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);
}
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);
}