pulsesequence() {
// Define Variables and Objects and Get Parameter Values
double aYxy8 = getval("aYxy8");
double pwYxy8 = getval("pwYxy8");
double nYxy8 = getval("nYxy8");
int cycles = (int) nYxy8/2.0;
nYxy8 = 2.0*cycles;
int counter = (int) (nYxy8 - 1.0);
initval((nYxy8 - 1.0),v8);
double onYxy8 = getval("onYxy8");
double srate = getval("srate");
DSEQ dec = getdseq("H");
strncpy(dec.t.ch,"dec",3);
putCmd("chHtppm='dec'\n");
strncpy(dec.s.ch,"dec",3);
putCmd("chHspinal='dec'\n");
DSEQ mix = getdseq("Hmix");
strncpy(mix.t.ch,"dec",3);
putCmd("chHmixtppm='mix'\n");
strncpy(mix.s.ch,"dec",3);
putCmd("chHmixspinal='mix'\n");
//--------------------------------------
// Copy Current Parameters to Processed
//-------------------------------------
putCmd("groupcopy('current','processed','acquisition')");
// Dutycycle Protection
DUTY d = init_dutycycle();
d.dutyon = getval("pwX90") + 4.0*nYxy8*pwYxy8 + getval("pwX180");
d.dutyoff = d1 + 4.0e-6;
d.c1 = d.c1 + (!strcmp(dec.seq,"tppm"));
d.c1 = d.c1 + ((!strcmp(dec.seq,"tppm")) && (dec.t.a > 0.0));
d.t1 = getval("rd") + getval("ad") + at;
d.c2 = d.c2 + (!strcmp(dec.seq,"spinal"));
d.c2 = d.c2 + ((!strcmp(dec.seq,"spinal")) && (dec.s.a > 0.0));
d.t2 = getval("rd") + getval("ad") + at;
d.c3 = d.c3 + (!strcmp(mix.seq,"tppm"));
d.c3 = d.c3 + ((!strcmp(mix.seq,"tppm")) && (mix.t.a > 0.0));
d.t3 = 2.0*nYxy8*(1.0/srate - 2.0*pwYxy8) + 1.0/srate - getval("pwX180");
d.c4 = d.c4 + (!strcmp(mix.seq,"spinal"));
d.c4 = d.c4 + ((!strcmp(mix.seq,"spinal")) && (mix.s.a > 0.0));
d.t4 = 2.0*nYxy8*(1.0/srate - 2.0*pwYxy8) + 1.0/srate - getval("pwX180");
d = update_dutycycle(d);
abort_dutycycle(d,10.0);
// Set Phase Tables
settable(phX90,4,table1);
settable(ph1Yxy8,8,table2);
settable(ph2Yxy8,4,table3);
settable(phX180,4,table4);
settable(phRec,4,table5);
if (counter < 0) tsadd(phRec,2,4);
setreceiver(phRec);
// Begin Sequence
txphase(phX90); decphase(zero);
obspwrf(getval("aX90"));
obsunblank(); decunblank(); _unblank34();
delay(d1);
sp1on(); delay(2.0e-6); sp1off(); delay(2.0e-6);
// X Single Pulse
rgpulse(getval("pwX90"),phX90,0.0,0.0);
// xy8Y Period One
obspwrf(getval("aX180"));
txphase(phX180);
if (counter >= 0) {
_dseqon(mix);
delay(pwYxy8/2.0);
dec2pwrf(aYxy8);
sub(v1,v1,v1);
if (counter >= 1) {
if (counter > 1) loop(v8,v9);
getelem(ph1Yxy8,v1,v4);
incr(v1);
getelem(ph2Yxy8,ct,v2);
add(v4,v2,v2);
dec2phase(v2);
delay(0.5/srate - pwYxy8);
if (onYxy8 == 2)
dec2rgpulse(pwYxy8,v2,0.0,0.0);
else
delay(pwYxy8);
if (counter > 1) endloop(v9);
}
// X Refocussing Pulse
delay(0.5/srate - pwYxy8/2.0 - getval("pwX180")/2.0);
rgpulse(getval("pwX180"),phX180,0.0,0.0);
dec2pwrf(aYxy8);
delay(0.5/srate - pwYxy8/2.0 - getval("pwX180")/2.0);
// xy8Y Period Two
if (counter >= 1) {
if (counter > 1) loop(v8,v9);
if (onYxy8 == 2)
dec2rgpulse(pwYxy8,v2,0.0,0.0);
else
delay(pwYxy8);
getelem(ph1Yxy8,v1,v4);
incr(v1);
getelem(ph2Yxy8,ct,v2);
add(v4,v2,v2);
dec2phase(v2);
delay(0.5/srate - pwYxy8);
if (counter > 1) endloop(v9);
}
delay(pwYxy8/2.0);
_dseqoff(mix);
}
// Begin Acquisition
_dseqon(dec);
obsblank(); _blank34();
delay(getval("rd"));
startacq(getval("ad"));
acquire(np, 1/sw);
endacq();
_dseqoff(dec);
obsunblank(); decunblank(); _unblank34();
}
pulsesequence()
{
/* DECLARE AND LOAD VARIABLES */
char f1180[MAXSTR], /* Flag to start t1 @ halfdwell */
C13refoc[MAXSTR], /* C13 sech/tanh pulse in middle of t1*/
Cshape[MAXSTR], /* CACO inversion 180 pulse */
