRITE);
/* Min TE ******************************************/
te1 = ss_grad.rfCenterBack + tref + 4e-6 + ss2_grad.rfCenterFront;
te2 = ss2_grad.rfCenterBack + alfa + ro_grad.timeToEcho;
minTE = 2*(te1 > te2 ? te1 : te2) + 2*4e-6;
if (minte[0] == 'y') {
te = minTE;
putvalue("te",ceil(te*1e6)*1e-6); /* round up to nearest us */
}
if (te < minTE) {
abort_message("TE too short. Minimum TE= %.2fms\n",minTE*1000);
}
te_delay1 = te/2 - te1;
te_delay2 = te/2 - te2;
/* Min TR ******************************************/
minTR = (GDELAY + ss_grad.rfCenterFront + te + ro_grad.timeFromEcho) * ns;
if (mintr[0] == 'y') {
tr = minTR + 4e-6;
putvalue("tr",tr);
}
if (tr < minTR + 4e-6) {
abort_message("TR too short. Minimum TR= %.2fms\n",(minTR + 4e-6)*1000);
}
tr_delay = (tr - minTR)/ns;
if (sglerror)
abort_message("Sequence has error(s) and will not execute - See error message(s)!\n");
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
/* PULSE SEQUENCE *************************************/
settable(t1,4,phr);
getelem(t1,ct,oph); /* receiver phase */
rotate();
obsoffset(resto);
delay(GDELAY);
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
/* RF pulse *******************************************/
obspower(tpwr1);
obspwrf(tpwr1f);
delay(GDELAY);
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);
/* Refocusing gradients ******************/
obl_shaped3gradient(ror_grad.name,"",ssr_grad.name,
ssr_grad.duration,
ror_grad.amp,0,-ssr_grad.amp,WAIT);
delay(te_delay1);
/* RF pulse *******************************************/
obspower(tpwr2);
obspwrf(tpwr2f);
delay(GDELAY);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
delay(te_delay2);
/* Readout gradient and acquisition ********************/
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);
endacq();
delay(ro_grad.atDelayBack);
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
}
pulsesequence() {
/* Acquisition variables */
double dw; /* nominal dwell time, = 1/sw */
double aqtm = getval("aqtm");
/* Delay variables */
double tref,
te_delay1, te_delay2, tr_delay, ti_delay,
del1, del2, del3, del4, del5, /* before and after diffusion gradients */
busy1, busy2, /* time spent on rf pulses etc. in TE periods */
seqtime, invTime;
int use_minte;
/* RF and receiver frequency variables */
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE]; /* frequencies for multi-slice */
int shape90=0, shape180=0, shapeIR=0; /* List ID for RF shapes */
double roff1, roff2, roffn; /* Receiver offsets when FOV is offset along readout */
/* Gradient amplitudes, may vary depending on "image" parameter */
double peramp, perinc, peamp, roamp, roramp;
/* diffusion variables */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
int diff_in_one = 0;
double tmp, tmp_ss2;
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl; /* bvalues*directions along RO, PE, and SL */
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* 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 */
/* loop variable */
int i;
/* Real-time variables used in this sequence **************/
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vnseg = v5; // Number of segments
int vnseg_ctr = v6; // Segment loop counter
int vetl = v7; // Number of choes in readout train
int vetl_ctr = v8; // etl loop counter
int vblip = v9; // Sign on blips in multi-shot experiment
int vssepi = v10; // Number of Gradient Steady States lobes
int vssepi_ctr = v11; // Steady State counter
int vacquire = v12; // Argument for setacqvar, to skip steady states
/******************************************************/
/* VARIABLE INITIALIZATIONS ***************************/
/******************************************************/
get_parameters();
euler_test();
if (tep < 0) { // adjust by reducing gpropdelay by that amount
gpropdelay += tep;
tep = 0;
}
setacqmode(WACQ|NZ); // Necessary for variable rate sampling
use_minte = (minte[0] == 'y');
/******************************************************/
/* CALCULATIONS ***************************************/
/******************************************************/
if (ix == 1) {
/* Calculate RF pulse */
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Calculate gradients: */
init_slice(&ss_grad,"ss",thk);
calc_slice(&ss_grad, &p1_rf,WRITE,"gss");
init_slice_refocus(&ssr_grad,"ssr");
calc_slice_refocus(&ssr_grad, &ss_grad, WRITE,"gssr");
if (spinecho[0] == 'y') {
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof1);
