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()
{
/* declaration of SGL kernel structures */
SGL_KERNEL_INFO_T read, phase, slice, ss_pre, ss_post;
/* declaration of internal variables */
double freqlist[MAXNSLICE];
double pe_steps;
int shapelist1, table;
double xtime, grad_duration, ror_pad,rod_pad;
double temp_tr;
double readAmp, phaseAmp, sliceAmp;
double tepad, tepad2, temin2, htrmin, delayToRF, delayRFToAcq, delayAcqToRF;
double rof_pad, delRof;
double sliceRephTrim, sliceDephTrim;
double readRephTrim, readDephTrim;
int rfPhase[2] = {0,2};
/* declaration of realtime 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 vss = v7;
int vssc = v8;
int vacquire = v9;
int vphase = v10;
settable(t2,2,rfPhase);
/* setup phase encoding order */
table = set_pe_order();
init_mri();
if( (sliceRephTrim = getvalnwarn("sliceRephTrim")) == 0.0 ) {
sliceRephTrim = 1.0;
}
if( (sliceDephTrim = getvalnwarn("sliceDephTrim")) == 0.0 ) {
sliceDephTrim = 1.0;
}
if( (readRephTrim = getvalnwarn("readRephTrim")) == 0.0 ) {
readRephTrim = 1.0;
}
if( (readDephTrim = getvalnwarn("readDephTrim")) == 0.0 ) {
readDephTrim = 1.0;
}
shape_rf( &p1_rf, "p1", p1pat, p1, flip1, rof1, rof2 ); // excitation pulse
init_slice( &ss_grad, "ss", thk ); // slice gradient
init_slice_refocus( &ssr_grad, "ssr" ); // slice refocus
init_slice_refocus( &ssd_grad, "ssd" ); // slice refocus
init_readout( &ro_grad, "ro", lro, np, sw ); // read gradient
init_readout_refocus( &ror_grad, "ror" ); // read dephase
init_readout_refocus( &rod_grad, "ror" ); // read dephase
init_phase( &pe_grad, "pe", lpe, nv ); // phase gradient
ss_grad.maxGrad = gmax * 0.57;
ssr_grad.maxGrad = gmax * 0.57;
ssd_grad.maxGrad = gmax * 0.57;
ro_grad.maxGrad = gmax * 0.57;
ror_grad.maxGrad = gmax * 0.57;
rod_grad.maxGrad = gmax * 0.57;
pe_grad.maxGrad = glimpe < 0.57? gmax*glimpe : gmax * 0.57;
/* calculate the RF pulses, gradient pulses and their interdependencies */
calc_rf( &p1_rf, "tpwr1", "tpwr1f" );
calc_slice( &ss_grad, &p1_rf, NOWRITE, "gss" );
ssr_grad.amp = ss_grad.amp;
ssr_grad.gmult = sliceRephTrim;
ssr_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE;
calc_slice_refocus( &ssr_grad, &ss_grad, NOWRITE, "gssr" );
ssd_grad.amp = ss_grad.amp;
ssd_grad.gmult = sliceDephTrim;
ssd_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE;
calc_slice_dephase( &ssd_grad, &ss_grad, NOWRITE, "gssd" );
calc_readout( &ro_grad, NOWRITE, "gro", "sw", "at" );
ror_grad.amp = ro_grad.amp;
ror_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE;
rod_grad.amp = ro_grad.amp;
rod_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE;
ror_grad.gmult = readRephTrim;
calc_readout_refocus( &ror_grad, &ro_grad, NOWRITE, "gror" );
rod_grad.gmult = readDephTrim;
calc_readout_rephase( &rod_grad, &ro_grad, NOWRITE, "grod" );
calc_phase( &pe_grad, NOWRITE, "gpe", "tpe" );
/* work out the position of the markers */
/* markerA */
/* ss_grad.rfDelayFront indicates the starting point of the
RF pulse measured from the start of the slice gradient
( rof1:pulse length:rof2 ) */
double granulatedRFDelayFront = granularity( ss_grad.rfDelayFront, GRADIENT_RES );
if( granulatedRFDelayFront > ss_grad.rfDelayFront ) {
granulatedRFDelayFront -= GRADIENT_RES;
}
/* ss_grad.rfDelayBack indicates the end point of the
RF pulse measured to the end of the slice gradient
( rof1:pulse length:rof2 ) */
double granulatedRFDelayBack = granularity( ss_grad.rfDelayBack, GRADIENT_RES );
if( granulatedRFDelayBack > ss_grad.rfDelayBack ) {
granulatedRFDelayBack -= GRADIENT_RES;
}
double granulatedRFDelay = granulatedRFDelayFront < granulatedRFDelayBack ? granulatedRFDelayFront : granulatedRFDelayBack;
double markerADelay = granulatedRFDelay;
/* read and phase gradients can overlap the start or end of the slice gradient by max of granulatedRFDElay */
double granulatedATDelayFront = granularity(ro_grad.atDelayFront, GRADIENT_RES);
if( granulatedATDelayFront > ro_grad.atDelayFront ) {
granulatedATDelayFront -= GRADIENT_RES;
}
double granulatedATDelayBack = granularity(ro_grad.atDelayBack, GRADIENT_RES);
if( granulatedATDelayBack > ro_grad.atDelayBack ) {
granulatedATDelayBack -= GRADIENT_RES;
}
double granulatedATDelay = granulatedATDelayFront < granulatedATDelayBack ? granulatedATDelayFront : granulatedATDelayBack;
/* longest gradient between RF pulse and acquire dominates */
xtime = ssr_grad.duration + granulatedRFDelay;
xtime = xtime > ssd_grad.duration + granulatedRFDelay ? xtime : ssd_grad.duration + granulatedRFDelay;
xtime = xtime > ror_grad.duration + granulatedATDelay ? xtime : ror_grad.duration + granulatedATDelay;
xtime = xtime > rod_grad.duration + granulatedATDelay ? xtime : rod_grad.duration + granulatedATDelay;
xtime = xtime > pe_grad.duration ? xtime : pe_grad.duration;
ror_pad = xtime - ror_grad.duration - granulatedATDelay;
rod_pad = xtime - rod_grad.duration - granulatedATDelay;
/* make a gradient list */
start_kernel( &sk );
add_gradient( (void*)&ss_grad, "slice", SLICE, START_TIME, "", 0.0, PRESERVE );
add_gradient( (void*)&ssr_grad, "sliceReph", SLICE, BEHIND, "slice", 0.0, INVERT );
