pulsesequence()
{
/* Internal variable declarations *********************/
double freq90[MAXNSLICE],freq180[MAXNSLICE];
double te_delay1,te_delay2,tr_delay,tau1,tau2,thk2fact,te_delay3=0.0,te_delay4=0.0,navTime=0.0;
double crushm0,pem0,gcrushr,gcrushp,gcrushs,pecrush;
double refsign=1,crushsign=1,navsign=1;
int shape90,shape180,table=0,sepRefocus;
char slprofile[MAXSTR];
/* sequence dependent diffusion variables */
double Gro,Gss; // "gdiff" for readout/readout refocus and slice/slice refocus
double dgro,dgss; // "delta" for readout/readout refocus and slice/slice refocus
double Dgro,Dgss; // "DELTA" for readout/readout refocus and slice/slice refocus
double dcrush,dgss2; // "delta" for crusher and gss2 gradients
double Dcrush,Dgss2; // "DELTA" for crusher and gss2 gradients
int i;
/* Real-time variables used in this sequence **********/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vpe_offset = v5; // PE/2 for non-table offset
int vpe_mult = v6; // PE multiplier, ranges from -PE/2 to PE/2
int vph180 = v7; // Phase of 180 pulse
int vph2 = v8; // alternate phase of 180 on odd transients
int vssc = v9; // Compressed steady-states
int vtrimage = v10; // Counts down from nt, trimage delay when 0
int vacquire = v11; // Argument for setacqvar, to skip steady state acquires
int vtrigblock = v12; // Number of slices per trigger block
/* Initialize paramaters *****************************/
init_mri();
thk2fact=getval("thk2fact");
pecrush=getval("pecrush");
sepRefocus=getvalnwarn("sepRefocus");
getstrnwarn("slprofile",slprofile);
/* Check for external PE table ***********************/
init_tablepar("pelist"); // Initialize pelist parameter
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
writetabletopar(t1,"pelist"); // Write t1 table to pelist parameter
table = 1;
}
/* RF Power & Bandwidth Calculations ******************/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Initialize gradient structures *********************/
init_slice(&ss_grad,"ss",thk);
init_slice(&ss2_grad,"ss2",thk*thk2fact);
init_dephase(&crush_grad,"crush");
init_slice_refocus(&ssr_grad,"ssr");
if (FP_LT(tcrushro,alfa)) tcrushro=alfa;
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_generic(&spoil_grad,"spoil",gspoil,tspoil);
/* Gradient calculations ******************************/
calc_readout(&ro_grad, WRITE,"gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
calc_generic(&spoil_grad,WRITE,"","");
/* Make sure crushing in PE dimension does not refocus signal from 180 */
crushm0=fabs(gcrush*tcrush);
pem0=0.0; gcrushp=0.0;
if (pecrush) pem0=pe_grad.m0;
calc_dephase(&crush_grad,WRITE,crushm0+pem0,"","");
gcrushr = crush_grad.amp*crushm0/crush_grad.m0;
if (pecrush) gcrushp = crush_grad.amp;
gcrushs = crush_grad.amp*crushm0/crush_grad.m0;
/* Allow phase encode and read dephase to be separated from slice refocus */
if (sepRefocus) {
/* Equalize read dephase and PE gradient durations */
calc_sim_gradient(&ror_grad,&pe_grad,&null_grad,0,WRITE);
crushsign=-1;
} else {
if (slprofile[0] == 'y') {
/* Combined slice refocusing and read dephasing,
reverse gradient sign if ror > ssr integral */
refsign = (ss_grad.m0ref > ro_grad.m0ref) ? 1.0 : -1.0;
ss_grad.m0ref -= ro_grad.m0ref;
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
}
/* Equalize both refocus and PE gradient durations */
calc_sim_gradient(&ror_grad,&pe_grad,&ssr_grad,0,WRITE);
}
/* Create optional prepulse events ********************/
if (fsat[0] == 'y') create_fatsat();
if (sat[0] == 'y') create_satbands();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') create_inversion_recovery();
if (diff[0] == 'y') init_diffusion(&diffusion,&diff_grad,"diff",gdiff,tdelta);
sgl_error_check(sglerror);
/* Min TE *********************************************/
te = granularity(te,2*GRADIENT_RES);
/* tau1, tau2 are the sum of events in each half echo period */
/* tau1, tau2 include a GRADIENT_RES as this is minimum delay time */
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront + 2*GRADIENT_RES;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho + GRADIENT_RES;
if (sepRefocus) tau2 += ror_grad.duration;
temin = 2*MAX(tau1,tau2);
/* Diffusion ******************************************/
if (diff[0] == 'y') {
/* granulate tDELTA */
tDELTA = granularity(tDELTA,GRADIENT_RES);
/* taudiff is the duration of events between diffusion gradients */
taudiff = ss2_grad.duration + 2*crush_grad.duration + GRADIENT_RES;
/* set minimum diffusion structure requirements for gradient echo: taudiff, tDELTA, te and minte[0] */
set_diffusion(&diffusion,taudiff,tDELTA,te,minte[0]);
/* set additional diffusion structure requirements for spin echo: tau1 and tau2 */
set_diffusion_se(&diffusion,tau1,tau2);
/* calculate the diffusion structure delays.