water_sat[MAXSTR]; /* saturate/non-saturate water flag */
int icosel; /* used to get n and p type */
double tau1, /* t1 delay */
tpwrs,
tpwrsf_d = getval("tpwrsf_d"), /* fine power adustment for first soft pulse(down)*/
tpwrsf_u = getval("tpwrsf_u"), /* fine power adustment for second soft pulse(up) */
pwHs = getval("pwHs"), /* H1 90 degree pulse length at tpwrs */
compH =getval("compH"),
lambda = 1.0/(4.0*getval("JNH")), /* 1/4J H1 evolution delay */
tNH = 1.0/(4.0*getval("JNH")), /* 1/4J N15 evolution delay */
tau_cp= getval("tau_cp"), /* 1/4 of overall relaxation increment */
ncyc=getval("ncyc"), /* number of pulsed cycles in relaxT */
pwClvl = getval("pwClvl"), /* coarse power for C13 pulse */
pwC = getval("pwC"), /* C13 90 degree pulse length at pwClvl */
C180pw=getval("C180pw"),
C180pwr=getval("C180pwr"), /* 13C decoupling pulse parameters */
compN = getval("compN"), /* adjustment for N15 amplifier compression */
compC = getval("compC"), /* adjustment for C13 amplifier compression */
pwNlvl = getval("pwNlvl"), /* power for N15 pulses */
pwN = getval("pwN"), /* N15 90 degree pulse length at pwNlvl */
sw1 = getval("sw1"),
gt1 = getval("gt1"),
gt2 = getval("gt2"),
/* coherence pathway gradients */
gzlvl1 = getval("gzlvl1"),
gzlvl2 = getval("gzlvl2"),
gt0 = getval("gt0"), /* other gradients */
gt3 = getval("gt3"),
gt4 = getval("gt4"),
gt5 = getval("gt5"),
gt6 = getval("gt6"),
gt7 = getval("gt7"),
gstab = getval("gstab"),
gzlvl0 = getval("gzlvl0"),
gzlvl3 = getval("gzlvl3"),
gzlvl4 = getval("gzlvl4"),
gzlvl5 = getval("gzlvl5"),
gzlvl6 = getval("gzlvl6"),
gzlvl7 = getval("gzlvl7");
getstr("f1180",f1180);
getstr("C13refoc",C13refoc);
getstr("Cshape",Cshape);
getstr("water_sat",water_sat);
tpwrs = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /*needs 1.69 times more*/
tpwrs = (int) (tpwrs); /*power than a square pulse */
if (tpwrsf_d<4095.0)
tpwrs=tpwrs+6.0; /* add 6dB to let tpwrsf_d control fine power ~2048*/
/* LOAD PHASE TABLE */
settable(t1,4,phi1);
settable(t2,4,phi2);
settable(t3,4,phi3);
settable(t10,1,phi10);
settable(t31,4,rec);
/* CHECK VALIDITY OF PARAMETER RANGES */
if((dm[A] == 'y' || dm[B] == 'y' || dm[C] == 'y' ))
{ text_error("incorrect dec1 decoupler flags! Should be 'nnn' "); psg_abort(1); }
if((dm2[A] == 'y' || dm2[B] == 'y'))
{ text_error("incorrect dec2 decoupler flags! Should be 'nny' "); psg_abort(1); }
if( dpwr2 > 50 )
{ text_error("don't fry the probe, DPWR2 too large! "); psg_abort(1); }
if( pw > 50.0e-6 )
{ text_error("dont fry the probe, pw too high ! "); psg_abort(1); }
if( pwN > 100.0e-6 )
{ text_error("dont fry the probe, pwN too high ! "); psg_abort(1); }
/* PHASES AND INCREMENTED TIMES */
/* Phase incrementation for hypercomplex 2D data, States-Haberkorn element */
icosel = -1;
if (phase1 == 1) {tsadd(t10,2,4); icosel = +1;}
/* Set up f1180 */
tau1 = d2;
if((f1180[A] == 'y') && (ni > 1.0))
{ tau1 += ( 1.0 / (2.0*sw1) ); if(tau1 < 0.2e-6) tau1 = 0.0; }
tau1 = tau1/2.0;
/* Calculate modifications to phases for States-TPPI acquisition */
if(d2_index % 2) { tsadd(t1,2,4); tsadd(t31,2,4); }
/* BEGIN PULSE SEQUENCE */
status(A);
obspower(tpwr);
decpower(pwClvl);
dec2power(pwNlvl);
txphase(zero);
decphase(zero);
dec2phase(zero);
delay(d1);
status(B);
dec2rgpulse(pwN, zero, 0.0, 0.0); /*destroy N15 magnetization*/
zgradpulse(gzlvl0, 0.5e-3);
delay(1.0e-4);
rgpulse(pw,zero,rof1,rof1); /* 1H pulse excitation */