add_gradient( (void*)&ror_grad, "readDeph", READ, BEHIND, "slice", -granulatedRFDelay + ror_pad, INVERT );
add_gradient( (void*)&ro_grad, "read", READ, BEHIND, "readDeph", 0.0, PRESERVE );
add_gradient( (void*)&pe_grad, "phase", PHASE, SAME_START, "readDeph", 0.0, PRESERVE );
add_gradient( (void*)&rod_grad, "readReph", READ, BEHIND, "read", 0.0, INVERT );
add_gradient( (void*)&pe_grad, "rewind", PHASE, SAME_END, "readReph", 0.0, INVERT );
add_gradient( (void*)&ss_grad, "nextSlice", SLICE, BEHIND, "readReph", rod_pad - granulatedRFDelay, PRESERVE );
add_gradient( (void*)&ssd_grad, "sliceDeph", SLICE, BEFORE, "nextSlice", 0, INVERT );
add_marker( "markerA", SAME_START, "slice", granulatedRFDelay );
add_marker( "markerB", SAME_START, "nextSlice", granulatedRFDelay );
/* get the minimum echo time */
temin = get_timing( FROM_RF_CENTER_OF, "slice", TO_ECHO_OF, "read" );
temin2 = get_timing( FROM_ECHO_OF, "read", TO_RF_CENTER_OF, "nextSlice" );
htrmin = MAX( temin, temin2 );
if( minte[0] == 'y' ){
te = htrmin;
}
tepad = granularity( te - temin, GRADIENT_RES );
tepad2 = granularity( te - temin2, GRADIENT_RES );
te = temin + tepad;
putCmd("setvalue('te', %f, 'current')\n", te );
if( tepad>0.0 ) change_timing( "readDeph", tepad );
if( tepad2>0.0 ) change_timing( "nextSlice", tepad2 );
tr = get_timing( FROM_START_OF, "slice", TO_START_OF, "nextSlice" );
putvalue("tr", tr );
delayRFToAcq = get_timing( FROM_RF_PULSE_OF, "slice", TO_ACQ_OF, "read" );
delayAcqToRF = get_timing( FROM_ACQ_OF, "read", TO_RF_PULSE_OF, "nextSlice" );
set_comp_info( &ss_pre, "ss_pre" );
write_comp_grads_snippet( NULL, NULL, &ss_pre, "START_OF_KERNEL", "markerA" );
set_comp_info( &read, "ro" );
set_comp_info( &phase, "pe" );
set_comp_info( &slice, "ss" );
write_comp_grads_snippet( &read, &phase, &slice, "markerA", "markerB" );
set_comp_info( &ss_post, "ss_post" );
write_comp_grads_snippet( NULL, NULL, &ss_post, "markerB", "END_OF_KERNEL" );
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp,0,freqlist,ns,seqcon[1]);
shapelist1 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freqlist,ns,ss_grad.rfFraction, seqcon[1]);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&pe_grad);/* profile[0] is n y or r */
F_initval(pe_steps/2.0,vpe_offset);
g_setExpTime(trmean*(ntmean*pe_steps*arraydim + (1+fabs(ssc))*arraydim));
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* PULSE SEQUENCE */
status( A );
rotate();
triggerSelect(trigger);
obsoffset( resto );
delay( GRADIENT_RES );
initval( 1+fabs( ssc ), vss );
obspower( p1_rf.powerCoarse );
obspwrf( p1_rf.powerFine );
delay( GRADIENT_RES );
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
obl_shapedgradient(ss_pre.name,ss_pre.dur,0,0,ss_pre.amp,NOWAIT);
sp1on();
delay(GRADIENT_RES);
sp1off();
delay(ss_pre.dur-GRADIENT_RES );
msloop( seqcon[1], ns, vms_slices, vms_ctr );
assign(vss,vssc);
peloop( seqcon[2], pe_steps, vpe_steps, vpe_ctr );
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);
}
if (table)
getelem(t1,vpe_ctr,vpe_index);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_index);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_index);
endif(vacquire);
}
pe_shaped3gradient( read.name, phase.name, slice.name,
read.dur, read.amp, 0, slice.amp,
-pe_grad.increment, vpe_index, NOWAIT );
delay(ss_grad.rfDelayFront - granulatedRFDelay);
shapedpulselist( shapelist1, ss_grad.rfDuration, oph, rof1, rof2, seqcon[1], vms_ctr );
delay( delayRFToAcq - alfa );
startacq(alfa);
acquire( np, 1/ro_grad.bandwidth );
endacq();
delay( delayAcqToRF - ss_grad.rfDelayFront + granulatedRFDelay - GRADIENT_RES );
sp1on();
delay(GRADIENT_RES);
sp1off();
endpeloop( seqcon[2], vpe_ctr );
endmsloop( seqcon[1], vms_ctr );
obl_shapedgradient(ss_post.name,ss_post.dur,0,0,ss_post.amp,WAIT);
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freqEx[MAXNSLICE];
double maxgradtime,spoilMoment,perTime,tau1,te_delay,tr_delay;
double te2=0.0,te3=0.0,te2min,te3min,tau2,tau3,te2_delay,te3_delay=0;
char minte2[MAXSTR],minte3[MAXSTR],spoilflag[MAXSTR];
int sepSliceRephase,sepReadRephase=0,readrev,table,shapeEx;
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 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
int vne = v13; // Number of echoes
int vne_ctr = v14; // Echo loop counter
int vneindex = v15; // Echo index, odd or even
int vnelast = v16; // Check for last echo
int vtrigblock = v17; // Number of slices per trigger block
/* Initialize paramaters **********************************/
init_mri();
getstr("spoilflag",spoilflag);
te2=getval("te2");
te3=getval("te3");
getstr("minte2",minte2);
getstr("minte3",minte3);
readrev=(int)getval("readrev");
/* 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 *************************/
shape_rf(&p1_rf,"p1",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
ro_grad.pad1=alfa; ro_grad.pad2=alfa;
init_readout_refocus(&ror_grad,"ror"); // dephase gradient
init_phase(&pe_grad,"pe",lpe,nv); // phase encode gradient
init_dephase(&spoil_grad,"spoil"); // optimized spoiler