address &temin is required in order to update temin accordingly */
calc_diffTime(&diffusion,&temin);
}
/* TE delays ******************************************/
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (FP_LT(te,temin)) {
abort_message("TE too short, minimum TE = %.3f ms\n",temin*1000);
}
te_delay1 = te/2 - tau1 + GRADIENT_RES;
te_delay2 = te/2 - tau2 + GRADIENT_RES;
if (navigator[0] == 'y') {
/* tau1, tau2 are the sum of events in each half echo period */
tau1 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho;
if (FP_GT(tau1,tau2)) {
te_delay3 = GRADIENT_RES;
te_delay4 = tau1-tau2+GRADIENT_RES;
} else {
te_delay3 = tau2-tau1+GRADIENT_RES;
te_delay4 = GRADIENT_RES;
}
navTime = te_delay3 + ss2_grad.duration + 2*crush_grad.duration + ro_grad.duration + te_delay4 + 2*GRADIENT_RES;
}
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Min TR *********************************************/
trmin = ss_grad.rfCenterFront + te + ro_grad.timeFromEcho + pe_grad.duration + 2*GRADIENT_RES;
/* Increase TR if any options are selected ************/
if (spoilflag[0] == 'y') trmin += spoil_grad.duration;
if (navigator[0] == 'y') trmin += navTime;
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (ticks > 0) trmin += GRADIENT_RES;
/* Adjust for all slices ******************************/
trmin *= ns;
/* Inversion recovery *********************************/
if (ir[0] == 'y') {
/* tauti is the additional time beyond IR component to be included in ti */
/* satTime, fsatTime and mtTime all included as those modules will be after IR */
tauti = satTime + fsatTime + mtTime + GRADIENT_RES + ss_grad.rfCenterFront;
/* calc_irTime checks ti and returns the time of all IR components */
trmin += calc_irTime(tauti,trmin,mintr[0],tr,&trtype);
}
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("TR too short, minimum TR = %.3f ms\n",trmin*1000);
}
/* TR delay *******************************************/
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Calculate B values *********************************/
if (ix == 1) {
/* Calculate bvalues according to main diffusion gradients */
calc_bvalues(&diffusion,"dro","dpe","dsl");
/* Add components from additional diffusion encoding imaging gradients peculiar to this sequence */
/* Initialize variables */
dgro = 0.5*(ror_grad.duration+ro_grad.timeToEcho);
Gro = ro_grad.m0ref/dgro; Dgro = dgro;
if (!sepRefocus) Dgro = te-ss_grad.rfCenterBack-ro_grad.timeToEcho;
dgss = 0.5*(ss_grad.rfCenterBack+ssr_grad.duration);
Gss = ss_grad.m0ref/dgss; Dgss = dgss;
dgss2 = ss2_grad.duration/2; Dgss2 = dgss2;
dcrush = crush_grad.duration-crush_grad.tramp; Dcrush = crush_grad.duration+ss2_grad.duration;
for (i = 0; i < diffusion.nbval; i++) {
/* set droval, dpeval and dslval */
set_dvalues(&diffusion,&droval,&dpeval,&dslval,i);
/* Readout */
diffusion.bro[i] += bval(Gro,dgro,Dgro);
diffusion.bro[i] += bval(crushsign*gcrushr,dcrush,Dcrush);
diffusion.bro[i] += bval_nested(gdiff*droval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
if (!sepRefocus) {
diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,gdiff*droval,tdelta,tDELTA);
diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,crushsign*gcrushr,dcrush,Dcrush);
}
/* Phase */
if (pecrush) {
diffusion.bpe[i] += bval(gcrushp,dcrush,Dcrush);
diffusion.bpe[i] += bval_nested(gdiff*dpeval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
}
/* Slice */
diffusion.bsl[i] += bval(Gss,dgss,Dgss);
diffusion.bsl[i] += bval(gcrushs,dcrush,Dcrush);
diffusion.bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
diffusion.bsl[i] += bval_nested(gcrushs,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
if (pecrush) diffusion.brp[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
if (!sepRefocus) {
diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gdiff*dpeval,tdelta,tDELTA);
if (pecrush) diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gcrushp,dcrush,Dcrush);
}
/* Readout/Slice Cross-terms */
diffusion.brs[i] += bval2(crushsign*gcrushr,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
if (!sepRefocus) {
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gdiff*dslval,tdelta,tDELTA);
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gcrushs,dcrush,Dcrush);
diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Slice/Phase Cross-terms */
diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,gcrushs,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
if (pecrush) {
diffusion.bsp[i] += bval2(gcrushs,gcrushp,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,gcrushp,dcrush,Dcrush);
diffusion.bsp[i] += bval_cross(gcrushp,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
}
