pulsesequence()
{
/* Internal variable declarations *************************/
double freqEx[MAXNSLICE];
double pespoil_amp,spoilMoment,maxgradtime,pe2_offsetamp=0.0,nvblock;
double tetime,te_delay,tr_delay,perTime;
int table=0,shapeEx=0,sepSliceRephase=0,image,blocknvs;
char spoilflag[MAXSTR],perName[MAXSTR],slab[MAXSTR];
/* Real-time variables used in this sequence **************/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vpe_offset = v3; // PE/2 for non-table offset
int vpe_mult = v4; // PE multiplier, ranges from -PE/2 to PE/2
int vper_mult = v5; // PE rewinder multiplier; turn off rewinder when 0
int vpe2_steps = v6; // Number of PE2 steps
int vpe2_ctr = v7; // PE2 loop counter
int vpe2_mult = v8; // PE2 multiplier
int vpe2_offset = v9; // PE2/2 for non-table offset
int vpe2r_mult = v10; // PE2 rewinder multiplier
int vtrigblock = v11; // Number of PE steps per trigger block
int vpe = v12; // Current PE step out of total PE*PE2 steps
/* Initialize paramaters *********************************/
init_mri();
getstr("spoilflag",spoilflag);
getstr("slab",slab);
image = getval("image");
blocknvs = (int)getval("blocknvs");
nvblock = getval("nvblock");
if (!blocknvs) nvblock=1; // If blocked PEs for trigger not selected nvblock=1
trmin = 0.0;
temin = 0.0;
/* Check for external PE table ***************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
if (ns > 1) abort_message("No of slices must be set to one");
/* RF Calculations ****************************************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2); /* hard pulse */
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2); /* soft pulse */
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Gradient calculations **********************************/
if (slab[0] == 'y') {
init_slice(&ss_grad,"ss",thk);
init_slice_refocus(&ssr_grad,"ssr");
calc_slice(&ss_grad,&p2_rf,WRITE,"gss");
calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr");
}
if (FP_GT(tcrushro,0.0))
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
else
init_readout(&ro_grad,"ro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
calc_readout(&ro_grad,WRITE,"gro","sw","at");
ro_grad.m0ref *= grof;
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
init_phase(&pe_grad,"pe",lpe,nv);
init_phase(&pe2_grad,"pe2",lpe2,nv2);
calc_phase(&pe_grad,NOWRITE,"gpe","tpe");
if (!blocknvs) nvblock=1;
calc_phase(&pe2_grad,NOWRITE,"gpe2","");
if (spoilflag[0] == 'y') { // Calculate spoil grad if spoiling is turned on
init_dephase(&spoil_grad,"spoil"); // Optimized spoiler
spoilMoment = ro_grad.acqTime*ro_grad.roamp; // Optimal spoiling is at*gro for 2pi per pixel
spoilMoment -= ro_grad.m0def; // Subtract partial spoiling from back half of readout
calc_dephase(&spoil_grad,WRITE,spoilMoment,"gspoil","tspoil");
}
/* Is TE long enough for separate slab refocus? ***********/
maxgradtime = MAX(ror_grad.duration,MAX(pe_grad.duration,pe2_grad.duration));
if (spoilflag[0] == 'y')
maxgradtime = MAX(maxgradtime,spoil_grad.duration);
tetime = maxgradtime + alfa + ro_grad.timeToEcho + 4e-6;
if (slab[0] == 'y') {
tetime += ss_grad.rfCenterBack + ssr_grad.duration;
if ((te >= tetime) && (minte[0] != 'y')) {
sepSliceRephase = 1; // Set flag for separate slice rephase
} else {
pe2_grad.areaOffset = ss_grad.m0ref; // Add slab refocus on pe2 axis
calc_phase(&pe2_grad,NOWRITE,"gpe2",""); // Recalculate pe2 to include slab refocus
}
}
/* Equalize refocus and PE gradient durations *************/
pespoil_amp = 0.0;
perTime = 0.0;
if ((perewind[0] == 'y') && (spoilflag[0] == 'y')) { // All four must be single shape
if (ror_grad.duration > spoil_grad.duration) { // calc_sim first with ror
calc_sim_gradient(&pe_grad,&pe2_grad,&ror_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
} else { // calc_sim first with spoil
calc_sim_gradient(&pe_grad,&pe2_grad,&spoil_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
}
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
putvalue("tspoil",perTime);
putvalue("gspoil",spoil_grad.amp);
} else { // post-acquire shape will be either pe or spoil, but not both
calc_sim_gradient(&ror_grad,&pe_grad,&pe2_grad,tpemin,WRITE);