init_dephase(&ref_grad,"ref"); // readout rephase
/* 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,WRITE,"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");
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
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 slice refocus? ******/
maxgradtime = MAX(ror_grad.duration,pe_grad.duration);
if (spoilflag[0] == 'y')
maxgradtime = MAX(maxgradtime,spoil_grad.duration);
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + maxgradtime + ro_grad.timeToEcho + GRADIENT_RES;
/* Equalize refocus and PE gradient durations *********/
if ((te >= tau1) && (minte[0] != 'y')) {
sepSliceRephase = 1; // Set flag for separate slice rephase
calc_sim_gradient(&ror_grad,&pe_grad,&spoil_grad,tpemin,WRITE);
} else {
sepSliceRephase = 0;
calc_sim_gradient(&ror_grad,&pe_grad,&ssr_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
}
perTime = 0.0;
if ((perewind[0] == 'y') || (spoilflag[0] == 'y'))
perTime = spoil_grad.duration;
if (spoilflag[0] == 'n')
spoil_grad.amp = 0.0;
/* 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') create_inversion_recovery();
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freqEx,ns,ss_grad.rfFraction,seqcon[1]);
/* Check that all Gradient calculations are ok ************/
sgl_error_check(sglerror);
/* Min TE ******************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + ro_grad.timeToEcho;
tau1 += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
temin = tau1 + GRADIENT_RES; /* ensure that te_delay is at least GRADIENT_RES */
te = granularity(te,GRADIENT_RES);
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (FP_LT(te,temin)) {
abort_message("TE too short. Minimum TE= %.3fms\n",temin*1000);
}
te_delay = te - tau1;
/* Min TE2 *****************************************/
tau2 = (readrev) ? 2*ro_grad.timeFromEcho : ro_grad.duration+ref_grad.duration;
te2min = tau2 + GRADIENT_RES;
te2 = granularity(te2,GRADIENT_RES);
if (minte2[0] == 'y') {
te2 = te2min;
putvalue("te2",te2);
}
if (FP_LT(te2,te2min)) {
abort_message("TE2 too short. Minimum TE2= %.3fms\n",te2min*1000);
}
if (readrev) te2_delay = te2 - tau2;
else {
tau2 = ro_grad.duration + 3*ror_grad.duration;
if (te2 >= tau2) {
sepReadRephase = 1; // Set flag for separate read rephase
te2_delay = te2 - ro_grad.duration - 2*ror_grad.duration;
} else {
sepReadRephase = 0;
if (te2 > te2min+GRADIENT_RES) {
ref_grad.duration = granularity(te2-ro_grad.duration-2*GRADIENT_RES,GRADIENT_RES);
ref_grad.calcFlag = AMPLITUDE_FROM_MOMENT_DURATION;
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
}
te2_delay = te2 - ro_grad.duration - ref_grad.duration;
}
}
/* Min TE3 *****************************************/
if (readrev) {
tau3 = 2*ro_grad.timeToEcho;
te3min = tau3 + GRADIENT_RES;
te3 = granularity(te3,GRADIENT_RES);
if (minte3[0] == 'y') {
te3 = te3min;
putvalue("te3",te3);
}
if (FP_LT(te3,te3min)) {
abort_message("TE3 too short. Minimum TE3= %.3fms\n",te3min*1000);
}
te3_delay = te3 - tau3;
}
/* Now set the TE array accordingly */
putCmd("TE = 0"); /* Re-initialize TE */
putCmd("TE[1] = %f",te*1000);
if (readrev) {
for (i=1;i<ne;i++) {
if (i%2 == 0) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te3*1000);
else putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
} else {
for (i=1;i<ne;i++) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Min TR ******************************************/
trmin = ss_grad.duration + te_delay + pe_grad.duration + ne*ro_grad.duration + perTime + 2*GRADIENT_RES;
trmin += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
if (readrev) trmin += (ne/2)*te2_delay + ((ne-1)/2)*te3_delay;
else trmin += (sepReadRephase) ? (ne-1)*(te2_delay+2*ror_grad.duration) : (ne-1)*(te2_delay+ref_grad.duration);
/* Increase TR if any options are selected *********/
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 = %.3fms\n",trmin*1000);
}
/* Calculate tr delay */
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&per_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);
/* PULSE SEQUENCE ***************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(GRADIENT_RES);
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
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
/* 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);
}
/* 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);
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);
}
/* TTL scope trigger **********************************/
sp1on(); delay(GRADIENT_RES); sp1off();
/* 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(shapeEx,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
if (sepSliceRephase) { // separate slice refocus gradient
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(te_delay); // delay between slab refocus and pe
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,
-pe_grad.increment,vpe_mult,WAIT);
} else {
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,-ssr_grad.amp,
-pe_grad.increment,vpe_mult,WAIT);
delay(te_delay); // delay after refocus/pe
}
F_initval(ne,vne);
loop(vne,vne_ctr);
if (readrev) {