} /* End for-all-directions */
/* Write the values */
write_bvalues(&diffusion,"bval","bvalue","max_bval");
}
/* Generate phase-ramped pulses ***********************/
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]);
shape180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]);
/* Set pe_steps for profile or full image *************/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
F_initval(pe_steps/2.0,vpe_offset);
/* Shift DDR for pro **********************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *******************/
if (ssc<0) {
if (seqcon[2] == 'c') g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*pe_steps*arraydim));
}
else g_setExpTime(trmean*ntmean*pe_steps*arraydim + tr*ssc);
/* Slice profile **************************************/
if (slprofile[0] == 'y' && !sepRefocus) ror_grad.amp = 0;
/* Set phase cycle table ******************************/
if (sepRefocus) settable(t2,1,ph180); // Phase encode is just before readout
else settable(t2,2,ph180);
/* PULSE SEQUENCE *************************************/
status(A); // Set status A
rotate(); // Set gradient rotation according to psi, phi and theta
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto); // Set spectrometer frequency
delay(GRADIENT_RES); // Delay for frequency setting
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
if (trtype) delay(ns*tr_delay); // relaxation delay
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vpe_ctr,vssc,vpe_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
if (seqcon[2] == 's')
assign(zero,vacquire); // Always acquire for non-compressed loop
else {
ifzero(vpe_ctr);
assign(zero,vacquire); // Start acquiring when vpe_ctr reaches zero
endif(vpe_ctr);
}
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_mult);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_mult);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states
endif(vacquire);
}
/* Phase cycle ****************************************/
getelem(t2,vpe_ctr,vph180); // For phase encoding with slice rephase
add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver
mod2(ct,vph2);
dbl(vph2,vph2);
add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (!trtype) delay(tr_delay); // Relaxation delay
if (ticks > 0) {
modn(vms_ctr,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(GRADIENT_RES);
elsenz(vtest);
delay(GRADIENT_RES);
endif(vtest);
}
sp1on(); delay(GRADIENT_RES); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (ir[0] == 'y') inversion_recovery();
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus gradient *****************************/
if (sepRefocus)
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
else
/* Include phase encode and readout dephase gradient if refocus gradients not separated */
pe_shapedgradient(pe_grad.name,pe_grad.duration,ror_grad.amp,0,-ssr_grad.amp*refsign,pe_grad.increment,vpe_mult,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d1);
diffusion_dephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d2);
}
else
delay(te_delay1);
/* Refocusing RF pulse ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT);
if (diff[0] == 'y') {
delay(diffusion.d3);
diffusion_rephase(&diffusion,dro,dpe,dsl);
delay(diffusion.d4);
}
else
delay(te_delay2);
/* Readout dephase, phase encode & readout gradients **/
roff = -poffset(pro,ro_grad.roamp); // incase inverted navigator is acquired
if (slprofile[0] == 'y') {
/* Readout gradient only if refocus gradients not separated */
if (sepRefocus)
obl_shapedgradient(ror_grad.name,ror_grad.duration,0,0,-ror_grad.amp,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,0,0,ro_grad.amp,NOWAIT);
} else {
/* Readout gradient only if refocus gradients not separated */
if (sepRefocus)
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,-pe_grad.increment,vpe_mult,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
}
/* Acquisition ****************************************/
delay(ro_grad.atDelayFront-alfa);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind Phase encoding ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT);
/* Navigator acquisition ******************************/
if (navigator[0] == 'y') {
delay(te_delay3);
obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT);
delay(te_delay4);
obl_shapedgradient(ro_grad.name,ro_grad.duration,navsign*ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
}
if (spoilflag[0] == 'y') {
obl_shapedgradient(spoil_grad.name,spoil_grad.duration,navsign*spoil_grad.amp,0,spoil_grad.amp,WAIT);
}
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
/* Duty cycle *****************************************/
calc_grad_duty(tr);
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE];