delay(gstab);
zgradpulse(gzlvl0, gt0);
delay(lambda - gt0 -gstab);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
txphase(one);
delay(lambda - gt0 -gstab);
zgradpulse(gzlvl0, gt0);
delay(gstab);
rgpulse(pw, one, rof1, rof1); /* on NzHz now */
if(water_sat[A]=='n') /* water to -Z */
{
obspower(tpwrs); obspwrf(tpwrsf_d);
shaped_pulse("H2osinc",pwHs,two,rof1,rof1);
obspower(tpwr); obspwrf(4095.0);
}
/* purge */
zgradpulse(gzlvl3, gt3);
delay(gstab);
/* HzNz-> Nz */
dec2rgpulse( pwN, zero, 0.0, 0.0);
delay(gstab);
zgradpulse(gzlvl6, gt0);
delay(lambda - gt0 -gstab);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
dec2phase(t3);
delay(lambda - gt0 -gstab);
zgradpulse(gzlvl6, gt0);
delay(gstab);
dec2rgpulse( pwN, t3, 0.0, 0.0);
/* purge */
zgradpulse(gzlvl7, gt7);
dec2phase(t3);
delay(gstab);
/* T1 relaxation delay */
if(ncyc > 0)
{
initval(ncyc,v4);
loop(v4,v5);
initval(2.0,v8);
loop(v8,v9);
if(water_sat[A]=='n') /* water to +Z */
{
delay(tau_cp-pw -rof1 -pwHs - 2.0*rof1-2.0*POWER_DELAY-WFG_START_DELAY -WFG_STOP_DELAY );
obspower(tpwrs); obspwrf(tpwrsf_d);
shaped_pulse("H2osinc",pwHs,two,rof1,rof1);
obspower(tpwr); obspwrf(4095.0);
rgpulse(2.0*pw, zero, rof1, rof1);
obspower(tpwrs); obspwrf(tpwrsf_u);
shaped_pulse("H2osinc",pwHs,two,rof1,rof1);
obspower(tpwr);
delay(tau_cp-pw -rof1 -pwHs - 2.0*rof1-2.0*POWER_DELAY-WFG_START_DELAY -WFG_STOP_DELAY );
}
else /* just don't bother about water */
{
delay(tau_cp-pw -rof1);
rgpulse(2.0*pw, zero, rof1, rof1);
delay(tau_cp-pw -rof1);
}
endloop(v9); /* repeat two times */
endloop(v5);
}
/* 15N evolution, t1 */
txphase(zero);
dec2phase(t1);
dec2rgpulse( pwN, t1, 0.0, 0.0);
delay(tau1);
rgpulse(2.0*pw, zero, 0.0, 0.0);
if(C13refoc[A]=='y')
{
decpower(C180pwr);
decshaped_pulse(Cshape, C180pw, zero, 0.0, 0.0);
decpower(pwClvl);
}
delay(tau1);
/* coding */
delay(lambda -gt1 -gstab -2.0*POWER_DELAY - C180pw);
if(C13refoc[A]!='y') delay(2.0*POWER_DELAY + C180pw);
zgradpulse(-icosel*gzlvl1, gt1); delay(gstab);
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
rgpulse(2.0*pw, zero, 0.0, 0.0);
zgradpulse(icosel*gzlvl1, gt1); delay(gstab); /* 2.0*GRADIENT_DELAY */
delay(lambda -gt1 -gstab);
dec2phase(t10);
/* reverse INEPT */
sim3pulse(pw, 0.0, pwN, zero, zero, t10, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
delay(gstab);
zgradpulse(gzlvl4, gt5);
delay(lambda -gt5 -gstab);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
txphase(one);
dec2phase(one);
delay(lambda - gt5 -gstab);
zgradpulse(gzlvl4, gt5);
delay(gstab);
sim3pulse(pw, 0.0, pwN, one, zero, one, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
delay(gstab);
zgradpulse( gzlvl5, gt5);
delay(lambda - gt5 -gstab);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
delay(lambda - gt5 -gstab);
zgradpulse(gzlvl5, gt5);
delay(gstab);
rgpulse(pw, zero, 0.0, 0.0);
delay(gt2 +gstab - 0.65*pw + 2.0*GRADIENT_DELAY + 2.0*POWER_DELAY);
rgpulse(2.0*pw, zero, rof1, rof1);
dec2power(dpwr2); decpower(dpwr); /* POWER_DELAY */
zgradpulse( gzlvl2, gt2); /* 2.0*GRADIENT_DELAY */
delay(gstab -10.0e-6);
statusdelay(C,10.0e-6);
setreceiver(t31);
}
pulsesequence()
{
/* Internal variable declarations *************************/
double freqEx[MAXNSLICE];
double maxgradtime,spoilMoment,perTime,tau1,te_delay,tr_delay;
double te2=0.0,te3=0.0,te2min,te3min,tau2,tau3,te2_delay,te3_delay=0;
char minte2[MAXSTR],minte3[MAXSTR],spoilflag[MAXSTR];