mod2(vne_ctr,vneindex);
ifzero(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te2_delay);
endif(vnelast);
elsenz(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,-ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te3_delay);
endif(vnelast);
endif(vneindex);
} else {
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
if (sepReadRephase) {
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
delay(te2_delay);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
} else {
obl_shapedgradient(ref_grad.name,ref_grad.duration,-ref_grad.amp,0,0,WAIT);
delay(te2_delay);
}
endif(vnelast);
}
endloop(vne_ctr);
/* Rewind / spoiler gradient **************************/
if ((perewind[0] == 'y') || (spoilflag[0] == 'y')) {
pe_shapedgradient(pe_grad.name,pe_grad.duration,spoil_grad.amp,0,0,pe_grad.increment,vper_mult,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);
}
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() {
/* 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 */
void pulsesequence() {
/* Internal variable declarations *********************/
int shapelist90,shapelist180,shapelistte=0;
double kzero,thk2fact,thk3fact;
double te1=0.0,te1_delay,te2_delay,te3_delay,tr_delay,te_delay1=0.0,te_delay2=0.0;
double crushm0,pem0,gcrushr,gcrushp,gcrushs;
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqte[MAXNSLICE];
char autocrush[MAXSTR];
/* Phase encode variables */
FILE *fp;
int tab[4096],petab[4096],odd,seg0,tabscheme;
char tabname[MAXSTR],tabfile[MAXSTR];
int i,j,k;
/* Diffusion variables */
double Gro,Gss; // "gdiff" for readout/readout refocus and slice/slice refocus
double dgro,Dgro; // delta and DELTA for readout dephase & readout
double dgss,Dgss; // delta and DELTA for excitation ss
double dgss3,Dgss3; // delta and DELTA for spin echo prep ss
double dcrush3,Dcrush3; // delta and DELTA for spin echo prep crusher
double dgss2,Dgss2; // delta and DELTA for refocus ss
double dcrush2,Dcrush2; // delta and DELTA for refocus crusher
/* 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 vpe2_steps = v10; // Number of PE2 steps
int vpe2_ctr = v11; // PE2 loop counter
int vpe2_mult = v12; // PE2 multiplier
int vpe2_offset = v13; // PE2/2 for non-table offset
int vssc = v14; // Compressed steady-states
int vtrimage = v15; // Counts down from nt, trimage delay when 0
int vacquire = v16; // Argument for setacqvar, to skip steady state acquires
int vphase180 = v17; // phase of 180 degree refocusing pulse
int vtrigblock = v18; // Number of slices per trigger block
/* Initialize paramaters ******************************/
init_mri();
kzero = getval("kzero");
getstr("autocrush",autocrush);
tabscheme = getval("tabscheme");
getstr("spoilflag",spoilflag);
/* Allow ROxPE2 projection ****************************/
if (profile[0] == 'y' && profile[1] == 'n') {
etl=1; kzero=1; nv=nv2;
} else {
/* Check kzero is valid *****************************/
if (kzero<1) kzero=1; if (kzero>etl) kzero=etl;
putCmd("kzero = %d",(int)kzero);
}
/* Set petable name and full path *********************/
sprintf(tabname,"fse%d_%d_%d",(int)nv,(int)etl,(int)kzero);
putCmd("petable = '%s'",tabname);
strcpy(tabfile,userdir);
strcat(tabfile,"/tablib/");
strcat(tabfile,tabname);
/* Generate phase encode table ************************/
if (tabscheme) { /* New scheme */
/* Calculate PE table for kzero=1 */
seg0=nseg/2;
for (j=0;j<seg0;j++) {
for (i=0;i<etl/2;i++) tab[j*(int)etl+i] = i*nseg+seg0-j;
for (i=1;i<=etl/2;i++) tab[(j+1)*(int)etl-i] = tab[j*(int)etl]-i*nseg;
}
for (j=seg0;j<nseg;j++) {
for (i=0;i<=etl/2;i++) tab[j*(int)etl+i] = i*nseg+seg0-j;
for (i=1;i<etl/2;i++) tab[(j+1)*(int)etl-i] = tab[j*(int)etl]-i*nseg;
}
/* Adjust for kzero */
for (i=0;i<nseg;i++) {
k=i*etl;
for (j=0;j<kzero-1;j++) petab[k+j]=tab[k+(int)etl-(int)kzero+j+1];
for (j=kzero-1;j<etl;j++) petab[k+j]=tab[k+j-(int)kzero+1];
}
} else { /* Original scheme */
/* Calculate PE table for kzero=1 */
odd=(int)nseg%2; seg0=nseg/2+odd;
k=0; for (i=0;i<etl;i++) for (j=seg0-odd*i%2-1;j>=0;j--) tab[j*(int)etl+i] = k--;
k=1; for (i=0;i<etl;i++) for (j=seg0-odd*i%2;j<nseg;j++) tab[j*(int)etl+i] = k++;
/* Adjust for kzero */
for (i=0;i<nseg;i++) {
k=i*etl;
for (j=0;j<kzero-1;j++) petab[k+j]=tab[k+(int)etl-j-1];
for (j=kzero-1;j<etl;j++) petab[k+j]=tab[k+j-(int)kzero+1];
}
}
/* Set petable name and full path *********************/
sprintf(tabname,"fse%d_%d_%d",(int)nv,(int)etl,(int)kzero);
putCmd("petable = '%s'",tabname);
strcpy(tabfile,userdir);
strcat(tabfile,"/tablib/");
strcat(tabfile,tabname);
/* Write to tabfile ***********************************/
fp=fopen(tabfile,"w");
fprintf(fp,"t1 =");
for (i=0;i<nseg;i++) {
fprintf(fp,"\n");
for (j=0;j<etl;j++) fprintf(fp,"%3d\t",petab[i*(int)etl+j]);
}
fclose(fp);
/* Set pelist to contain table order ******************/
putCmd("pelist = 0"); /* Re-initialize pelist */
for (i=0;i<nseg*etl;i++) putCmd("pelist[%d] = %d",i+1,petab[i]);
/* Avoid gradient slew rate errors */
for (i=0;i<nseg*etl;i++) if (abs(petab[i]) > nv/2) petab[i]=0;
/* Set phase encode table *****************************/