int shape90=0, shape180=0, shapeIR=0;
double te_delay1, te_delay2, tr_delay, ti_delay = 0;
double del1=0, del2=0, del3=0, del4=0;
double tau1=0, tau2=0, difftime=0, tetime=0;
int table=0;
/* Diffusion parameters */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl,
i;
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* and the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* Real-time variables ************************************/
int vpe_steps = v1;
int vpe_ctr = v2;
int vms_slices = v3;
int vms_ctr = v4;
int vpe_offset = v5;
int vpe_index = v6;
int vph180 = v7; // Phase of 180 pulse
int vph2 = v8; // alternate phase of 180 on odd transients
/* Initialize paramaters *********************************/
init_mri();
/* Check for external PE table ***************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
if ((diff[0] == 'y') && (gcrush < 4))
warn_message("Advisory: set gcrush to higher value to avoid image artifacts");
/* Initialize gradient structures *************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof2,rof2);
init_slice(&ss_grad,"ss",thk);
init_slice_butterfly(&ss2_grad,"ss2",thk*1.1,gcrush,tcrush);
init_slice_refocus(&ssr_grad,"ssr");
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
if (p2_rf.header.rfFraction != 0.5)
abort_message("RF pulse for refocusing (%s) must be symmetric",p2pat);
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
calc_slice_refocus(&ssr_grad, &ss_grad, NOWRITE,"gssr");
calc_readout(&ro_grad, WRITE, "gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad, &ro_grad, NOWRITE, "gror");
calc_phase(&pe_grad, NOWRITE, "gpe","tpe");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad, &pe_grad, &ssr_grad,0,WRITE);
/* Set up diffusion gradient */
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
calc_generic(&diff_grad,NOWRITE,"","");
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if (ix == 1) diff_grad.duration += diff_grad.tramp;
calc_generic(&diff_grad,WRITE,"","");
}
/* Min TE *************************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + 4e-6 + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + ror_grad.duration + ro_grad.timeToEcho + alfa;
temin = 2*(MAX(tau1,tau2) + 2*4e-6); /* have at least 4us between gradient events */
/* Calculate te_delays with the current TE, then later see how diffusion fits */
if ((minte[0] == 'y') || (te < temin)) {
te_delay1 = temin/2 - tau1;
te_delay2 = temin/2 - tau2;
}
else {
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
}
if (diff[0] =='y') {
/* Is tDELTA long enough for RF refocusing gradient? */
if (tDELTA < diff_grad.duration + ss2_grad.duration)
abort_message("DELTA too short, increase to %.2fms",
(diff_grad.duration + ss2_grad.duration)*1000+0.005);
/* Is tDELTA too long for TE dead time? */
difftime = tDELTA + diff_grad.duration; // tDELTA + front & back half diff_grad
tetime = ss2_grad.duration + te_delay1 + te_delay2;
if (difftime > tetime) {
temin += (difftime - tetime);
}
}
/* We now know the minimum TE incl. diffusion */
if (minte[0] == 'y') {
te = temin;
putvalue("te",ceil(te*1e6)*1e-6); /* round up to nearest us */
}
if (te < temin) {
if (diff[0] == 'n') {
abort_message("TE too short. Minimum TE = %.2fms\n",temin*1000);
}
else {
abort_message("TE too short, increase to %.2fms or reduce DELTA to %.2fms",
temin*1000,(tetime-diff_grad.duration)*1000);
}
}
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
/* Set up delays around diffusion gradients */
/* RF1 - del1 - diff - del2 - RF2 - del3 - diff - del4 - ACQ */
if (diff[0] == 'y') {
del1 = (tetime - difftime)/2;
del4 = del1;
del2 = te_delay1 - diff_grad.duration;
del3 = te_delay2 - diff_grad.duration;
if (del3 < 0.0) { // shift diff block to right
del1 += del3;
del2 -= del3;
del4 -= del3;
del3 = 0;
} else if (del2 < 0.0) { // shift diff block to left
del1 -= del2;
del3 -= del2;
del4 += del2;
del2 = 0;
}
}
else { /* No diffusion */
del1 = 0;
del3 = 0;
del2 = te_delay1;
del4 = te_delay2;
}
/* Min TR *************************************************/
trmin = (ss_grad.duration - ss_grad.rfCenterBack) + te + ro_grad.timeFromEcho;
if (navigator[0] == 'y')
trmin += (pe_grad.duration + ro_grad.duration);
/* Optional prepulse calculations *************************/
if (sat[0] == 'y') {
create_satbands();
trmin += satTime;
}
if (fsat[0] == 'y') {
create_fatsat();
trmin += fsatTime;
}
if (mt[0] == 'y') {
create_mtc();
trmin += mtTime;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof2,rof2);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrushir,tcrushir);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
tau1 = ss_grad.duration - ss_grad.rfCenterBack; /* duration of ss_grad before RF center */
