void shape_rf (RF_PULSE_T *rf, char rfBase[MAX_STR], char rfName[MAX_STR], double pw, double flip,
double rof1, double rof2)
{
if ((ix > 1) && !sglarray) {
rf->flip = flip;
return;
}
initRf(rf);
strcpy(rf->pulseBase,rfBase);
strcpy(rf->pulseName,rfName);
strcpy(rf->rfcoil,rfcoil);
rf->rfDuration = pw;
rf->flip = flip;
rf->flipmult = 1.0;
rf->rof1 = rof1;
rf->rof2 = rof2;
/* Generate the pulse shape if rf->pulseName is appropriate */
genRf(rf);
/* If the pulse shape has not been generated proceed as for init_rf */
switch (rf->type) {
case RF_NULL:
rf->rfDuration = shapelistpw(rfName,pw); /* Round to 200ns resolution*/
readRfPulse(rf);
/* Set actual bandwidth according to pulse duration */
if ((FP_LT(rf->flip,FLIPLIMIT_LOW)) || (FP_GT(rf->flip,FLIPLIMIT_HIGH)))
/* use excitation bandwidth */
rf->bandwidth = rf->header.bandwidth/rf->rfDuration;
else
/* use inversion bandwidth */
rf->bandwidth = rf->header.inversionBw/rf->rfDuration;
break;
default:
/* Even though shape is properly quantized for some reason we need to
use shapelistpw to round to 200ns resolution, otherwise duration may
be significantly wrong ?? */
rf->rfDuration = shapelistpw(rf->pulseName,pw);
break;
}
switch (rf->error) {
case ERR_RF_SHAPE_MISSING:
sgl_abort_message("ERROR: Can not find RF shape '%s.RF'",rfName);
break;
case ERR_RF_HEADER_ENTRIES:
sgl_abort_message("ERROR rf shape '%s': incorrect header information",rfName);
break;
default:
break;
}
if ((rf->header.rfFraction < 0) || (rf->header.rfFraction > 1))
sgl_abort_message("ERROR rf shape '%s': RF Fraction must be between 0 and 1",rfName);
}
int lw_segment_envelope_intersects(const POINT2D *p1, const POINT2D *p2, const POINT2D *q1, const POINT2D *q2)
{
double minq=FP_MIN(q1->x,q2->x);
double maxq=FP_MAX(q1->x,q2->x);
double minp=FP_MIN(p1->x,p2->x);
double maxp=FP_MAX(p1->x,p2->x);
if (FP_GT(minp,maxq) || FP_LT(maxp,minq))
return LW_FALSE;
minq=FP_MIN(q1->y,q2->y);
maxq=FP_MAX(q1->y,q2->y);
minp=FP_MIN(p1->y,p2->y);
maxp=FP_MAX(p1->y,p2->y);
if (FP_GT(minp,maxq) || FP_LT(maxp,minq))
return LW_FALSE;
return LW_TRUE;
}
pulsesequence()
{
/* Internal variable declarations *********************/
char txphase[MAXSTR];
char rxphase[MAXSTR];
char blankmode[MAXSTR]={0};
double postDelay;
double rfDuration;
double acqt;
int i,ret=-1;
static int phs1[4] = {0,2,1,3}; /* from T1meas.c */
/*************************************************/
/* Initialize paramter **************************/
i = 0;
postDelay = 0.5;
acqt = 0.0;
getstr("rxphase",rxphase);
getstr("txphase",txphase);
ret = P_getstring(GLOBAL,"blankmode",blankmode,1,MAXSTR);
//getparm("blankmode","string",GLOBAL,blankmode,MAXSTR);
postDelay = tr - at;
//printf("blankmode=%s\n",blankmode);
/*************************************************/
/* check phase setting ***************************/
if ( (txphase[0] =='n') && (rxphase[0] =='n') )
{
abort_message("ERROR - Select at least one phase [Tx or Rx]\n");
}
/**************************************************/
/* check pulse width *****************************/
rfDuration = shapelistpw(p1pat, p1); /* assign exitation pulse duration */
acqt = rfDuration + rof1 - alfa;
if (FP_GT(acqt, at))
{