settable(t1,(int)etl*nseg,petab);
/* 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");
/* Calculate thk2fact to ensure gss=gss2 for the choice of p1 and p2
so that the sequence remains robust in the absence of correct
balancing of slice select and slice refocus gradients */
thk2fact=p2_rf.bandwidth/p1_rf.bandwidth;
putvalue("thk2fact",thk2fact);
/* Initialize gradient structures *********************/
init_readout(&ro_grad,"ro",lro,np,sw);
ro_grad.pad1=alfa; ro_grad.pad2=alfa;
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_phase(&pe2_grad,"pe2",lpe2,nv2);
init_slice(&ss_grad,"ss",thk);
init_slice(&ss2_grad,"ss2",thk*thk2fact);
init_slice_refocus(&ssr_grad,"ssr");
init_dephase(&crush_grad,"crush");
/* Gradient calculations ******************************/
calc_readout(&ro_grad,WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,WRITE,"gror");
calc_phase(&pe_grad,NOWRITE,"","");
calc_phase(&pe2_grad,NOWRITE,"","");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
/* Equalize refocus gradient durations ****************/
calc_sim_gradient(&ror_grad,&null_grad,&ssr_grad,0.0,WRITE);
/* Equalize PE gradient durations *********************/
calc_sim_gradient(&pe_grad,&pe2_grad,&null_grad,0.0,WRITE);
/* Set crushing gradient moment ***********************/
crushm0=fabs(gcrush*tcrush);
if (spoilflag[0] == 'y') {
init_generic(&spoil_grad,"spoil",gspoil,tspoil);
calc_generic(&spoil_grad,WRITE,"gspoil","tspoil");
}
/* 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') create_inversion_recovery();
if (diff[0] == 'y') init_diffusion(&diffusion,&diff_grad,"diff",gdiff,tdelta);
if (diff[0] == 'y') { /* Diffusion encoding is during spin echo preparation */
spinecho[0]='y';
putCmd("spinecho='y'");
}
if (spinecho[0] == 'y') { /* spin echo preparation */
shape_rf(&p3_rf,"p3",p3pat,p3,flip3,rof1,rof2);
calc_rf(&p3_rf,"tpwr3","tpwr3f");
/* Calculate thk3fact to ensure gss=gss2=gss3 for the choice of
p1, p2 and p3 so that the sequence remains robust in the absence
of correct balancing of slice select and slice refocus gradients */
thk3fact=p3_rf.bandwidth/p1_rf.bandwidth;
putvalue("thk3fact",thk3fact);
init_slice(&ss3_grad,"ss3",thk*thk3fact);
calc_slice(&ss3_grad,&p3_rf,WRITE,"");
putvalue("gss3",ss3_grad.ssamp);
offsetlist(pss,ss3_grad.ssamp,0,freqte,ns,seqcon[1]);
shapelistte = shapelist(p3_rf.pulseName,ss3_grad.rfDuration,freqte,ns,ss3_grad.rfFraction,seqcon[1]);
/* Automatically set crushers to avoid unwanted echoes */
if (autocrush[0] == 'y') {
if (crushm0 < 0.6*ro_grad.m0) crushm0=0.6*ro_grad.m0;
}
}
/* Make sure crushing in PE dimensions does not refocus signal from 180 */
pem0 = (pe_grad.m0 > pe2_grad.m0) ? pe_grad.m0 : pe2_grad.m0;
calc_dephase(&crush_grad,WRITE,crushm0+pem0,"","");
gcrushr = crush_grad.amp*crushm0/crush_grad.m0;
gcrushp = crush_grad.amp*(crushm0+pe_grad.m0)/crush_grad.m0;
gcrushs = crush_grad.amp*(crushm0+pe2_grad.m0)/crush_grad.m0;
sgl_error_check(sglerror);
/* Set up frequency offset pulse shape list ***********/
offsetlist(pss,ss_grad.amp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shapelist90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]);
shapelist180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]);
/* To ensure proper overlap spin and stimulated echoes ensure that the
middle of the refocusing RF pulse is the centre of the pulse and that
echoes are formed in the centre of the acquisition window */
if (ss2_grad.rfFraction != 0.5)
abort_message(
"ERROR %s: Refocusing RF pulse must be symmetric (RF fraction = %.2f)",
seqfil,ss2_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 ****/
esp = granularity(esp,2*GRADIENT_RES);
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront + GRADIENT_RES;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + pe_grad.duration + ro_grad.timeToEcho + GRADIENT_RES;
tau3 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront + GRADIENT_RES;
espmin = 2*MAX(MAX(tau1,tau2),tau3); // Minimum echo spacing
if (minesp[0] == 'y') {
esp = espmin;
putvalue("esp",esp);
}
if (FP_LT(esp,espmin)) {
abort_message("ERROR %s: Echo spacing too small, minimum is %.3fms\n",seqfil,espmin*1000);
}
te1_delay = esp/2.0 - tau1 + GRADIENT_RES; // Intra-esp delays
te2_delay = esp/2.0 - tau2 + GRADIENT_RES;
te3_delay = esp/2.0 - tau3 + GRADIENT_RES;
/* Spin echo preparation ******************************/
if (spinecho[0] == 'y') {
te = granularity(te,2*GRADIENT_RES);
te1 = te-kzero*esp;
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss3_grad.duration/2.0 + GRADIENT_RES;
tau2 = ss3_grad.duration/2.0 + crush_grad.duration + GRADIENT_RES;
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 = ss3_grad.duration + 2*crush_grad.duration;
/* set minimum diffusion structure requirements for gradient echo: taudiff, tDELTA, te and minte[0] */
set_diffusion(&diffusion,taudiff,tDELTA,te1,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') {
te1 = temin;
te = te1+kzero*esp;
putvalue("te",te);
}
te_delay1 = te1/2 - tau1 + GRADIENT_RES;
te_delay2 = te1/2 - tau2 + GRADIENT_RES;
if (FP_LT(te,temin+kzero*esp)) {