int sepSliceRephase,sepReadRephase=0,readrev,table,shapeEx;
int i;
/* Real-time variables used in this sequence **************/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vpe_offset = v5; // PE/2 for non-table offset
int vpe_mult = v6; // PE multiplier, ranges from -PE/2 to PE/2
int vper_mult = v7; // PE rewinder multiplier; turn off rewinder when 0
int vssc = v8; // Compressed steady-states
int vacquire = v9; // Argument for setacqvar, to skip steady state acquires
int vrfspoil_ctr = v10; // RF spoil counter
int vrfspoil = v11; // RF spoil multiplier
int vtrimage = v12; // Counts down from nt, trimage delay when 0
int vne = v13; // Number of echoes
int vne_ctr = v14; // Echo loop counter
int vneindex = v15; // Echo index, odd or even
int vnelast = v16; // Check for last echo
int vtrigblock = v17; // Number of slices per trigger block
/* Initialize paramaters **********************************/
init_mri();
getstr("spoilflag",spoilflag);
te2=getval("te2");
te3=getval("te3");
getstr("minte2",minte2);
getstr("minte3",minte3);
readrev=(int)getval("readrev");
/* Check for external PE table ***************************/
table = 0;
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
/* Set Rcvr/Xmtr phase increments for RF Spoiling ********/
/* Ref: Zur, Y., Magn. Res. Med., 21, 251, (1991) *******/
if (rfspoil[0] == 'y') {
rcvrstepsize(rfphase);
obsstepsize(rfphase);
}
/* Initialize gradient structures *************************/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2 ); // excitation pulse
init_slice(&ss_grad,"ss",thk); // slice select gradient
init_slice_refocus(&ssr_grad,"ssr"); // slice refocus gradient
init_readout(&ro_grad,"ro",lro,np,sw); // readout gradient
ro_grad.pad1=alfa; ro_grad.pad2=alfa;
init_readout_refocus(&ror_grad,"ror"); // dephase gradient
init_phase(&pe_grad,"pe",lpe,nv); // phase encode gradient
init_dephase(&spoil_grad,"spoil"); // optimized spoiler
init_dephase(&ref_grad,"ref"); // readout rephase
/* RF Calculations ****************************************/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Gradient calculations **********************************/
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice_refocus(&ssr_grad, &ss_grad,WRITE,"gssr");
calc_readout(&ro_grad, WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad, NOWRITE,"gpe","tpe");
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
spoilMoment = ro_grad.acqTime*ro_grad.roamp; // Optimal spoiling is at*gro for 2pi per pixel
spoilMoment -= ro_grad.m0def; // Subtract partial spoiling from back half of readout
calc_dephase(&spoil_grad,WRITE,spoilMoment,"gspoil","tspoil");
/* Is TE long enough for separate slice refocus? ******/
maxgradtime = MAX(ror_grad.duration,pe_grad.duration);
if (spoilflag[0] == 'y')
maxgradtime = MAX(maxgradtime,spoil_grad.duration);
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + maxgradtime + ro_grad.timeToEcho + GRADIENT_RES;
/* Equalize refocus and PE gradient durations *********/
if ((te >= tau1) && (minte[0] != 'y')) {
sepSliceRephase = 1; // Set flag for separate slice rephase
calc_sim_gradient(&ror_grad,&pe_grad,&spoil_grad,tpemin,WRITE);
} else {
sepSliceRephase = 0;
calc_sim_gradient(&ror_grad,&pe_grad,&ssr_grad,tpemin,WRITE);
calc_sim_gradient(&ror_grad,&spoil_grad,&null_grad,tpemin,NOWRITE);
}
perTime = 0.0;
if ((perewind[0] == 'y') || (spoilflag[0] == 'y'))