if ((perewind[0] == 'y') && (spoilflag[0] == 'n')) { // Rewinder, no spoiler
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
spoil_grad.amp = 0.0;
putvalue("tpe",perTime);
} else if ((perewind[0] == 'n') && (spoilflag[0] == 'y')) { // Spoiler, no rewinder
strcpy(perName,spoil_grad.name);
perTime = spoil_grad.duration;
pespoil_amp = spoil_grad.amp; // Apply spoiler on PE & PE2 axis if no rewinder
}
}
if (slab[0] == 'y') pe2_offsetamp = sepSliceRephase ? 0.0 : pe2_grad.offsetamp; // pe2 slab refocus
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
sgl_error_check(sglerror); // Check for any SGL errors
/* Min TE ******************************************/
tetime = pe_grad.duration + alfa + ro_grad.timeToEcho;
if (slab[0] == 'y') {
tetime += ss_grad.rfCenterBack;
tetime += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
}
else if (ws[0] == 'y')
tetime += p2/2.0 + rof2; /* soft pulse */
else
tetime += p1/2.0 + rof2; /* hard pulse */
temin = tetime + 4e-6; // Ensure that te_delay is at least 4us
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (te < temin) {
abort_message("TE too short. Minimum TE= %.2fms\n",temin*1000+0.005);
}
te_delay = te - tetime;
/* Min TR ******************************************/
trmin = te_delay + pe_grad.duration + ro_grad.duration + perTime;
if (slab[0] == 'y') {
trmin += ss_grad.duration;
trmin += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
}
else if (ws[0] == 'y')
trmin += p2 +rof1 + rof2; /* soft pulse */
else
trmin += p1 +rof1 + rof2; /* hard pulse */
trmin += 8e-6;
/* Increase TR if any options are selected *********/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (ticks > 0) trmin += 4e-6;
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000+0.005);
}
/* Calculate tr delay */
tr_delay = granularity(tr-trmin,GRADIENT_RES);
if(slab[0] == 'y') {
/* Generate phase-ramped pulses: 90 */
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1pat,ss_grad.rfDuration,freqEx,ns,ss_grad.rfFraction,seqcon[1]);
}
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad);
F_initval(pe_steps/2.0,vpe_offset);
pe2_steps = prep_profile(profile[1],nv2,&pe2_grad,&null_grad);
F_initval(pe2_steps/2.0,vpe2_offset);
assign(zero,oph);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *******************/
g_setExpTime(tr*(nt*pe_steps*pe2_steps));
/* PULSE SEQUENCE *************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(4e-6);
/* trigger */
if (ticks > 0) F_initval((double)nvblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
delay(tr_delay); // relaxation delay
sub(vpe_ctr,vpe_offset,vpe_mult);
sub(vpe2_ctr,vpe2_offset,vpe2_mult);
mult(vpe2_ctr,vpe_steps,vpe);
add(vpe_ctr,vpe,vpe);
/* PE rewinder follows PE table; zero if turned off ***/
if (perewind[0] == 'y') {
assign(vpe_mult,vper_mult);
assign(vpe2_mult,vpe2r_mult);
}
else {
assign(zero,vper_mult);
assign(zero,vpe2r_mult);
}
if (ticks > 0) {
modn(vpe,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
elsenz(vtest);
delay(4e-6);
endif(vtest);
}
sp1on(); delay(4e-6); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (slab[0] == 'y') {
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapeEx,ss_grad.rfDuration,zero,rof1,rof2,seqcon[1],zero);
delay(ss_grad.rfDelayBack);
if (sepSliceRephase) {
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(te_delay + tau); /* tau is current B0 encoding delay */
}
} else {
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
if (ws[0] == 'y')
shapedpulse(p2pat,p2,zero,rof1,rof2); /* soft CS pulse */
else
shapedpulse(p1pat,p1,zero,rof1,rof2); /* hard pulse */
delay(te_delay + tau); /* tau is current B0 encoding delay */
}
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp*image,0,-pe2_offsetamp,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
if ((slab[0] == 'y') && !sepSliceRephase) delay(te_delay + tau); /* tau is current B0 encoding delay */
/* Readout gradient and acquisition ********************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp*image,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
/* Rewind / spoiler gradient *********************************/