abort_message("ERROR %s: TE too short, minimum TE = %.3f ms\n",seqfil,temin*1000);
}
}
else
putvalue("te",kzero*esp); // Return effective TE
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* 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); // readout dephase & readout delta
Gro = ro_grad.m0ref/dgro; // readout dephase & readout gradient strength
Dgro = dgro+2*crush_grad.duration+ss2_grad.duration+te2_delay+pe_grad.duration; // readout dephase & readout DELTA
dgss = 0.5*(ss_grad.rfCenterBack+ssr_grad.duration); // slice & slice refocus delta
Gss = ss_grad.m0ref/dgss; // slice & slice refocus gradient strength
Dgss = dgss; // slice & slice refocus DELTA
dgss2 = (ss2_grad.duration-ss2_grad.tramp)/2.0; // refocus slice select delta
Dgss2 = dgss2; // refocus slice select DELTA
dcrush2 = crush_grad.duration-crush_grad.tramp; // refocus crusher delta
Dcrush2 = crush_grad.duration+ss2_grad.duration; // refocus crusher DELTA
dcrush3 = crush_grad.duration-crush_grad.tramp; // spin echo prep crusher delta
Dcrush3 = crush_grad.duration+ss3_grad.duration; // spin echo prep crusher DELTA
dgss3 = (ss3_grad.duration-ss3_grad.tramp)/2.0; // spin echo prep slice select delta
Dgss3 = dgss3; // spin echo prep slice select DELTA
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(gcrushr,dcrush2,Dcrush2);
diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,gcrushr,dcrush2,Dcrush2);
/* Phase */
diffusion.bpe[i] += bval(gcrushp,dcrush2,Dcrush2);
/* Slice */
diffusion.bsl[i] += bval(Gss,dgss,Dgss);
diffusion.bsl[i] += bval(gcrushs,dcrush2,Dcrush2);
diffusion.bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
diffusion.bsl[i] += bval_nested(gcrushs,dcrush2,Dcrush2,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
diffusion.brp[i] += bval2(gcrushr,gcrushp,dcrush2,Dcrush2);
/* Readout/Slice Cross-terms */
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gcrushs,dcrush2,Dcrush2);
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,ss2_grad.ssamp,dgss2,Dgss2);
diffusion.brs[i] += bval2(gcrushr,gcrushs,dcrush2,Dcrush2);
diffusion.brs[i] += bval_cross(gcrushr,dcrush2,Dcrush2,ss2_grad.ssamp,dgss2,Dgss2);
/* Slice/Phase Cross-terms */
diffusion.bsp[i] += bval2(gcrushs,gcrushp,dcrush2,Dcrush2);
diffusion.bsp[i] += bval_cross(gcrushp,dcrush2,Dcrush2,ss2_grad.ssamp,dgss2,Dgss2);
if (spinecho[0] == 'y') {
/* Readout */
diffusion.bro[i] += bval(crush_grad.amp,dcrush3,Dcrush3);
diffusion.bro[i] += bval_nested(gdiff*droval,tdelta,tDELTA,crush_grad.amp,dcrush3,Dcrush3);
/* Slice */
diffusion.bsl[i] += bval(ss3_grad.amp,dgss3,Dgss3);
diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,ss3_grad.ssamp,dgss3,Dgss3);
/* Readout/Slice Cross-terms */
diffusion.brs[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,crush_grad.amp,dcrush3,Dcrush3);
diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,ss3_grad.amp,dgss3,Dgss3);
diffusion.brs[i] += bval_cross(crush_grad.amp,dcrush3,Dcrush3,ss3_grad.amp,dgss3,Dgss3);
/* Readout/Phase Cross-terms */
diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crush_grad.amp,dcrush3,Dcrush3);
/* Slice/Phase Cross-terms */
diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,ss3_grad.amp,dgss3,Dgss3);
}
} /* End for-all-directions */
/* Write the values */
write_bvalues(&diffusion,"bval","bvalue","max_bval");
}
/* Minimum TR *****************************************/
trmin = ss_grad.rfCenterFront + etl*esp + ro_grad.timeFromEcho + pe_grad.duration + te3_delay + 2*GRADIENT_RES;
if (spoilflag[0] == 'y') trmin += spoil_grad.duration;
/* Increase TR if any options are selected ************/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (spinecho[0] == 'y') trmin += te1;
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("ERROR %s: TR too short, minimum TR = %.3fms\n",seqfil,trmin*1000);
}
/* Calculate tr delay *********************************/
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set number of segments for profile or full image ***/
nseg = prep_profile(profile[0],nseg,&pe_grad,&null_grad);
pe2_steps = prep_profile(profile[1],nv2,&pe2_grad,&null_grad);
F_initval(pe2_steps/2.0,vpe2_offset);
/* Shift DDR for pro **********************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *******************/
if (ssc<0) {
if (seqcon[2] == 's' && seqcon[3]=='s') g_setExpTime(trmean*ntmean*arraydim - ssc*arraydim);
else if (seqcon[2]=='s') g_setExpTime(trmean*nseg*(ntmean*pe2_steps*arraydim - ssc*arraydim));
else if (seqcon[3]=='s') g_setExpTime(trmean*pe2_steps*(ntmean*nseg*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*pe2_steps*arraydim - ssc*arraydim));
}
else g_setExpTime(trmean*ntmean*nseg*pe2_steps*arraydim + tr*ssc);
/* 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' && seqcon[3]=='s') assign(zero,vssc); // Zero for standard peloop and pe2loop
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);
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],nseg,vseg,vseg_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);
if (seqcon[2] == 'c')
sub(vseg_ctr,vssc,vseg_ctr); // vseg_ctr counts up from -ssc