perTime = spoil_grad.duration;
if (spoilflag[0] == 'n')
spoil_grad.amp = 0.0;
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') create_inversion_recovery();
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp,0,freqEx,ns,seqcon[1]);
shapeEx = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freqEx,ns,ss_grad.rfFraction,seqcon[1]);
/* Check that all Gradient calculations are ok ************/
sgl_error_check(sglerror);
/* Min TE ******************************************/
tau1 = ss_grad.rfCenterBack + pe_grad.duration + ro_grad.timeToEcho;
tau1 += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
temin = tau1 + GRADIENT_RES; /* ensure that te_delay is at least GRADIENT_RES */
te = granularity(te,GRADIENT_RES);
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (FP_LT(te,temin)) {
abort_message("TE too short. Minimum TE= %.3fms\n",temin*1000);
}
te_delay = te - tau1;
/* Min TE2 *****************************************/
tau2 = (readrev) ? 2*ro_grad.timeFromEcho : ro_grad.duration+ref_grad.duration;
te2min = tau2 + GRADIENT_RES;
te2 = granularity(te2,GRADIENT_RES);
if (minte2[0] == 'y') {
te2 = te2min;
putvalue("te2",te2);
}
if (FP_LT(te2,te2min)) {
abort_message("TE2 too short. Minimum TE2= %.3fms\n",te2min*1000);
}
if (readrev) te2_delay = te2 - tau2;
else {
tau2 = ro_grad.duration + 3*ror_grad.duration;
if (te2 >= tau2) {
sepReadRephase = 1; // Set flag for separate read rephase
te2_delay = te2 - ro_grad.duration - 2*ror_grad.duration;
} else {
sepReadRephase = 0;
if (te2 > te2min+GRADIENT_RES) {
ref_grad.duration = granularity(te2-ro_grad.duration-2*GRADIENT_RES,GRADIENT_RES);
ref_grad.calcFlag = AMPLITUDE_FROM_MOMENT_DURATION;
calc_dephase(&ref_grad,WRITE,ro_grad.m0,"","");
}
te2_delay = te2 - ro_grad.duration - ref_grad.duration;
}
}
/* Min TE3 *****************************************/
if (readrev) {
tau3 = 2*ro_grad.timeToEcho;
te3min = tau3 + GRADIENT_RES;
te3 = granularity(te3,GRADIENT_RES);
if (minte3[0] == 'y') {
te3 = te3min;
putvalue("te3",te3);
}
if (FP_LT(te3,te3min)) {
abort_message("TE3 too short. Minimum TE3= %.3fms\n",te3min*1000);
}
te3_delay = te3 - tau3;
}
/* Now set the TE array accordingly */
putCmd("TE = 0"); /* Re-initialize TE */
putCmd("TE[1] = %f",te*1000);
if (readrev) {
for (i=1;i<ne;i++) {
if (i%2 == 0) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te3*1000);
else putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
} else {
for (i=1;i<ne;i++) putCmd("TE[%d] = TE[%d]+%f",i+1,i,te2*1000);
}
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Min TR ******************************************/
trmin = ss_grad.duration + te_delay + pe_grad.duration + ne*ro_grad.duration + perTime + 2*GRADIENT_RES;
trmin += (sepSliceRephase) ? ssr_grad.duration : 0.0; // Add slice refocusing if separate event
if (readrev) trmin += (ne/2)*te2_delay + ((ne-1)/2)*te3_delay;
else trmin += (sepReadRephase) ? (ne-1)*(te2_delay+2*ror_grad.duration) : (ne-1)*(te2_delay+ref_grad.duration);
/* Increase TR if any options are selected *********/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (ticks > 0) trmin += GRADIENT_RES;
/* Adjust for all slices ***************************/
trmin *= ns;
/* Inversion recovery *********************************/
if (ir[0] == 'y') {
/* tauti is the additional time beyond IR component to be included in ti */
/* satTime, fsatTime and mtTime all included as those modules will be after IR */