ti_delay = ti - (ssi_grad.rfCenterBack + tau1);
if (ti_delay < 0) {
abort_message("TI too short, Minimum TI = %.2fms\n",(ti-ti_delay)*1000);
}
irTime = ti + ssi_grad.duration - ssi_grad.rfCenterBack; /* time to add to TR */
trmin += irTime;
trmin -= tau1; /* but subtract out ss_grad which was already included in TR */
}
trmin *= ns;
if (mintr[0] == 'y'){
tr = trmin + ns*4e-6;
putvalue("tr",tr);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000);
}
tr_delay = (tr - trmin)/ns > 4e-6 ? (tr - trmin)/ns : 4e-6;
/***************************************************/
/* CALCULATE B VALUES ******************************/
if (diff[0] == 'y') {
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
/* Readout */
Dro = ror_grad.duration;
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
bro[i] += bval(ro_grad.amp,ro_grad.timeToEcho,Dro);
/* Slice */
dgss2 = Dgss2 = ss_grad.rfCenterFront;
dcrush = tcrush; //"delta" for crusher part of butterfly
Dcrush = dcrush + ss_grad.rfDuration; //"DELTA" for crusher
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*slarr[i],gdiff*pearr[i],tdelta,tDELTA);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Generate phase-ramped pulses: 90, 180, and IR */
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
if (ir[0] == 'y') {
offsetlist(pss,ssi_grad.ssamp,0,freqIR,ns,seqcon[1]);
shapeIR = shapelist(pipat,ssi_grad.rfDuration,freqIR,ns,0,seqcon[1]);
}
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
initval(pe_steps/2.0,vpe_offset);
sgl_error_check(sglerror);
/* Return parameters to VnmrJ */
putvalue("rgss",ss_grad.tramp); //90 slice ramp
if (ss2_grad.enableButterfly) { //180 slice ramps
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgss2",ss2_grad.tramp);
}
if (ro_grad.enableButterfly) {
putvalue("rgro",ro_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgro",ro_grad.tramp); //RO ramp
}
putvalue("tror",ror_grad.duration); //ROR duration
putvalue("rgror",ror_grad.tramp); //ROR ramp
putvalue("gpe",pe_grad.peamp); //PE max amp
putvalue("gss",ss_grad.ssamp);
putvalue("gro",ro_grad.roamp);
g_setExpTime(tr*(nt*pe_steps*arraydim + ssc));
/* PULSE SEQUENCE *************************************/
rotate();
obsoffset(resto);
roff = -poffset(pro,ro_grad.roamp);
delay(4e-6);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_index);
else
sub(vpe_ctr,vpe_offset,vpe_index);
settable(t2,2,ph180); // initialize phase tables and variables
getelem(t2,vpe_ctr,vph180);
add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver
mod2(ct,vph2);
dbl(vph2,vph2);
add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
}
/* TTL scope trigger **********************************/
sp1on(); delay(5e-6); sp1off();
/* Prepulses ******************************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Optional IR pulse **********************************/
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0,0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayFront);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,-ssr_grad.amp,
pe_grad.increment,vpe_index,WAIT);
delay(del1); // delay to start of first diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del2); // delay from end of diffusion to slice refocusing
/* Refocusing RF pulse ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
delay(del3); // delay from slice refocusing to second diffusion gradient
if (diff[0] == 'y') {
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
}
delay(del4); // delay from end of diffusion gradient to readout event
/* Readout gradient and acquisition ********************/
roff = -poffset(pro,ro_grad.roamp);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind Phase encoding ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,
pe_grad.increment,vpe_index,WAIT);
if (navigator[0] == 'y') {
roff = -poffset(pro,-ro_grad.roamp);
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
}
/* Relaxation delay ***********************************/
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
}
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() {
/* 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;
double seqtime,tau1,tau2,tau3,te1_delay,te2_delay,te3_delay,tr_delay;
double freq90[MAXNSLICE], freq180[MAXNSLICE];
/* Diffusion variables */
double te1, te1min, del1, del2, del3, del4;
double te_diff1, te_diff2, tmp1, tmp2;
double diffamp;
char diffpat[MAXSTR];
/* Navigator variables */
double etlnav;
/* Variable crushers */
double cscale;
double vcrush; // flag
/* Diffusion parameters */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl,
i;