calc_rf(&p2_rf,"tpwr2","tpwr2f");
init_slice_butterfly(&ss2_grad,"ss2",thk,gcrush,tcrush);
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
}
else ss2_grad.duration = 0; /* used for diffusion calculations */
init_readout(&epiro_grad,"epiro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
init_phase(&epipe_grad, "epipe",lpe,nv);
init_phase(&per_grad,"per",lpe,nv);
init_readout(&nav_grad,"nav",lro,np,sw);
init_epi(&epi_grad);
if (!strcmp(orient,"oblique")) {
if ((phi != 90) || (psi != 90) || (theta != 90)) {
/* oblique slice - this should take care of most cases */
epiro_grad.slewRate /= 3; /* = gmax/trise */
epipe_grad.slewRate /= 3;
}
}
calc_epi(&epi_grad,&epiro_grad,&epipe_grad,&ror_grad,&per_grad,&nav_grad,NOWRITE);
/* Make sure the slice refocus, readout refocus,
and phase dephaser fit in the same duration */
tref = calc_sim_gradient(&ror_grad, &per_grad, &null_grad, getval("tpe"), WRITE);
if (sgldisplay) displayEPI(&epi_grad);
/* calc_sim_gradient recalculates per_grad, so reset its
base amplitude for centric ordering or fractional k-space*/
switch(ky_order[0]) {
case 'l':
per_grad.amp *= (fract_ky/(epipe_grad.steps/2));
break;
case 'c':
per_grad.amp = (nseg/2-1)*per_grad.increment;
break;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof1,rof1);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrush,tcrush);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
}
if (fsat[0] == 'y') {
create_fatsat();
}
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
diff_grad.maxGrad = gmax;
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,"","");
}
}
/* Acquire top-down or bottom-up ? */
if (ky_order[1] == 'r') {
epipe_grad.amp *= -1;
per_grad.amp *= -1;
per_grad.increment *= -1;
}
} /* end gradient setup if ix == 1 */
/* Load table used to determine multi-shot direction */
settable(t2,(int) nseg,epi_grad.table2);
/* What is happening in the 2 TE/2 periods (except for diffusion)? */
busy1 = ss_grad.rfCenterBack + ssr_grad.duration;
busy2 = tep + nav_grad.duration*(epi_grad.center_echo + 0.5);
if (navigator[0] == 'y')
busy2 += (tep + nav_grad.duration + per_grad.duration);
/* How much extra time do we have in each TE/2 period? */
if (spinecho[0] == 'y') {
busy1 += (GDELAY + ss2_grad.rfCenterFront);
busy2 += ss2_grad.rfCenterBack;
temin = MAX(busy1,busy2)*2;
if (use_minte) te = temin;
te_delay1 = te/2 - busy1;
te_delay2 = te/2 - busy2;
if (temin > te) { /* Use min TE and try and catch further violations of min TE */
te_delay1 = temin/2 - busy1;
te_delay2 = temin/2 - busy2;
}
}
else { /* Gradient echo */
temin = (busy1 + busy2);
if (use_minte) te = temin;
te_delay1 = te - temin;
te_delay2 = 0;
if (temin > te) te_delay1 = 0;
}
/* Now fill in the diffusion delays:
del1 = between 90 and 1st diffusion gradient
del2 = after 1st diffusion gradient
del3 = before 2nd diffusion gradient when both in same TE/2 period
del4 = before 2nd diffusion gradient when in different TE/2 period
del5 = before acquisition
Ie, the order is:
90 - del1 - diff - del2 - (diff - del3) - 180 - (del4 - diff) - del5 - acq
where one and only one of the two options (diff - del3) or (del4 - diff) is used
*/
if (diff[0] == 'y') {
tmp_ss2 = GDELAY + ss2_grad.duration; /* ss2 grad + 4us delay */
del1 = del2 = del3 = del4 = del5 = 0;
if (tDELTA < (diff_grad.duration + tmp_ss2)) /* Minimum DELTA */
abort_message("ERROR %s: tDELTA is too short, minimum is %.2fms\n",
seqfil,(diff_grad.duration + tmp_ss2)*1000+0.005);
if (tDELTA + diff_grad.duration > te_delay1 + tmp_ss2 + te_delay2) {
if (!use_minte) {
abort_message("ERROR %s: Maximum tDELTA is %.2fms",
seqfil,te_delay1 + ss2_grad.duration + te_delay2 - diff_grad.duration);
}
else {
tmp = (tDELTA + diff_grad.duration) - (te_delay1 + tmp_ss2 + te_delay2);
if (spinecho[0] == 'y') {
te_delay1 += (tmp/2);
te_delay2 += (tmp/2);
}
else
te_delay1 += tmp;
temin += tmp;
}
}
if (spinecho[0] == 'y') {
if (te_delay1 >= (tDELTA + diff_grad.duration)) { /* Put them both in 1st TE/2 period, */
diff_in_one = (diff[0] == 'y'); /* no need to increase temin */
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = te_delay1 - (tDELTA+diff_grad.duration); /* time after diffusion gradients */
del5 = te_delay2; /* delay in second TE/2 period */
}
else { /* put them on each side of the 180 */
diff_in_one = 0;
busy1 += diff_grad.duration;
busy2 += diff_grad.duration;
temin = 2*MAX(busy1,busy2);
/* Optimally, the 2nd diff grad is right after the 180 */