tauti = satTime + fsatTime + mtTime + GRADIENT_RES + ss_grad.rfCenterFront;
/* calc_irTime checks ti and returns the time of all IR components */
trmin += calc_irTime(tauti,trmin,mintr[0],tr,&trtype);
}
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("TR too short. Minimum TR = %.3fms\n",trmin*1000);
}
/* Calculate tr delay */
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&per_grad);
F_initval(pe_steps/2.0,vpe_offset);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *********************/
if (ssc<0) {
if (seqcon[2] == 'c') g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*pe_steps*arraydim));
}
else g_setExpTime(trmean*ntmean*pe_steps*arraydim + tr*ssc);
/* PULSE SEQUENCE ***************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(GRADIENT_RES);
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
assign(zero,vrfspoil_ctr); // RF spoil phase counter
assign(zero,vrfspoil); // RF spoil multiplier
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
if (trtype) delay(ns*tr_delay); // relaxation delay
/* Compressed steady-states:
1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vpe_ctr,vssc,vpe_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
if (seqcon[2] == 's')
assign(zero,vacquire); // Always acquire for non-compressed loop
else {
ifzero(vpe_ctr);
assign(zero,vacquire); // Start acquiring when vpe_ctr reaches zero
endif(vpe_ctr);
}
/* Set rcvr/xmtr phase for RF spoiling *******************/
if (rfspoil[0] == 'y') {
incr(vrfspoil_ctr); // vrfspoil_ctr = 1 2 3 4 5 6
add(vrfspoil,vrfspoil_ctr,vrfspoil); // vrfspoil = 1 3 6 10 15 21
xmtrphase(vrfspoil);
rcvrphase(vrfspoil);
}
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_mult);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_mult);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states
endif(vacquire);
}
/* PE rewinder follows PE table; zero if turned off ***/
if (perewind[0] == 'y') assign(vpe_mult,vper_mult);
else assign(zero,vper_mult);
/* Begin multislice loop ******************************/
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (!trtype) delay(tr_delay); // Relaxation delay
if (ticks > 0) {
modn(vms_ctr,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(GRADIENT_RES);
elsenz(vtest);
delay(GRADIENT_RES);
endif(vtest);
}
/* TTL scope trigger **********************************/
sp1on(); delay(GRADIENT_RES); sp1off();
/* Prepulse options ***********************************/
if (ir[0] == 'y') inversion_recovery();
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* Slice select RF pulse ******************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapeEx,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Phase encode, refocus, and dephase gradient ********/
if (sepSliceRephase) { // separate slice refocus gradient
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(te_delay); // delay between slab refocus and pe
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,
-pe_grad.increment,vpe_mult,WAIT);
} else {
pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,-ssr_grad.amp,
-pe_grad.increment,vpe_mult,WAIT);
delay(te_delay); // delay after refocus/pe
}
F_initval(ne,vne);
loop(vne,vne_ctr);
if (readrev) {
mod2(vne_ctr,vneindex);
ifzero(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te2_delay);
endif(vnelast);