if (perewind[0] == 'y' || (spoilflag[0] == 'y')) {
pe2_shapedgradient(perName,perTime,spoil_grad.amp,pespoil_amp,pespoil_amp,
pe_grad.increment,pe2_grad.increment,vper_mult,vpe2r_mult,WAIT);
}
endpeloop(seqcon[2],vpe_ctr);
endpeloop(seqcon[3],vpe2_ctr);
}
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);
}
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);
}
void pulsesequence()
{
/* Internal variable declarations *************************/
double freqEx[MAXNSLICE];
double pespoil_amp,maxgradtime,spoilMoment,perTime,pe2_offsetamp,tau1,te_delay,tr_delay;
double te2=0.0,te3=0.0,te2min,te3min,tau2,tau3,te2_delay,te3_delay=0;
char minte2[MAXSTR],minte3[MAXSTR],spoilflag[MAXSTR],perName[MAXSTR];
int sepSliceRephase,sepReadRephase=0,readrev,table,shapeEx;
int i;
/* Real-time variables used in this sequence **************/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vpe_offset = v5; // PE/2 for non-table offset
int vpe_mult = v6; // PE multiplier, ranges from -PE/2 to PE/2
int vper_mult = v7; // PE rewinder multiplier; turn off rewinder when 0
int vpe2_steps = v8; // Number of PE2 steps
int vpe2_ctr = v9; // PE2 loop counter
int vpe2_mult = v10; // PE2 multiplier
int vpe2_offset = v11; // PE2/2 for non-table offset
int vpe2r_mult = v12; // PE2 rewinder multiplier
int vssc = v13; // Compressed steady-states
int vacquire = v14; // Argument for setacqvar, to skip steady state acquires
int vrfspoil_ctr = v15; // RF spoil counter
int vrfspoil = v16; // RF spoil multiplier
int vtrimage = v17; // Counts down from nt, trimage delay when 0
int vne = v18; // Number of echoes
int vne_ctr = v19; // Echo loop counter
int vneindex = v20; // Echo index, odd or even
int vnelast = v21; // Check for last echo
int vtrigblock = v22; // Number of slices per trigger block
/* Initialize paramaters **********************************/
init_mri();
getstr("spoilflag",spoilflag);
te2=getval("te2");
te3=getval("te3");
getstr("minte2",minte2);
getstr("minte3",minte3);
readrev=(int)getval("readrev");
/* Check for external PE table ***************************/
table = 0;
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
/* Set Rcvr/Xmtr phase increments for RF Spoiling ********/
/* Ref: Zur, Y., Magn. Res. Med., 21, 251, (1991) *******/
if (rfspoil[0] == 'y') {
rcvrstepsize(rfphase);
obsstepsize(rfphase);
}
/* Initialize gradient structures *************************/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2 ); // excitation pulse
init_slice(&ss_grad,"ss",thk); // slice select gradient
init_slice_refocus(&ssr_grad,"ssr"); // slice refocus gradient
init_readout(&ro_grad,"ro",lro,np,sw); // readout gradient
init_readout_refocus(&ror_grad,"ror"); // dephase gradient
init_phase(&pe_grad,"pe",lpe,nv); // phase encode gradient
init_phase(&pe2_grad,"pe2",lpe2,nv2); // 2nd phase encode gradient
init_dephase(&spoil_grad,"spoil"); // optimized spoiler
init_dephase(&ref_grad,"ref"); // readout rephase
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice_refocus(&ssr_grad, &ss_grad, WRITE,"gssr");
calc_readout(&ro_grad, WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad, NOWRITE,"gpe","tpe");
calc_phase(&pe2_grad,NOWRITE,"gpe2","");
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
if (spoilflag[0] == 'y') {
spoilMoment = ro_grad.acqTime*ro_grad.roamp; // Optimal spoiling is at*gro for 2pi per pixel
spoilMoment -= ro_grad.m0def; // Subtract partial spoiling from back half of readout
if (perewind[0] == 'y')
calc_dephase(&spoil_grad,NOWRITE,spoilMoment,"gspoil","tspoil");
else
calc_dephase(&spoil_grad,WRITE,spoilMoment,"gspoil","tspoil");
}
/* Is TE long enough for separate slab refocus? *******/
maxgradtime = MAX(ror_grad.duration,pe_grad.duration);
if (spoilflag[0] == 'y')
maxgradtime = MAX(maxgradtime,spoil_grad.duration);
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + maxgradtime + alfa + ro_grad.timeToEcho + 4e-6;
if ((te >= tau1) && (minte[0] != 'y')) sepSliceRephase = 1; // Set flag for separate slice rephase
else {
sepSliceRephase = 0;
pe2_grad.areaOffset = ss_grad.m0ref; // Add slab refocus on pe2 axis
calc_phase(&pe2_grad,NOWRITE,"gpe2",""); // Recalculate pe2 to include slab refocus