else if (seqcon[3] == 'c')
sub(vpe2_ctr,vssc,vpe2_ctr); // vpe2_ctr counts up from -ssc
assign(zero,vssc);
if (seqcon[2] == 's' && seqcon[3]=='s')
assign(zero,vacquire); // Always acquire for non-compressed loop
else {
if (seqcon[2] == 'c') {
ifzero(vseg_ctr);
assign(zero,vacquire); // Start acquiring when vseg_ctr reaches zero
endif(vseg_ctr);
}
else if (seqcon[3] == 'c') {
ifzero(vpe2_ctr);
assign(zero,vacquire); // Start acquiring when vpe2_ctr reaches zero
endif(vpe2_ctr);
}
}
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* Use standard encoding order for 2nd PE dimension */
ifzero(vacquire);
sub(vpe2_ctr,vpe2_offset,vpe2_mult);
elsenz(vacquire);
sub(zero,vpe2_offset,vpe2_mult);
endif(vacquire);
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();
/* 90 degree 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(shapelist90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Spin echo preparation ******************************/
if (spinecho[0] == 'y') {
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0.0,0.0,-ssr_grad.amp,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d1);
diffusion_dephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d2);
}
else
delay(te_delay1);
obspower(p3_rf.powerCoarse);
obspwrf(p3_rf.powerFine);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0.0,0.0,WAIT);
obl_shapedgradient(ss3_grad.name,ss3_grad.duration,0,0,ss3_grad.amp,NOWAIT);
delay(ss3_grad.rfDelayFront);
shapedpulselist(shapelistte,ss3_grad.rfDuration,vphase180,rof1,rof2,seqcon[1],vms_ctr);
delay(ss3_grad.rfDelayBack);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0.0,0.0,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d3);
diffusion_rephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d4);
}
else
delay(te_delay2);
delay(ss_grad.duration/2.0);
delay(te1_delay);
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
obl_shapedgradient(ror_grad.name,ror_grad.duration,ror_grad.amp,0.0,0.0,WAIT);
}
else {
/* 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);
}
F_initval(etl,vetl);
loop(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 *********************************/
obl_shapedgradient(crush_grad.name,crush_grad.duration,gcrushr,gcrushp,gcrushs,WAIT);
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);
obl_shapedgradient(crush_grad.name,crush_grad.duration,gcrushr,gcrushp,gcrushs,WAIT);
/* Second half-TE period ****************************/
delay(te2_delay);
/* Phase-encode gradient ****************************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Readout gradient *********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquire data *************************************/
startacq(alfa);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ******************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
/* Second half-TE delay *****************************/
delay(te3_delay);
endloop(vetl_ctr);
if (spoilflag[0] == 'y')
obl_shapedgradient(spoil_grad.name,spoil_grad.duration,spoil_grad.amp,spoil_grad.amp,spoil_grad.amp,WAIT);
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vseg_ctr);
endpeloop(seqcon[3],vpe2_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence() {
/* Internal variable declarations *************************/
int shapelist90,shapelist180;
int table = 0;
double tau1,tau2,tau3,te1_delay,te2_delay,te3_delay,tr_delay;
double freq90[MAXNSLICE],freq180[MAXNSLICE];
double thk2fact,crush_step,neby2,crush_ind;
int suppressSTE,*crushtab;
char crushmod[MAXSTR];
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 vpe_mult = v3; // PE multiplier, ranges from -PE/2 to PE/2
int vpe_offset = v4; // PE/2 for non-table offset
int vms_slices = v5; // Number of slices
int vms_ctr = v6; // Slice loop counter
int vne = v7; // Number of echoes
int vne_ctr = v8; // Echo loop counter
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 vphase90 = v12; // Phase of 90 degree excitation pulse
int vphase180 = v13; // Phase of 180 degree refocusing pulse
int vphindex = v14; // Phase cycle index
int vneindex = v15; // Echo index, odd or even
int vcrush = v16; // Crusher modulation
int vtrigblock = v17; // Number of slices per trigger block
/* Initialize paramaters **********************************/
init_mri();
getstr("crushmod",crushmod);
suppressSTE=getval("suppressSTE");
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
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");
/* Calculate thk2fact to ensure gss=gss2 for the choice of p1 and p2
so that the sequence remains robust in the absence of correct
balancing of slice select and slice refocus gradients */
thk2fact=p2_rf.bandwidth/p1_rf.bandwidth;
putvalue("thk2fact",thk2fact);
/* Initialize gradient structures *************************/
init_readout(&ro_grad,"ro",lro,np,sw);
ro_grad.pad1=alfa; ro_grad.pad2=alfa;
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_slice(&ss_grad,"ss",thk);
init_slice(&ss2_grad,"ss2",thk*thk2fact);
init_slice_refocus(&ssr_grad,"ssr");
init_generic(&crush_grad,"crush",gcrush,tcrush);