del2 = tDELTA - diff_grad.duration - tmp_ss2; /* This is always > 0, or we would have aborted above */
del1 = te_delay1 - (diff_grad.duration + del2);
if (del1 < 0) {
del1 = 0; /* Place the 1st right after the 90 and push the 2nd out */
del4 = tDELTA - te_delay1 - ss2_grad.duration;
}
del5 = te_delay2 - (del4 + diff_grad.duration);
/* del5 could still be < 0, when te_delay2 < diff_grad.duration */
if (del5 < 0) {
del1 += fabs(del5); /* Increase each TE/2 period by abs(del5) */
del5 = 0;
}
}
}
else { /* gradient echo */
diff_in_one = (diff[0] == 'y');
del1 = 0;
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = 0;
del4 = 0;
if (!use_minte) /* user defined TE */
del5 = te_delay1 - (tDELTA + diff_grad.duration);
}
} /* End of Diffusion block */
else {
del1 = te_delay1;
del5 = te_delay2;
del2 = del3 = del4 = 0;
}
if (sgldisplay) {
text_message("busy1/2, temin = %f, %f, %f",busy1*1e3, busy2*1e3, temin*1e3);
text_message("te_delay1/2 = %f, %f",te_delay1*1e3, te_delay2*1e3);
text_message("delays 1-5: %.2f, %.2f, %.2f, %.2f, %.2fms\n",del1*1000,del2*1000,del3*1000,del4*1000,del5*1000);
}
/* Check if TE is long enough */
temin = ceil(temin*1e6)/1e6; /* round to nearest us */
if (use_minte) {
te = temin;
putvalue("te",te);
}
else if (temin > te) {
abort_message("TE too short, minimum is %.2f ms\n",temin*1000);
}
if (ir[0] == 'y') {
ti_delay = ti - (pi*ssi_grad.rfFraction + rof2 + ssi_grad.rfDelayBack)
- (ss_grad.rfDelayFront + rof1 + p1*(1-ss_grad.rfFraction));
if (ti_delay < 0) {
abort_message("TI too short, minimum is %.2f ms\n",(ti-ti_delay)*1000);
}
}
else ti_delay = 0;
invTime = GDELAY + ssi_grad.duration + ti_delay;
/* Minimum TR per slice, w/o options */
seqtime = GDELAY + ss_grad.rfCenterFront // Before TE
+ te
+ (epiro_grad.duration - nav_grad.duration*(epi_grad.center_echo+0.5)); // After TE
/* Add in time for options outside of TE */
if (ir[0] == 'y') seqtime += invTime;
if (fsat[0] == 'y') seqtime += fsatTime;
trmin = seqtime + 4e-6; /* ensure a minimum of 4us in tr_delay */
trmin *= ns;
if (tr - trmin < 0.0) {
abort_message("%s: Requested tr too short. Min tr = %.2f ms\n",
seqfil,ceil(trmin*100000)/100.00);
}
/* spread out multi-slice acquisition over total TR */
tr_delay = (tr - ns*seqtime)/ns;
/******************************************************/
/* Return gradient values to VnmrJ interface */
/******************************************************/
putvalue("etl",epi_grad.etl+2*ssepi);
putvalue("gro",epiro_grad.amp);
putvalue("rgro",epiro_grad.tramp);
putvalue("gror",ror_grad.amp);
putvalue("tror",ror_grad.duration);
putvalue("rgror",ror_grad.tramp);
putvalue("gpe",epipe_grad.amp);
putvalue("rgpe",epipe_grad.tramp);
putvalue("gped",per_grad.amp);
putvalue("tped",per_grad.duration);
putvalue("rgped",per_grad.tramp);
putvalue("gss",ss_grad.amp);
putvalue("gss2",ss2_grad.ssamp);
putvalue("rgss",ss_grad.tramp);
putvalue("gssr",ssr_grad.amp);
putvalue("tssr",ssr_grad.duration);
putvalue("rgssr",ssr_grad.tramp);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
putvalue("rgssi",ssi_grad.crusher1RampToSsDuration);
putvalue("rgcrush",ssi_grad.crusher1RampToCrusherDuration);
putvalue("at_full",epi_grad.duration);
putvalue("at_one",nav_grad.duration);
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("np_ramp",epi_grad.np_ramp);
putvalue("np_flat",epi_grad.np_flat);
if (diff[0] == 'y') { /* CALCULATE B VALUES */
/* 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++) {
/* We need to worry about slice gradients & crushers for slice gradients */
/* Everything else is outside diffusion gradients, and thus constant */
/* for all b-values/directions */
/* Readout */
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Slice */
dgss2 = p2/2; Dgss2 = dgss2;
dcrush = tcrush; Dcrush = dcrush + p2;
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
}
if (!diff_in_one) {
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);
}
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
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);
/* Set all gradients depending on whether we do */
/* Use separate variables, because we only initialize & calculate gradients for ix==1 */
peamp = epipe_grad.amp;
perinc = per_grad.increment;
peramp = per_grad.amp;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
switch ((int)image) {
case 1: /* Real image scan, don't change anything */
break;
case 0: /* Normal reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
break;
case -1: /* Inverted image scan */