abort_message("Pulse duration too long. max [%.3f] ms\n",(at-rof1+alfa)*1000.0);
}
if(ret==0 && blankmode[0]=='u')
obsunblank();
delay(postDelay);
settable(t1,4,phs1); /*from T1meas.c */
getelem(t1,ct,v11); /*from T1meas.c */
setreceiver(t1);
/*==============================================*/
/* START LOOPBACK PULSE SEQUENCE */
/*==============================================*/
status(A);
obsoffset(resto);
/* TTL trigger to scope sequence ****************************/
sp1on();
/* Relaxation delay ***********************************/
xgate(ticks);
/* RF pulse *******************************************/
obspower(tpwr);
obspwrf(tpwrf);
ShapedXmtNAcquire(p1pat, rfDuration, v11, rof1, OBSch);
endacq();
sp1off();
if(ret==0 && blankmode[0]=='u')
obsunblank();
}
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 gaussRf(RF_PULSE_T *rf)
{
int i;
double t;
double a,b;
/* Set gauss shape type */
rf->type = RF_GAUSS;
/* Set shape name */
setshapeRf(rf);
/* Get pulse parameters */
getparsRf(rf);
/* Round pulse resolution & duration and set the number of pulse points */
roundparsRf(rf);
/* Set default cutoff (% of maximum) */
if (rf->cutoff < 0.001) rf->cutoff = 1.0;
/* Otherwise make sure cutoff is 0.1, 0.5, 1.0, 5.0 or 10.0 */
if (rf->cutoff < 0.25) rf->cutoff = 0.1;
else if ((rf->cutoff >= 0.25) && (rf->cutoff < 0.75))
rf->cutoff = 0.5;
else if ((rf->cutoff >= 0.75) && (rf->cutoff < 2.5))
rf->cutoff = 1.0;
else if ((rf->cutoff >= 2.5) && (rf->cutoff < 7.5))
rf->cutoff = 5.0;
else if (rf->cutoff >= 7.5) rf->cutoff = 10.0;
/* Set excitation and inversion bandwidths */
if (rf->cutoff == 0.1) {
rf->header.bandwidth = 3.308;
rf->header.inversionBw = 1.863;
}
if (rf->cutoff == 0.5) {
rf->header.bandwidth = 2.896;
rf->header.inversionBw = 1.635;
}
if (rf->cutoff == 1.0) {
rf->header.bandwidth = 2.705;
rf->header.inversionBw = 1.528;
}
if (rf->cutoff == 5.0) {
rf->header.bandwidth = 2.216;
rf->header.inversionBw = 1.263;
}
if (rf->cutoff == 10.0) {
rf->header.bandwidth = 1.997;
rf->header.inversionBw = 1.1455;
}
/* Set modulation type */
strcpy(rf->header.modulation,"amplitude");
/* Set rf fraction */
rf->header.rfFraction = 0.5;
/* Set pulse type */
strcpy(rf->header.type,"selective");
/* Set actual bandwidth of pulse */
if ((FP_LT(rf->flip,FLIPLIMIT_LOW)) || (FP_GT(rf->flip,FLIPLIMIT_HIGH)))
/* use excitation bandwidth */
rf->bandwidth = rf->header.bandwidth/rf->rfDuration;
else
/* use inversion bandwidth */
rf->bandwidth = rf->header.inversionBw/rf->rfDuration;
/* Set SPL version */
rf->header.version = SPLVERSION;
/* Allocate memory for pulse shape */
if ((rf->amp=(double *)malloc(rf->pts*sizeof(double))) == NULL) nomem();
if ((rf->phase=(double *)malloc(rf->pts*sizeof(double))) == NULL) nomem();
/* Generate shape */
a = -log(rf->cutoff/100.0)*4.0/(rf->rfDuration*rf->rfDuration);
b = -rf->rfDuration/2.0 + rf->res/2.0;
for (i=0;i<rf->pts;i++) {
t = b+rf->res*i;
rf->amp[i]=exp(-a*t*t);
rf->phase[i]=0.0;
}
/* Calculate area under pulse */
calcintRf(rf);
/* Scale amplitude so max is 1023.0 */
scaleampRf(rf);
/* Write the pulse to disk */
writeRf(rf);
/* Write pulse parameters */
putparsRf(rf);
/* Update pulseName with new shape name */
strcpy(rf->pulseName,rf->shapeName);