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* and the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* Real-time variables used in this sequence **************/
int vpe_ctr = v1; // PE loop counter
int vpe_mult = v2; // PE multiplier, ranges from -PE/2 to PE/2
int vpe2_ctr = v3; // PE loop counter
int vpe2_mult = v4; // PE multiplier, ranges from -PE/2 to PE/2
int vpe2_offset = v5;
int vpe2_steps = v6;
int vms_slices = v7; // Number of slices
int vms_ctr = v8; // Slice loop counter
int vseg = v9; // Number of ETL segments
int vseg_ctr = v10; // Segment counter
int vetl = v11; // Echo train length
int vetl_ctr = v12; // Echo train loop counter
int vssc = v13; // Compressed steady-states
int vtrimage = v14; // Counts down from nt, trimage delay when 0
int vacquire = v15; // Argument for setacqvar, to skip steady state acquires
int vphase180 = v16; // phase of 180 degree refocusing pulse
int vetl_loop = v17; // Echo train length MINUS ONE, used on etl loop
int vnav = v18; // Echo train length
int vcr_ctr = v19; // variable crusher, index into table
int vcr1 = v20; // multiplier along RO
int vcr2 = v21; // multiplier along PE
int vcr3 = v22; // multiplier along SL
int vetl1 = v23; // = etl-1, determine navigator echo location in echo loop
int vcr_reset = v24; // check for navigator echoes, reset crushers
/* Initialize paramaters **********************************/
get_parameters();
te1 = getval("te1"); /* te1 is the echo time for the first echo */
cscale = getval("cscale"); /* Scaling factor on first 180 crushers */
vcrush = getval("vcrush"); /* Variable crusher or set amplitude? */
getstr("diffpat",diffpat);
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
} else {
abort_message("petable undefined");
}
/* Hold variable crushers in tables 5, 6, 7 */
settable(t5,8,crro);
settable(t6,8,crpe);
settable(t7,8,crss);
seqtime = 0.0;
espmin = 0.0;
/* RF Power & Bandwidth Calculations **********************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
// 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_readout(&ro_grad,"ro",lro,np,sw);
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); /* NOTE assume same band widths for p1 and p2 */
init_slice(&ss2_grad,"ss2",thk); /* not butterfly, want to scale crushers w/ echo */
init_slice_refocus(&ssr_grad,"ssr");
/* Gradient calculations **********************************/
calc_readout(&ro_grad,WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
calc_phase(&pe2_grad,NOWRITE,"gpe2","tpe2");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p1_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad,&pe_grad,&pe2_grad,0.0,WRITE);
/* Variable crusher */
init_generic(&crush_grad,"crush",gcrush,tcrush);
calc_generic(&crush_grad,WRITE,"","");
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
/* Optional Diffusion gradient */
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
if (!strcmp("sine",diffpat)) {
diff_grad.shape = SINE;
diffamp = gdiff*1;
}
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if ((ix == 1) && (diff_grad.shape == TRAPEZOID)) {
calc_generic(&diff_grad,NOWRITE,"","");
diff_grad.duration += diff_grad.tramp;
}
calc_generic(&diff_grad,WRITE,"","");
}
/* 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,0,seqcon[1]);
shapelist180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
/* same slice selection gradient and RF pattern used */
if (ss_grad.rfFraction != 0.5)
abort_message("RF pulse must be symmetric (RF fraction = %.2f)",ss_grad.rfFraction);
if (ro_grad.echoFraction != 1)
abort_message("Echo Fraction must be 1");
/*****************************************************/
/* TIMING FOR ECHOES *********************************/
/*****************************************************/
/* First echo time, without diffusion */
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + crush_grad.duration + pe_grad.duration + ro_grad.timeToEcho;
te1min = 2*MAX(tau1,tau2);
if (te1 < te1min + 2*4e-6) {
abort_message("First echo time too small, minimum is %.2fms\n",(te1min+2*4e-6)*1000);
}
/* Each half-echo period in the ETL loop ********/
tau3 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(tau2,tau3); // Minimum echo spacing
if (minesp[0] == 'y') {
esp = espmin + 2*4e-6;
putvalue("esp",esp);
}
if (esp - (espmin + 2*4e-6) < -12.5e-9) {
abort_message("Echo spacing too small, minimum is %.2fms\n",(espmin+2*4e-6)*1000);
}
te1_delay = te1/2.0 - tau1;
te2_delay = esp/2.0 - tau2;
te3_delay = esp/2.0 - tau3;
/*****************************************************/
/* TIMING FOR DIFFUSION ******************************/
/*****************************************************/
del1 = te1/2.0 - tau1;
del2 = 0;
del3 = te1/2.0 - tau2;
del4 = 0;
if (diff[0] == 'y') {