elsenz(vneindex);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,-ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,-ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
delay(te3_delay);
endif(vnelast);
endif(vneindex);
} else {
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Readout gradient ********************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquisition ***************************************/
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
sub(vne,vne_ctr,vnelast);
sub(vnelast,one,vnelast);
ifzero(vnelast);
elsenz(vnelast);
if (sepReadRephase) {
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
delay(te2_delay);
obl_shapedgradient(ror_grad.name,ror_grad.duration,-ror_grad.amp,0,0,WAIT);
} else {
obl_shapedgradient(ref_grad.name,ref_grad.duration,-ref_grad.amp,0,0,WAIT);
delay(te2_delay);
}
endif(vnelast);
}
endloop(vne_ctr);
/* Rewind / spoiler gradient **************************/
if ((perewind[0] == 'y') || (spoilflag[0] == 'y')) {
pe_shapedgradient(pe_grad.name,pe_grad.duration,spoil_grad.amp,0,0,pe_grad.increment,vper_mult,WAIT);
}
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence()
{
/* DECLARE VARIABLES */
char f1180[MAXSTR],
C13refoc[MAXSTR],
wtg3919[MAXSTR];
int t1_counter;
double
tofHN = 0.0,
tau1, /* t1/2 */
taua = getval("taua"), /* 2.25ms */
pwN = getval("pwN"), /* PW90 for N-nuc */
pwNlvl = getval("pwNlvl"), /* power level for N hard pulses */
pwC = getval("pwC"), /* PW90 for N-nuc */
pwClvl = getval("pwClvl"), /* power level for N hard pulses */
relaxT = getval("relaxT"), /* total time for NOE measuring */
ncyc = 0, /* number of pulsed cycles in relaxT */
compH = getval("compH"),
pwHs = getval("pwHs"), /* H1 90 degree pulse length at tpwrs */
tpwrs, /* power for the pwHs ("H2Osinc") pulse */
tpwrsf_a = getval("tpwrsf_a"), /* fine power for the pwHs ("H2Osinc") pulse */
tpwrsf_u = getval("tpwrsf_u"), /* fine power for the pwHs ("H2Osinc") pulse */
tpwrsf_d = getval("tpwrsf_d"), /* fine power for the pwHs ("H2Osinc") pulse */
phincr_a = getval("phincr_a"), /* fine power for the pwHs ("H2Osinc") pulse */
phincr_u = getval("phincr_u"), /* fine power for the pwHs ("H2Osinc") pulse */
phincr_d = getval("phincr_d"), /* fine power for the pwHs ("H2Osinc") pulse */
d3919 = getval("d3919"),
pwHs_dly,
wtg_dly,
gstab = getval("gstab"),
gt0 = getval("gt0"),
gt3 = getval("gt3"),
gt4 = getval("gt4"),
gt5 = getval("gt5"),
gzlvl0 = getval("gzlvl0"),
gzlvl3 = getval("gzlvl3"),
gzlvl4 = getval("gzlvl4"),
gzlvl5 = getval("gzlvl5");
/* LOAD VARIABLES */
getstr("f1180",f1180);
getstr("wtg3919",wtg3919);
getstr("C13refoc",C13refoc);
if (find("tofHN")>1) tofHN=getval("tofHN");
if (tofHN == 0.0) tofHN=tof;
/* selective H20 one-lobe sinc pulse */
tpwrs = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /* needs 1.69 times more */
tpwrs = (int) (tpwrs); /* power than a square pulse */
pwHs_dly = pwHs +WFG_START_DELAY +2.0e-6 +2.0*POWER_DELAY +2.0*SAPS_DELAY;
if (tpwrsf_a < 4095.0) pwHs_dly = pwHs_dly +2.0*PWRF_DELAY; /* if one flipback is calibrated */
if (phincr_a != 0.0) pwHs_dly = pwHs_dly +2.0*SAPS_DELAY; /* so will probably be the others */
if (wtg3919[0] != 'y')
wtg_dly = pwHs_dly;
else
wtg_dly = pw*2.385 +7.0*rof1 +d3919*2.5 +SAPS_DELAY;
/* LOAD VARIABLES */
assign(one,v11);
assign(three,v12);
settable(t2, 4, phi2);
settable(t3, 1, phi3);
settable(t10, 4, phi10);
settable(t14, 4, rec);
/* Phase incrementation for hypercomplex data */
if ( phase1 == 2 ) /* Hypercomplex in t1 */