/* 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,&p2_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
calc_generic(&crush_grad,WRITE,"","");
/* Equalize slice 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') create_inversion_recovery();
sgl_error_check(sglerror);
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.amp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shapelist90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]);
shapelist180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]);
/* To ensure proper overlap spin and stimulated echoes ensure that the
middle of the refocusing RF pulse is the centre of the pulse and that
echoes are formed in the centre of the acquisition window */
if (ss2_grad.rfFraction != 0.5)
abort_message("ERROR %s: Refocusing RF pulse must be symmetric (RF fraction = %.2f)",
seqfil,ss2_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 + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + pe_grad.duration + crush_grad.duration + ro_grad.timeToEcho;
tau3 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(MAX(tau1,tau2),tau3); // Minimum echo spacing
espmin += 2*GRADIENT_RES; // Ensure that each delay is at least GRADIENT_RES
te = granularity(te,2*GRADIENT_RES);
if (minesp[0] == 'y') {
te = espmin;
putvalue("te",te);
}
if (FP_LT(te,espmin)) {
abort_message("ERROR %s: Echo time too small, minimum is %.3fms\n",seqfil,espmin*1000);
}
te1_delay = te/2.0 - tau1; // Intra-esp delays
te2_delay = te/2.0 - tau2;
te3_delay = te/2.0 - tau3;
/* Now set the TE processing array accordingly */
putCmd("TE = 0"); /* Re-initialize TE */
for (i=0;i<ne;i++) putCmd("TE[%d] = %f",i+1,te*1000*(i+1));
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Minimum TR **************************************/
trmin = ss_grad.rfCenterFront + ne*te + ro_grad.timeFromEcho + pe_grad.duration + te3_delay + 2*GRADIENT_RES;
/* Increase TR if any options are selected *********/
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("ERROR %s: TR too short, minimum TR is %.3fms\n",seqfil,trmin*1000);
}
/* Calculate tr delay */
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&per_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);
/* Set phase cycle tables */
if (suppressSTE) {
if ((int)nt%2 == 1)
abort_message("STE suppression requires a 2 step phase cycle. Set nt as a multiple of 2\n");
settable(t2,4,phref1s);
settable(t3,4,phref2s);
settable(t4,4,phrec1s);
settable(t5,4,phrec2s);
} else {
settable(t2,4,phref1);
settable(t3,4,phref2);
settable(t4,4,phrec1);
settable(t5,4,phrec2);
}
/* Set crusher table */
crushtab=malloc((int)ne*sizeof(int));
neby2=ceil(ne/2.0 - US); // US to handle precision errors
crush_step=gcrush/neby2;
for (i=0; i<ne; i++) {
crush_ind = (1.0-2.0*(i%2))*(neby2-floor(i/2));
crushtab[i] = (int)(crush_ind);
}
settable(t6,(int)ne,crushtab);
/* PULSE SEQUENCE ***************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(GRADIENT_RES);
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
/* Phase for excitation pulse */
assign(zero,vphase90);
/* 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);
}
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();
/* 90 degree 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(shapelist90,ss_grad.rfDuration,vphase90,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* 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);
F_initval(ne,vne);
loop(vne,vne_ctr);
/* Phase cycle for refocusing pulse and receiver */
mod4(ct,vphindex);
mod2(vne_ctr,vneindex);
ifzero(vneindex);
getelem(t2,vphindex,vphase180);
getelem(t4,vphindex,oph);
elsenz(vneindex);
getelem(t3,vphindex,vphase180);
getelem(t5,vphindex,oph);
endif(vneindex);
/* Crusher gradient modulation */
assign(one,vcrush);
if (crushmod[0] == 'y') {
assign(zero,vcrush);
ifzero(vneindex);
add(vcrush,one,vcrush);
elsenz(vneindex);
sub(vcrush,one,vcrush);
endif(vneindex);
}
if (crushmod[0] == 'p') {
getelem(t6,vne_ctr,vcrush);
crush_grad.amp=crush_step;
}
/* 180 degree pulse *******************************/
if (crushmod[0] == 'y' || crushmod[0] == 'p')
var3_shapedgradient(crush_grad.name,crush_grad.duration,0.0,0.0,0.0,0.0,0.0,crush_grad.amp,zero,zero,vcrush,WAIT);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0,crush_grad.amp,WAIT);
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);
if (crushmod[0] == 'y' || crushmod[0] == 'p')
var3_shapedgradient(crush_grad.name,crush_grad.duration,0.0,0.0,0.0,0.0,0.0,crush_grad.amp,zero,zero,vcrush,WAIT);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0,crush_grad.amp,WAIT);
/* Second half-TE period ******************************/
delay(te2_delay);
/* Phase-encode gradient ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,-pe_grad.increment,vpe_mult,WAIT);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquire data ****************************************/
startacq(alfa);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode 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);
endloop(vne_ctr);
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);
}