}
/* Equalize refocus and PE gradient durations *************/
pespoil_amp = 0.0;
perTime = 0.0;
if ((perewind[0] == 'y') && (spoilflag[0] == 'y')) { // All four must be single shape
if (ror_grad.duration > spoil_grad.duration) { // calc_sim first with ror
calc_sim_gradient(&pe_grad,&pe2_grad,&ror_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
} else { // calc_sim first with spoil
calc_sim_gradient(&pe_grad,&pe2_grad,&spoil_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,WRITE);
}
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
} else { // post-acquire shape will be either pe or spoil, but not both
calc_sim_gradient(&ror_grad,&pe_grad,&pe2_grad,tpemin,WRITE);
if ((perewind[0] == 'y') && (spoilflag[0] == 'n')) { // Rewinder, no spoiler
strcpy(perName,pe_grad.name);
perTime = pe_grad.duration;
spoil_grad.amp = 0.0;
} else if ((perewind[0] == 'n') && (spoilflag[0] == 'y')) { // Spoiler, no rewinder
strcpy(perName,spoil_grad.name);
perTime = spoil_grad.duration;
pespoil_amp = spoil_grad.amp; // Apply spoiler on PE & PE2 axis if no rewinder
}
}
pe2_offsetamp = sepSliceRephase ? 0.0 : pe2_grad.offsetamp; // pe2 slab refocus
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') create_inversion_recovery();
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freqEx,ns,ss_grad.rfFraction,seqcon[1]);
/* Check that all Gradient calculations are ok ************/
sgl_error_check(sglerror);
/* Min TE ******************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + alfa + ro_grad.timeToEcho;
tau1 += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
temin = tau1 + 4e-6; /* ensure that te_delay is at least 4us */
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (te < temin) {
abort_message("TE too short. Minimum TE= %.2fms\n",temin*1000+0.005);
}
te_delay = te - tau1;
/* Min TE2 *****************************************/
tau2 = (readrev) ? 2*ro_grad.timeFromEcho+alfa : ro_grad.duration+ref_grad.duration;
te2min = tau2 + 4e-6;
if (minte2[0] == 'y') {
te2 = te2min;
putvalue("te2",te2);
}
if (te2 < te2min) {
abort_message("TE2 too short. Minimum TE2= %.2fms\n",te2min*1000+0.005);
}
if (readrev) te2_delay = te2 - tau2;
else {
tau2 = ro_grad.duration + 2*ror_grad.duration;
if (te2 >= tau2) {
sepReadRephase = 1; // Set flag for separate read rephase
te2_delay = te2 - ro_grad.duration - 2*ror_grad.duration;
} else {
sepReadRephase = 0;
if (te2 > te2min+4e-6) {
ref_grad.duration = granularity(te2-ro_grad.duration-8e-6,GRADIENT_RES);
ref_grad.calcFlag = AMPLITUDE_FROM_MOMENT_DURATION;
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
}
te2_delay = te2 - ro_grad.duration - ref_grad.duration;
}
}
/* Min TE3 *****************************************/
if (readrev) {
tau3 = 2*ro_grad.timeToEcho + alfa;
te3min = tau3 + 4e-6;
if (minte3[0] == 'y') {
te3 = te3min;
putvalue("te3",te3);
}
if (te3 < te3min) {
abort_message("TE3 too short. Minimum TE3= %.2fms\n",te3min*1000+0.005);
}
te3_delay = te3 - tau3;
}
/* Now set the TE array accordingly */
putCmd("TE = 0"); /* Re-initialize TE */
putCmd("TE[1] = %f",te*1000);
if (readrev) {
for (i=1;i<ne;i++) {
if (i%2 == 0) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te3*1000);
else putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
} else {
for (i=1;i<ne;i++) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Min TR ******************************************/
trmin = ss_grad.duration + te_delay + pe_grad.duration + ne*ro_grad.duration + perTime + 8e-6;
trmin += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
if (readrev) trmin += (ne/2)*te2_delay + ((ne-1)/2)*te3_delay;
else trmin += (sepReadRephase) ? (ne-1)*(te2_delay+2*ror_grad.duration) : (ne-1)*(te2_delay+ref_grad.duration);
/* Increase TR if any options are selected *********/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (ticks > 0) trmin += 4e-6;
/* Adjust for all slices ***************************/
trmin *= ns;
/* Inversion recovery *********************************/
if (ir[0] == 'y') {
/* tiaddTime 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 */
tiaddTime = satTime + fsatTime + mtTime + 4e-6 + ss_grad.rfCenterFront;