tau1 += diff_grad.duration;
tau2 += diff_grad.duration;
te1min = 2*MAX(tau1,tau2);
if (te1 < te1min + 4*4e-6) { /* te1 is split into 4 delays, each of which must be >= 4us */
abort_message("ERROR %s: First echo time too small, minimum is %.2fms\n",seqfil,te1min*1000);
}
/* te1 is the echo time for the first echo */
te_diff1 = te1/2 - tau1; /* Available time in first half of first echo */
te_diff2 = te1/2 - tau2; /* Available time in second half of first echo */
tmp1 = ss2_grad.duration + 2*crush_grad.duration; /* duration of 180 block */
/* Is tDELTA long enough? */
if (tDELTA < diff_grad.duration + tmp1)
abort_message("DELTA too short, increase to %.2fms",
(diff_grad.duration + tmp1)*1000);
/* Is tDELTA too long? */
tmp2 = diff_grad.duration + te_diff1 + tmp1 + te_diff2;
if (tDELTA > tmp2) {
abort_message("DELTA too long, increase te1 to %.2fms",
(te1 + (tDELTA-tmp2))*1000);
}
/* First attempt to put lobes right after slice select, ie del1 = 0 */
del1 = 4e-6; /* At least 4us after setting power for 180 */
del2 = te_diff1 - del1;
del3 = tDELTA - (diff_grad.duration + del2 + tmp1);
if (del3 < 4e-6) { /* shift diffusion block towards acquisition */
del3 = 4e-6;
del2 = tDELTA - (diff_grad.duration + tmp1 + del3);
}
del1 = te_diff1 - del2;
del4 = te_diff2 - del3;
if (fabs(del4) < 12.5e-9) del4 = 0;
}
te = te1 + (kzero-1)*esp; // Return effective TE
putvalue("te",te);
/* How many echoes in the echo loop, including navigators? */
etlnav = (etl-1)+(navigator[0]=='y')*2.0;
/* Minimum TR **************************************/
seqtime = 4e-6 + 2*nseg*ns*4e-6; /* count all the 4us delays */
seqtime += ns*(ss_grad.duration/2 + te1 + (etlnav)*esp + ro_grad.timeFromEcho + pe_grad.duration + te3_delay);
/* Increase TR if any options are selected****************/
if (sat[0] == 'y') seqtime += ns*satTime;
if (fsat[0] == 'y') seqtime += ns*fsatTime;
if (mt[0] == 'y') seqtime += ns*mtTime;
trmin = seqtime + ns*4e-6; /* Add 4us to ensure that tr_delay is always >= 4us */
if (mintr[0] == 'y'){
tr = trmin;
putvalue("tr",tr+1e-6);
}
if (tr < trmin) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000);
}
tr_delay = (tr - seqtime)/ns;
/* Set number of segments for profile or full image **********/
nseg = prep_profile(profile[0],nv/etl,&pe_grad,&per_grad);
pe2_steps = prep_profile(profile[1],nv2,&pe2_grad,&pe2r_grad);
/* Calculate total scan time */
g_setExpTime(tr*(nt*nseg*pe2_steps*arraydim + ssc));
/***************************************************/
/* CALCULATE B VALUES ******************************/
if (diff[0] == 'y') {
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
dcrush = crush_grad.duration; //"delta" for crusher
Dcrush = dcrush + ss_grad.duration; //"DELTA" for crusher
/* Readout */
Dro = ror_grad.duration;
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
bro[i] += bval(ro_grad.amp,ro_grad.timeToEcho,Dro);
bro[i] += bval(crush_grad.amp,dcrush,Dcrush);
bro[i] += bval_nested(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Slice */
dgss2 = Dgss2 = ss_grad.rfCenterFront;
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
bsl[i] += bval(crush_grad.amp,dcrush,Dcrush);
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval_nested(ss2_grad.ssamp,dgss2,Dgss2,
crush_grad.amp,dcrush,Dcrush);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
bpe[i] += bval(crush_grad.amp,dcrush,Dcrush);
bpe[i] += bval_nested(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
brs[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
ss2_grad.ssamp,dgss2,Dgss2);
brs[i] += bval_cross(crush_grad.amp,dcrush,Dcrush,
ss2_grad.ssamp,dgss2,Dgss2);
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
brp[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
brp[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
brp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*pearr[i],gdiff*slarr[i],tdelta,tDELTA);
bsp[i] += bval2(crush_grad.amp,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*slarr[i],tdelta,tDELTA,
crush_grad.amp,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,
ss2_grad.ssamp,dgss2,Dgss2);
bsp[i] += bval_cross(crush_grad.amp,dcrush,Dcrush,
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);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* PULSE SEQUENCE *************************************/
if (ix == 1) grad_advance(tep);
initval(fabs(ssc),vssc); // Compressed steady-state counter
setacqvar(vacquire); // Control acquisition through vacquire
assign(one,vacquire); // Turn on acquire when vacquire is zero
/* Phase cycle: Alternate 180 phase to cancel residual FID */
mod2(ct,vphase180); // 0101
dbl(vphase180,vphase180); // 0202
add(vphase180,one,vphase180); // 1313 Phase difference from 90