/* Free memory */
free(rf->amp);
free(rf->phase);
}
/*----------------------------------*/
void sincRf(RF_PULSE_T *rf)
{
int i;
double t;
double a,b;
/* Set sinc shape type */
rf->type = RF_SINC;
/* Set shape name */
setshapeRf(rf);
/* Get pulse parameters */
getparsRf(rf);
/* Round pulse resolution & duration and set the number of pulse points */
roundparsRf(rf);
/* Set default number of lobes */
if (rf->lobes == 0) rf->lobes = 5;
/* Otherwise make sure lobes is odd and between 1 and 13 */
if (rf->lobes < 1) rf->lobes = 1;
if (rf->lobes > 13) rf->lobes = 13;
if (rf->lobes%2 == 0) rf->lobes++;
/* Set excitation and inversion bandwidths */
switch (rf->lobes) {
case 1:
rf->header.bandwidth = 1.998;
rf->header.inversionBw = 1.252;
break;
case 3:
rf->header.bandwidth = 4.018;
rf->header.inversionBw = 2.598;
break;
case 5:
rf->header.bandwidth = 5.944;
rf->header.inversionBw = 4.702;
break;
case 7:
rf->header.bandwidth = 7.884;
rf->header.inversionBw = 6.298;
break;
case 9:
rf->header.bandwidth = 9.856;
rf->header.inversionBw = 8.398;
break;
case 11:
rf->header.bandwidth = 11.790;
rf->header.inversionBw = 9.985;
break;
case 13:
rf->header.bandwidth = 13.783;
rf->header.inversionBw = 11.918;
break;
}
/* Set modulation type */
strcpy(rf->header.modulation,"amplitude");
/* Set rf fraction */
rf->header.rfFraction = 0.5;
/* Set pulse type */
strcpy(rf->header.type,"selective");
/* Set actual bandwidth of pulse */
if ((FP_LT(rf->flip,FLIPLIMIT_LOW)) || (FP_GT(rf->flip,FLIPLIMIT_HIGH)))
/* use excitation bandwidth */
rf->bandwidth = rf->header.bandwidth/rf->rfDuration;
else
/* use inversion bandwidth */
rf->bandwidth = rf->header.inversionBw/rf->rfDuration;
/* Set SPL version */
rf->header.version = SPLVERSION;
/* Allocate memory for pulse shape */
if ((rf->amp=(double *)malloc(rf->pts*sizeof(double))) == NULL) nomem();
if ((rf->phase=(double *)malloc(rf->pts*sizeof(double))) == NULL) nomem();
/* Generate shape */
a = -rf->rfDuration/2.0 + rf->res/2.0;
b = M_PI*(rf->lobes + 1)/(rf->rfDuration - rf->res);
for (i=0;i<rf->pts;i++) {
t = b*(a+rf->res*i);
if (t == 0.0) rf->amp[i]=1.0;
else rf->amp[i]=sin(t)/t;
rf->phase[i]=0.0;
}
/* Calculate area under pulse */
calcintRf(rf);
/* Scale amplitude so max is 1023.0 */
scaleampRf(rf);
/* Pulse amplitudes can't be negative, so set opposite phase instead */
absampRf(rf);
/* Write the pulse to disk */
writeRf(rf);
/* Write pulse parameters */
putparsRf(rf);
/* Update pulseName with new shape name */
strcpy(rf->pulseName,rf->shapeName);
/* Free memory */
free(rf->amp);
free(rf->phase);
}
BOX3D *
lwcircle_compute_box3d(POINT4D *p1, POINT4D *p2, POINT4D *p3)
{
double x1, x2, y1, y2, z1, z2;
double angle, radius, sweep;
/* angles from center */
double a1, a2, a3;
/* angles from center once a1 is rotated to zero */
double r2, r3;
double xe = 0.0, ye = 0.0;
POINT4D *center;
int i;
BOX3D *box;
LWDEBUG(2, "lwcircle_compute_box3d called.");
radius = lwcircle_center(p1, p2, p3, ¢er);
if (radius < 0.0)
{
LWDEBUG(3, "lwcircle_compute_box3d: zero radius");
/*
* We've got a straight line here. Look to the end points for extents.
* It's worth noting that when lwcircle_center returns < 0, center hasn't been allocated.