/* calc_irTime checks ti and returns the time of all IR components */
trmin += calc_irTime(tiaddTime,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 = %.2fms\n",trmin*1000+0.005);
}
/* Calculate tr delay */
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&per_grad);
F_initval(pe_steps/2.0,vpe_offset);
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') g_setExpTime(trmean*ntmean*pe_steps*pe2_steps*arraydim);
else if (seqcon[3]=='s') g_setExpTime(trmean*pe2_steps*(ntmean*pe_steps*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*pe2_steps*arraydim - ssc*arraydim));
} else {
if (seqcon[2]=='s') g_setExpTime(trmean*ntmean*pe_steps*pe2_steps*arraydim);
else g_setExpTime(trmean*ntmean*pe_steps*pe2_steps*arraydim + tr*ssc);
}
/* Return parameters to VnmrJ */
putvalue("tror",ror_grad.duration); // ROR duration
putvalue("gpe",pe_grad.peamp); // PE max grad amp
putvalue("gss",ss_grad.ssamp); // Excitation slice grad
putvalue("gro",ro_grad.roamp); // RO grad
/* PULSE SEQUENCE ***************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(4e-6);
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
assign(zero,vrfspoil_ctr); // RF spoil phase counter
assign(zero,vrfspoil); // RF spoil multiplier
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop2(seqcon[3],pe2_steps,vpe2_steps,vpe2_ctr);
/* 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);
}
/* 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);
/* Set rcvr/xmtr phase for RF spoiling *******************/
if (rfspoil[0] == 'y') {
incr(vrfspoil_ctr); // vrfspoil_ctr = 1 2 3 4 5 6
add(vrfspoil,vrfspoil_ctr,vrfspoil); // vrfspoil = 1 3 6 10 15 21
xmtrphase(vrfspoil);
rcvrphase(vrfspoil);
}
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_mult);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_mult);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states
endif(vacquire);
}
/* PE rewinder follows PE table; zero if turned off ***/
if (perewind[0] == 'y') {
assign(vpe_mult,vper_mult);
assign(vpe2_mult,vpe2r_mult);
}
else {
assign(zero,vper_mult);
assign(zero,vpe2r_mult);
}
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (!trtype) delay(tr_delay); // Relaxation delay
if (ticks > 0) {
modn(vms_ctr,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
elsenz(vtest);
delay(4e-6);
endif(vtest);
}
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* Prepulse options ***********************************/
if (ir[0] == 'y') inversion_recovery();
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapeEx,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
if (sepSliceRephase) { // separate slice refocus gradient
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(te_delay); // delay between slab refocus and pe
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,-pe2_offsetamp,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
} else {
pe2_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,-pe2_offsetamp,
-pe_grad.increment,-pe2_grad.increment,vpe_mult,vpe2_mult,WAIT);
delay(te_delay); // delay after refocus/pe
}
F_initval(ne,vne);
loop(vne,vne_ctr);
if (readrev) {
mod2(vne_ctr,vneindex);
ifzero(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te2_delay);
endif(vnelast);
elsenz(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,-ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te3_delay);
endif(vnelast);
endif(vneindex);
} else {
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
if (sepReadRephase) {
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
delay(te2_delay);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
} else {
obl_shapedgradient(ref_grad.name,ref_grad.duration,-ref_grad.amp,0,0,WAIT);
delay(te2_delay);
}
endif(vnelast);
}
endloop(vne_ctr);
/* Rewind / spoiler gradient **************************/
if ((perewind[0] == 'y') || (spoilflag[0] == 'y')) {
pe2_shapedgradient(perName,perTime,spoil_grad.amp,pespoil_amp,pespoil_amp,
pe_grad.increment,pe2_grad.increment,vper_mult,vpe2r_mult,WAIT);
}
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
endpeloop(seqcon[3],vpe2_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}