add(vphase180,oph,vphase180);
obsoffset(resto);
delay(4e-6);
initval(nseg,vseg);
initval(pe2_steps/2.0,vpe2_offset);
initval(etl,vetl);
initval(etl-1,vetl1);
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
/* Use standard encoding order for 2nd PE dimension */
sub(vpe2_ctr,vpe2_offset,vpe2_mult);
loop(vseg,vseg_ctr);
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vseg_ctr,vssc,vseg_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
ifzero(vseg_ctr);
assign(zero,vacquire); // Start acquiring when vseg_ctr reaches zero
endif(vseg_ctr);
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (ticks) {
xgate(ticks);
grad_advance(tep);
}
sp1on(); delay(4e-6); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* 90 degree pulse ************************************/
rotate();
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapelist90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Read dephase and Slice refocus *********************/
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0.0,0.0,-ssr_grad.amp,WAIT);
/* First half-TE delay ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(del1);
/* DIFFUSION GRADIENT */
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del2);
/*****************************************************/
/* FIRST ECHO OUTSIDE LOOP ***************************/
/*****************************************************/
ifzero(vacquire); // real acquisition, get PE multiplier from table
mult(vseg_ctr,vetl,vpe_ctr);
getelem(t1,vpe_ctr,vpe_mult);
elsenz(vacquire); // steady state scan
assign(zero,vpe_mult);
endif(vacquire);
/* Variable crusher */
assign(zero,vcr_ctr);
getelem(t5,vcr_ctr,vcr1);
getelem(t6,vcr_ctr,vcr2);
getelem(t7,vcr_ctr,vcr3);
if(vcrush)
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp*cscale,crush_grad.amp*cscale,crush_grad.amp*cscale, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,
crush_grad.amp,crush_grad.amp,crush_grad.amp,WAIT);
/* 180 degree pulse *******************************/
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 (vcrush)
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp*cscale,crush_grad.amp*cscale,crush_grad.amp*cscale, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,
crush_grad.amp,crush_grad.amp,crush_grad.amp,WAIT);
delay(del3);
/* DIFFUSION GRADIENT */
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del4);
/* Phase-encode gradient ******************************/
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,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);
/* Acquire data ****************************************/
startacq(10e-6);
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);
/*****************************************************/
/* LOOP THROUGH THE REST OF ETL **********************/
/*****************************************************/
peloop(seqcon[2],etlnav,vetl_loop,vetl_ctr);
ifzero(vacquire); // real acquisition, get PE multiplier from table
mult(vseg_ctr,vetl,vpe_ctr);
add(vpe_ctr,vetl_ctr,vpe_ctr);
add(vpe_ctr,one,vpe_ctr);
getelem(t1,vpe_ctr,vpe_mult);
elsenz(vacquire); // steady state scan
assign(zero,vpe_mult);
endif(vacquire);
/* But don't phase encode navigator echoes */
ifrtGE(vetl_ctr,vetl1,vnav);
assign(zero,vpe_mult);
endif(vnav);
/* Variable crusher */
incr(vcr_ctr); /* Get next crusher level */
/* Except if we're doing navigators, start over */
sub(vetl1,vetl_ctr,vcr_reset);
ifzero(vcr_reset);
assign(zero,vcr_ctr);
endif(vcr_reset);
getelem(t5,vcr_ctr,vcr1);
getelem(t6,vcr_ctr,vcr2);
getelem(t7,vcr_ctr,vcr3);
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp,crush_grad.amp,crush_grad.amp, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
/* 180 degree pulse *******************************/
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);
/* Variable crusher */
phase_encode3_oblshapedgradient(crush_grad.name,crush_grad.name,crush_grad.name,
crush_grad.duration,
(double)0,(double)0,(double)0, // base levels
crush_grad.amp,crush_grad.amp,crush_grad.amp, // step size
vcr1,vcr2,vcr3, // multipliers
(double)1.0,(double)1.0,(double)1.0, // upper limit on multipliers
1,WAIT,0);
/* 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 period ******************************/
delay(te2_delay);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(10e-6);
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);
endpeloop(seqcon[2],vetl_ctr);
/* Relaxation delay ***********************************/
if (!trtype)
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr);
if (trtype)
delay(ns*tr_delay);
endloop(vseg_ctr);
endpeloop(seqcon[3],vpe2_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}