*/
x1 = (FP_LT(p1->x, p3->x)) ? p1->x : p3->x;
x2 = (FP_GT(p1->x, p3->x)) ? p1->x : p3->x;
y1 = (FP_LT(p1->y, p3->y)) ? p1->y : p3->y;
y2 = (FP_GT(p1->y, p3->y)) ? p1->y : p3->y;
z1 = (FP_LT(p1->z, p2->z)) ? p1->z : p2->z;
z1 = (FP_LT(z1, p3->z)) ? z1 : p3->z;
z2 = (FP_GT(p1->z, p2->z)) ? p1->z : p2->z;
z2 = (FP_GT(z2, p3->z)) ? z2 : p3->z;
box = lwalloc(sizeof(BOX3D));
box->xmin = x1;
box->xmax = x2;
box->ymin = y1;
box->ymax = y2;
box->zmin = z1;
box->zmax = z2;
LWDEBUGF(3, "lwcircle_compute_box3d: extents %.16f %.16f %.16f, %.16f %.16f %.16f", x1, y1, z1, x2, y2, z2);
return box;
}
/*
top = center->y + radius;
left = center->x - radius;
LWDEBUGF(3, "lwcircle_compute_box3d: center (%.16f, %.16f)", center->x, center->y);
*/
x1 = MAXFLOAT;
x2 = -1 * MAXFLOAT;
y1 = MAXFLOAT;
y2 = -1 * MAXFLOAT;
a1 = atan2(p1->y - center->y, p1->x - center->x);
a2 = atan2(p2->y - center->y, p2->x - center->x);
a3 = atan2(p3->y - center->y, p3->x - center->x);
/* Rotate a2 and a3 such that a1 = 0 */
r2 = a2 - a1;
r3 = a3 - a1;
LWDEBUGF(4, "a1 %.16f, a2 %.16f, a3 %.16f", a1, a2, a3);
LWDEBUGF(4, "r2 %.16f, r3 %.16f", r2, r3);
/*
* There are six cases here I'm interested in
* Clockwise:
* 1. a1-a2 < 180 == r2 < 0 && (r3 > 0 || r3 < r2)
* 2. a1-a2 > 180 == r2 > 0 && (r3 > 0 && r3 < r2)
* 3. a1-a2 > 180 == r2 > 0 && (r3 > r2 || r3 < 0)
* Counter-clockwise:
* 4. a1-a2 < 180 == r2 > 0 && (r3 < 0 || r3 > r2)
* 5. a1-a2 > 180 == r2 < 0 && (r3 < 0 && r3 > r2)
* 6. a1-a2 > 180 == r2 < 0 && (r3 < r2 || r3 > 0)
* 3 and 6 are invalid cases where a3 is the midpoint.
* BBOX is fundamental, so these cannot error out and will instead
* calculate the sweep using a3 as the middle point.
*/
/* clockwise 1 */
if (FP_LT(r2, 0) && (FP_GT(r3, 0) || FP_LT(r3, r2)))
{
sweep = (FP_GT(r3, 0)) ? (r3 - 2 * M_PI) : r3;
}
/* clockwise 2 */
else if (FP_GT(r2, 0) && FP_GT(r3, 0) && FP_LT(r3, r2))
{
sweep = (FP_GT(r3, 0)) ? (r3 - 2 * M_PI) : r3;
}
/* counter-clockwise 4 */
else if (FP_GT(r2, 0) && (FP_LT(r3, 0) || FP_GT(r3, r2)))
{
sweep = (FP_LT(r3, 0)) ? (r3 + 2 * M_PI) : r3;
}
/* counter-clockwise 5 */
else if (FP_LT(r2, 0) && FP_LT(r3, 0) && FP_GT(r3, r2))
{
sweep = (FP_LT(r3, 0)) ? (r3 + 2 * M_PI) : r3;
}
/* clockwise invalid 3 */
else if (FP_GT(r2, 0) && (FP_GT(r3, r2) || FP_LT(r3, 0)))
{
sweep = (FP_GT(r2, 0)) ? (r2 - 2 * M_PI) : r2;
}
/* clockwise invalid 6 */
else
{
sweep = (FP_LT(r2, 0)) ? (r2 + 2 * M_PI) : r2;
}
LWDEBUGF(3, "a1 %.16f, a2 %.16f, a3 %.16f, sweep %.16f", a1, a2, a3, sweep);
angle = 0.0;
for (i=0; i < 6; i++)
{
switch (i)
{
/* right extent */
case 0:
angle = 0.0;
xe = center->x + radius;
ye = center->y;
break;
/* top extent */
case 1:
angle = M_PI_2;
xe = center->x;
ye = center->y + radius;
break;
/* left extent */
case 2:
angle = M_PI;
xe = center->x - radius;