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
case -2: /* Inverted reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
default: break;
}
/* 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]);
if (spinecho[0] == 'y') {
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]);
}
sgl_error_check(sglerror);
roff1 = -poffset(pro,epi_grad.amppos);
roff2 = -poffset(pro,epi_grad.ampneg);
roffn = -poffset(pro,nav_grad.amp);
roff1 = -poffset(pro,epi_grad.amppos*roamp/epiro_grad.amp);
roff2 = -poffset(pro,epi_grad.ampneg*roamp/epiro_grad.amp);
roffn = -poffset(pro,nav_grad.amp);
dw = granularity(1/sw,1/epi_grad.ddrsr);
/* Total Scan Time */
g_setExpTime(tr*nt*nseg*arraydim);
/******************************************************/
/* PULSE SEQUENCE *************************************/
/******************************************************/
rotate();
F_initval(epi_grad.etl/2, vetl);
/* vetl is the loop counter in the acquisition loop */
/* that includes both a positive and negative readout lobe */
F_initval(nseg, vnseg);
/* NB. F_initval(-ssepi,vssepi); currently gives errors */
initval(-ssepi,vssepi); /* gradient steady state lobes */
obsoffset(resto); delay(GDELAY);
ifzero(rtonce); grad_advance(gpropdelay); endif(rtonce);
loop(vnseg,vnseg_ctr); /* Loop through segments in segmented EPI */
msloop(seqcon[1],ns,vms_slices,vms_ctr); /* Multislice loop */
assign(vssepi,vssepi_ctr);
sp1on(); delay(4e-6); sp1off(); /* Output trigger to look at scope */
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
getelem(t2,vnseg_ctr,vblip); /* vblip = t2[vnseg_ctr]; either 1 or -1 for pos/neg blip */
/* Optional FAT SAT */
if (fsat[0] == 'y') {
fatsat();
}
/* Optional IR + TI delay */
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0.0,0.0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayBack);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* 90 ss degree pulse */
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0.0,0.0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,p1_rf.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus */
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(del1);
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);
if (diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
-diff_grad.amp*dro,-diff_grad.amp*dpe,-diff_grad.amp*dsl,WAIT);
delay(del3);
/* Optional 180 ss degree pulse with crushers */
if (spinecho[0] == 'y') {
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0.0,0.0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
}
delay(del4);
if ((diff[0] == 'y') && !diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del5);
/* Optional navigator echo */
if (navigator[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,roramp,0,0,WAIT);
obl_shapedgradient(nav_grad.name,nav_grad.duration,
-nav_grad.amp,0,0,NOWAIT);
delay(tep);
roff = roffn; /* Set receiver offset for navigator gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
/* Phase encode dephaser here if navigator echo was acquired */
var_shapedgradient(per_grad.name,per_grad.duration,0,-peramp,0,perinc,vnseg_ctr,WAIT);
}
else {
var_shapedgradient(per_grad.name,per_grad.duration,
-roramp,-peramp,0,perinc,vnseg_ctr,WAIT);
}
/* Start readout and phase encode gradient waveforms, NOWAIT */
/* If alternating ky-ordering, get polarity on blips from table */
var_shaped3gradient(epiro_grad.name,epipe_grad.name,"", /* patterns */
epiro_grad.duration, /* duration */
roamp,0,0, /* amplitudes */
peamp,vblip, /* step and multiplier */
NOWAIT); /* Don't wait */
delay(tep);
/* Acquisition loop */
assign(one,vacquire); // real-time acquire flag
nowait_loop(epi_grad.etl/2 + ssepi,vetl,vetl_ctr);
ifzero(vssepi_ctr); //vssepi_ctr = -ssepi, -ssepi+1, ..., 0, 1,2,...
assign(zero,vacquire); // turn on acquisition after all ss lobes
endif(vssepi_ctr);
incr(vssepi_ctr);
setacqvar(vacquire); // Set acquire flag
roff = roff1; /* Set receiver offset for positive gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw); //dw = 1/sw
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
roff = roff2; /* Set receiver offset for negative gradient */
delay(epi_grad.skip-alfa);
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
nowait_endloop(vetl_ctr);
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr); /* end multislice loop */
endloop(vnseg_ctr); /* end segments loop */
} /* end pulsesequence */
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);
}