ye = center->y;
break;
/* bottom extent */
case 3:
angle = -1 * M_PI_2;
xe = center->x;
ye = center->y - radius;
break;
/* first point */
case 4:
angle = a1;
xe = p1->x;
ye = p1->y;
break;
/* last point */
case 5:
angle = a3;
xe = p3->x;
ye = p3->y;
break;
}
/* determine if the extents are outside the arc */
if (i < 4)
{
if (FP_GT(sweep, 0.0))
{
if (FP_LT(a3, a1))
{
if (FP_GT(angle, (a3 + 2 * M_PI)) || FP_LT(angle, a1)) continue;
}
else
{
if (FP_GT(angle, a3) || FP_LT(angle, a1)) continue;
}
}
else
{
if (FP_GT(a3, a1))
{
if (FP_LT(angle, (a3 - 2 * M_PI)) || FP_GT(angle, a1)) continue;
}
else
{
if (FP_LT(angle, a3) || FP_GT(angle, a1)) continue;
}
}
}
LWDEBUGF(3, "lwcircle_compute_box3d: potential extreame %d (%.16f, %.16f)", i, xe, ye);
x1 = (FP_LT(x1, xe)) ? x1 : xe;
y1 = (FP_LT(y1, ye)) ? y1 : ye;
x2 = (FP_GT(x2, xe)) ? x2 : xe;
y2 = (FP_GT(y2, ye)) ? y2 : ye;
}
LWDEBUGF(3, "lwcircle_compute_box3d: extreames found (%.16f %.16f, %.16f %.16f)", x1, y1, x2, y2);
/*
x1 = center->x + x1 * radius;
x2 = center->x + x2 * radius;
y1 = center->y + y1 * radius;
y2 = center->y + y2 * radius;
*/
z1 = (FP_LT(p1->z, p2->z)) ? p1->z : p2->z;
z1 = (FP_LT(z1, p3->z)) ? z1 : p3->z;
z2 = (FP_GT(p1->z, p2->z)) ? p1->z : p2->z;
z2 = (FP_GT(z2, p3->z)) ? z2 : p3->z;
box = lwalloc(sizeof(BOX3D));
box->xmin = x1;
box->xmax = x2;
box->ymin = y1;
box->ymax = y2;
box->zmin = z1;
box->zmax = z2;
lwfree(center);
return box;
}
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);
}
static int lwcircle_calculate_gbox(POINT4D p1, POINT4D p2, POINT4D p3, GBOX *gbox)
{
double x1, x2, y1, y2, z1, z2, m1, m2;
double angle, radius, sweep;
/* angles from center */
double a1, a2, a3;
/* angles from center once a1 is rotated to zero */
double r2, r3;
double xe = 0.0, ye = 0.0;
POINT4D *center;
int i;
LWDEBUG(2, "lwcircle_calculate_gbox called.");
radius = lwcircle_center(&p1, &p2, &p3, ¢er);
if (radius < 0.0) return G_FAILURE;
x1 = MAXFLOAT;
x2 = -1 * MAXFLOAT;
y1 = MAXFLOAT;
y2 = -1 * MAXFLOAT;
a1 = atan2(p1.y - center->y, p1.x - center->x);
a2 = atan2(p2.y - center->y, p2.x - center->x);
a3 = atan2(p3.y - center->y, p3.x - center->x);
/* Rotate a2 and a3 such that a1 = 0 */
r2 = a2 - a1;
r3 = a3 - a1;
/*
* There are six cases here I'm interested in
* Clockwise:
* 1. a1-a2 < 180 == r2 < 0 && (r3 > 0 || r3 < r2)
* 2. a1-a2 > 180 == r2 > 0 && (r3 > 0 && r3 < r2)
* 3. a1-a2 > 180 == r2 > 0 && (r3 > r2 || r3 < 0)
* Counter-clockwise:
* 4. a1-a2 < 180 == r2 > 0 && (r3 < 0 || r3 > r2)
* 5. a1-a2 > 180 == r2 < 0 && (r3 < 0 && r3 > r2)
* 6. a1-a2 > 180 == r2 < 0 && (r3 < r2 || r3 > 0)
* 3 and 6 are invalid cases where a3 is the midpoint.
* BBOX is fundamental, so these cannot error out and will instead
* calculate the sweep using a3 as the middle point.
*/
/* clockwise 1 */
if (FP_LT(r2, 0) && (FP_GT(r3, 0) || FP_LT(r3, r2)))
{
sweep = (FP_GT(r3, 0)) ? (r3 - 2 * M_PI) : r3;
}
/* clockwise 2 */
else if (FP_GT(r2, 0) && FP_GT(r3, 0) && FP_LT(r3, r2))
{
sweep = (FP_GT(r3, 0)) ? (r3 - 2 * M_PI) : r3;
}
/* counter-clockwise 4 */
else if (FP_GT(r2, 0) && (FP_LT(r3, 0) || FP_GT(r3, r2)))
{
sweep = (FP_LT(r3, 0)) ? (r3 + 2 * M_PI) : r3;
}
/* counter-clockwise 5 */
else if (FP_LT(r2, 0) && FP_LT(r3, 0) && FP_GT(r3, r2))
{
sweep = (FP_LT(r3, 0)) ? (r3 + 2 * M_PI) : r3;
}
/* clockwise invalid 3 */
else if (FP_GT(r2, 0) && (FP_GT(r3, r2) || FP_LT(r3, 0)))
{
sweep = (FP_GT(r2, 0)) ? (r2 - 2 * M_PI) : r2;
}
/* clockwise invalid 6 */
else
{
sweep = (FP_LT(r2, 0)) ? (r2 + 2 * M_PI) : r2;
}
LWDEBUGF(3, "a1 %.16f, a2 %.16f, a3 %.16f, sweep %.16f", a1, a2, a3, sweep);
angle = 0.0;
for (i=0; i < 6; i++)
{
switch (i)
{
/* right extent */
case 0:
angle = 0.0;
xe = center->x + radius;
ye = center->y;
break;
/* top extent */
case 1:
angle = M_PI_2;
xe = center->x;
ye = center->y + radius;
break;
/* left extent */
case 2:
angle = M_PI;
xe = center->x - radius;
ye = center->y;
break;
/* bottom extent */
case 3:
angle = -1 * M_PI_2;
xe = center->x;
ye = center->y - radius;
break;
/* first point */
case 4:
angle = a1;
xe = p1.x;
ye = p1.y;
break;
/* last point */
case 5:
angle = a3;
xe = p3.x;
ye = p3.y;
break;
}
/* determine if the extents are outside the arc */
if (i < 4)
{
if (FP_GT(sweep, 0.0))
{
if (FP_LT(a3, a1))
{
if (FP_GT(angle, (a3 + 2 * M_PI)) || FP_LT(angle, a1)) continue;
}
else
{
if (FP_GT(angle, a3) || FP_LT(angle, a1)) continue;
}
}
else
{
if (FP_GT(a3, a1))
{
if (FP_LT(angle, (a3 - 2 * M_PI)) || FP_GT(angle, a1)) continue;
}
else
{
if (FP_LT(angle, a3) || FP_GT(angle, a1)) continue;
}
}
}
LWDEBUGF(3, "lwcircle_calculate_gbox: potential extreame %d (%.16f, %.16f)", i, xe, ye);
x1 = (FP_LT(x1, xe)) ? x1 : xe;
y1 = (FP_LT(y1, ye)) ? y1 : ye;
x2 = (FP_GT(x2, xe)) ? x2 : xe;
y2 = (FP_GT(y2, ye)) ? y2 : ye;
}
LWDEBUGF(3, "lwcircle_calculate_gbox: extreames found (%.16f %.16f, %.16f %.16f)", x1, y1, x2, y2);
z1 = FP_MIN(p1.z, p2.z);
z1 = FP_MIN(z1, p3.z);
z2 = FP_MAX(p1.z, p2.z);
z2 = FP_MAX(z2, p3.z);
m1 = FP_MIN(p1.m, p2.m);
m1 = FP_MIN(m1, p3.m);
m2 = FP_MAX(p1.m, p2.m);
m2 = FP_MAX(m2, p3.m);
gbox->xmin = x1;
gbox->xmax = x2;
gbox->ymin = y1;
gbox->ymax = y2;
if ( FLAGS_GET_Z(gbox->flags) )
{
gbox->zmin = z1;
gbox->zmax = z2;
}
if ( FLAGS_GET_M(gbox->flags) )
{
gbox->mmin = m1;
gbox->mmax = m2;
}
return G_SUCCESS;
}
/**
** @brief returns the kind of #CG_SEGMENT_INTERSECTION_TYPE behavior of lineseg 1 (constructed from p1 and p2) and lineseg 2 (constructed from q1 and q2)
** @param p1 start point of first straight linesegment
** @param p2 end point of first straight linesegment
** @param q1 start point of second line segment
** @param q2 end point of second line segment
** @return a #CG_SEGMENT_INTERSECTION_TYPE
** Returns one of
** SEG_ERROR = -1,
** SEG_NO_INTERSECTION = 0,
** SEG_COLINEAR = 1,
** SEG_CROSS_LEFT = 2,
** SEG_CROSS_RIGHT = 3,
*/
int lw_segment_intersects(const POINT2D *p1, const POINT2D *p2, const POINT2D *q1, const POINT2D *q2)
{
double pq1, pq2, qp1, qp2;
/* No envelope interaction => we are done. */
if (!lw_segment_envelope_intersects(p1, p2, q1, p2))
{
return SEG_NO_INTERSECTION;
}
/* Are the start and end points of q on the same side of p? */
pq1=lw_segment_side(p1,p2,q1);
pq2=lw_segment_side(p1,p2,q2);
if ((pq1>0 && pq2>0) || (pq1<0 && pq2<0))
{
return SEG_NO_INTERSECTION;
}
/* Are the start and end points of p on the same side of q? */
qp1=lw_segment_side(q1,q2,p1);
qp2=lw_segment_side(q1,q2,p2);
if ( (qp1 > 0.0 && qp2 > 0.0) || (qp1 < 0.0 && qp2 < 0.0) )
{
return SEG_NO_INTERSECTION;
}
/* Nobody is on one side or another? Must be colinear. */
if ( pq1 == 0.0 && pq2 == 0.0 && qp1 == 0.0 && qp2 == 0.0 )
{
return SEG_COLINEAR;
}
/*
** When one end-point touches, the sidedness is determined by the
** location of the other end-point. Only touches by the first point
** will be considered "real" to avoid double counting.
*/
LWDEBUGF(4, "pq1=%.15g pq2=%.15g", pq1, pq2);
LWDEBUGF(4, "qp1=%.15g qp2=%.15g", qp1, qp2);
/* Second point of p or q touches, it's not a crossing. */
if ( pq2 == 0.0 || qp2 == 0.0 )
{
return SEG_NO_INTERSECTION;
}
/* First point of p touches, it's a "crossing". */
if ( pq1 == 0.0 )
{
if ( FP_GT(pq2,0.0) )
return SEG_CROSS_RIGHT;
else
return SEG_CROSS_LEFT;
}
/* First point of q touches, it's a crossing. */
if ( qp1 == 0.0 )
{
if ( FP_LT(pq1,pq2) )
return SEG_CROSS_RIGHT;
else
return SEG_CROSS_LEFT;
}
/* The segments cross, what direction is the crossing? */
if ( FP_LT(pq1,pq2) )
return SEG_CROSS_RIGHT;
else
return SEG_CROSS_LEFT;
/* This should never happen! */
return SEG_ERROR;
}
pulsesequence()
{
/* Internal variable declarations *********************/
char txphase[MAXSTR];
char rxphase[MAXSTR];
char my_p1pat[MAXSTR];
char my_p4pat[MAXSTR];
char my_p2pat[MAXSTR];
char my_p3pat[MAXSTR];
char blankmode[MAXSTR]={0};
char tmpstr[MAXSTR];
double postDelay;
double rfDuration;
double acqt;
int i,ret=-1;
static int phs1[4] = {0,2,1,3}; /* from T1meas.c */
int my_pulseID;
double my_offsets[64];
double my_tpwr[64];
double my_tpwrf[64];
int my_on_off[64];
double mytmp;
int my_numrfch;
int my_retval;
for(i=0;i<64;i++) my_offsets[i] = 0.0;
/*************************************************/
/* Initialize paramter **************************/
i = 0;
postDelay = 0.5;
acqt = 0.0;
// getstr("rxphase",rxphase);
// getstr("txphase",txphase);
getstr("p1pat",my_p1pat);
getstr("p2pat",my_p2pat);
getstr("p3pat",my_p3pat);
getstr("p4pat",my_p4pat);
ret = P_getstring(GLOBAL,"blankmode",blankmode,1,MAXSTR);
if ( P_getreal(CURRENT,"ampargs",&mytmp,2) < 0 )
mytmp = 0.0;
if ( P_getreal(GLOBAL, "numrfch", &mytmp, 1) < 0 )
abort_message("Cannot proceed without global numrfch\n");
my_numrfch = (int)(mytmp+0.05);
if(my_numrfch<2) abort_message("this is a single transmit system and you don't need this pulse sequence\n");
if(my_numrfch>16) abort_message("numrfch > 16 not supported \n");
printf("mytmp=%f\n",mytmp);
// if((P_getstring(GLOBAL,"rfGroupMap",tmpstr,1,MAXSTR) < 0) || (strlen(tmp) < 2))
// {
// abort_message("global rfGroupMap doesn't exist or is too short\n");
// }
// else // rfGroupMap is set to all 1's for the same number as numrfch so we control everything here in the sequence
//{
strncpy(tmpstr,"111111111111111111111111111111111111111111111111111111111111111111",(size_t)my_numrfch);
tmpstr[my_numrfch]=0;
P_setstring(CURRENT, "rfGroupMap", tmpstr, 1);
// }
//getparm("blankmode","string",GLOBAL,blankmode,MAXSTR);
postDelay = tr - at;
//printf("blankmode=%s\n",blankmode);
/*************************************************/
/* check phase setting ***************************/
// if ( (txphase[0] =='n') && (rxphase[0] =='n') )
// {
// abort_message("ERROR - Select at least one phase [Tx or Rx]\n");
// }
/**************************************************/
/* check pulse width *****************************/
rfDuration = shapelistpw(p1pat, pw); /* assign exitation pulse duration */
printf("p1pat: %s\n",my_p1pat);
printf("duration: %e\n",rfDuration);
acqt = rfDuration + rof1 - alfa;
if (FP_GT(acqt, at))
{
abort_message("Pulse duration too long. max [%.3f] ms\n",(at-rof1+alfa)*1000.0);
}
if(ret==0 && blankmode[0]=='u')
obsunblank();
delay(postDelay);
settable(t1,4,phs1); /*from T1meas.c */
getelem(t1,ct,v11); /*from T1meas.c */
setreceiver(t1);
printf("mytmp=%d\n",my_numrfch);
my_pulseID = initRFGroupPulse(rfDuration, my_p1pat, 's', 0.0, 0.0, v11, &my_offsets[0], my_numrfch-1);
printf("pulse id = %d\n",my_pulseID);
//modifyRFGroupName(my_pulseID,2,my_p2pat);
//modifyRFGroupName(my_pulseID,3,my_p3pat);
// modifyRFGroupName(my_pulseID,4,my_p4pat);
for(i=0;i<64;i++) my_tpwr[i]=0.0;
for(i=0;i<64;i++) my_tpwrf[i]=0.0;
for(i=0;i<64;i++) my_on_off[i]=0;
//SAS turn everything off
for(i=0;i<my_numrfch-1;i++)
{
modifyRFGroupOnOff(my_pulseID, i+1,0);
printf("here is i=%d\n",i);
}
for(i=0;i<my_numrfch-1;i++) modifyRFGroupPwrf(my_pulseID, i+1, 0.0);
for(i=0;i<my_numrfch-1;i++) modifyRFGroupPwrC(my_pulseID, i+1, 0.0);
//SAS get the parameter arrays into the local arrays
my_retval=(int)getarray("my_tpwr",my_tpwr);
/*
printf("my tpwr0 was: %e\n",my_tpwr[0]);
printf("my tpwr1 was: %e\n",my_tpwr[1]);
printf("my tpwr2 was: %e\n",my_tpwr[2]);
printf("my tpwr3 was: %e\n",my_tpwr[3]);
printf("my tpwr4 was: %e\n",my_tpwr[4]);
printf("my tpwr5 was: %e\n",my_tpwr[5]);
printf("my tpwr6 was: %e\n",my_tpwr[6]);
printf("my tpwr7 was: %e\n",my_tpwr[7]);
*/
my_retval=(int)getarray("my_on_off",my_tpwrf); //dump the array of reals into a real array
for(i=0;i<my_numrfch;i++) my_on_off[i] = (int)my_tpwrf[i]; //convert to integer
/*
printf("my on_off_0 was: %d\n",my_on_off[0]);
printf("my on_off_1 was: %d\n",my_on_off[1]);
printf("my on_off_2 was: %d\n",my_on_off[2]);
printf("my on_off_3 was: %d\n",my_on_off[3]);
printf("my on_off_4 was: %d\n",my_on_off[4]);
printf("my on_off_5 was: %d\n",my_on_off[5]);
printf("my on_off_6 was: %d\n",my_on_off[6]);
printf("my on_off_7 was: %d\n",my_on_off[7]);
*/
for(i=0;i<64;i++) my_tpwrf[i]=2047.0;
//SAS set everything to array values
for(i=0;i<my_numrfch;i++) modifyRFGroupOnOff(my_pulseID, i+1,my_on_off[i]);
for(i=0;i<my_numrfch;i++) modifyRFGroupPwrf(my_pulseID, i+1, my_tpwrf[i]);
for(i=0;i<my_numrfch;i++) modifyRFGroupPwrC(my_pulseID, i+1, my_tpwr[i]);
/*==============================================*/
/* START LOOPBACK PULSE SEQUENCE */
/*==============================================*/
status(A);
obsoffset(resto);
/* TTL trigger to scope sequence ****************************/
sp1on();
/* Relaxation delay ***********************************/
xgate(ticks);
/* RF pulse *******************************************/
GroupPulse(my_pulseID, rof1, rof2, v11, 0);
endacq();
sp1off();
if(ret==0 && blankmode[0]=='u')
obsunblank();
}