{ ttadd(t14,t10,4); tsadd(t3,2,4); }
/* calculate modification to phases based on current t1 values
to achieve States-TPPI acquisition */
if(ix == 1) d2_init = d2;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5);
if (t1_counter %2)
{ tsadd(t2,2,4); tsadd(t14,2,4); }
/* Set up f1180 */
tau1 = d2;
if((f1180[A] == 'y') && (ni > 1.0))
{ tau1 += ( 1.0 / (2.0*sw1) ); if(tau1 < 0.2e-6) tau1 = 0.0; }
tau1 = tau1/2.0;
/* Set up phincr corrections */
if (phincr_a < 0.0) phincr_a=phincr_a+360.0;
if (phincr_u < 0.0) phincr_u=phincr_u+360.0;
if (phincr_d < 0.0) phincr_d=phincr_d+360.0;
/* BEGIN ACTUAL PULSE SEQUENCE */
status(A);
obspower(tpwr);
decpower(pwClvl);
dec2power(pwNlvl);
txphase(zero);
dec2phase(zero);
obsstepsize(1.0);
rcvroff();
initval(ncyc+0.1,v10);
delay(1.0e-5);
/* destroy magnetization of proton and nitrogen */
rgpulse(pw,zero,0.0,0.0);
initval(phincr_u,v14);
txphase(two); if (phincr_u != 0) xmtrphase(v14);
if (tpwrsf_u < 4095.0) { obspwrf(tpwrsf_u); obspower(tpwrs+6.0); }
else obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, two, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_u < 4095.0) obspwrf(4095.0);
txphase(t3); if (phincr_u != 0) xmtrphase(zero);
dec2rgpulse(pwN, zero, 0.0, 0.0);
zgradpulse(gzlvl0,gt0);
dec2phase(one);
delay(gstab);
dec2rgpulse(pwN, one, 0.0, 0.0);
zgradpulse(0.7*gzlvl0,gt0);
dec2phase(zero);
delay(gstab);
/* Saturation of 1H to produce NOE */
status(B);
if (tofHN != tof) obsoffset(tofHN);
delay(0.5e-5);
if (relaxT < 1.0e-4 )
{
ncyc = (int)(200.0*d1 + 0.5); /* no H1 saturation */
initval(ncyc,v1);
obspower(-15.0); obspwrf(0.0); /* powers set to minimum, but amplifier is unblancked identically */
loop(v1,v2);
delay(2.5e-3 - 4.0*compH*1.34*pw);
rgpulse(4.0*compH*1.34*pw, zero, 5.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 5.0e-6);
delay(2.5e-3 - 4.0*compH*1.34*pw);
endloop(v2);
}
else
{
ncyc = (int)(200.0*relaxT + 0.5); /* H1 saturation */
initval(ncyc,v1);
if (ncyc > 0)
{
obspower(tpwr-12);
loop(v1,v2);
delay(2.5e-3 - 4.0*compH*1.34*pw);
rgpulse(4.0*compH*1.34*pw, zero, 5.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 0.0e-6);
rgpulse(4.0*compH*1.34*pw, zero, 0.0e-6, 5.0e-6);
delay(2.5e-3 - 4.0*compH*1.34*pw);
endloop(v2);
}
}
obspower(tpwr); obspwrf(4095.0);
if (tofHN != tof) obsoffset(tof);
/* two spin state mixing */
zgradpulse(0.7*gzlvl3,gt3);
delay(gstab);
rgpulse(pw,zero,0.0,0.0);
initval(phincr_u,v14);
txphase(two); if (phincr_u != 0) xmtrphase(v14);
if (tpwrsf_u < 4095.0) { obspwrf(tpwrsf_u); obspower(tpwrs+6.0); }
else obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, two, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_u < 4095.0) obspwrf(4095.0);
txphase(t3); if (phincr_u != 0) xmtrphase(zero);
zgradpulse(gzlvl3,gt3);
delay(gstab);
/*********************************************/
/* inept of 15N and 1H and evolution of t1 */
/*********************************************/
dec2rgpulse(pwN,t2,0.0,0.0);
/* H1 EVOLUTION BEGINS */
txphase(t3); dec2phase(zero);
if (C13refoc[A]=='y' && (tau1 -2.0*pwC -3.0*SAPS_DELAY) > 0.2e-6)
{
delay(tau1 -2.0*pwC -3.0*SAPS_DELAY);
decrgpulse(pwC, zero, 0.0, 0.0);
decphase(one);
decrgpulse(2.0*pwC, one, 0.0, 0.0);
decphase(zero);
decrgpulse(pwC, zero, 0.0, 0.0);
delay(tau1 -2.0*pwC -SAPS_DELAY);
}
else if (2.0*tau1 -2.0*SAPS_DELAY > 0.2e-6)
delay(2.0*tau1 -2.0*SAPS_DELAY);
/* H1 EVOLUTION ENDS */
rgpulse(pw, t3, 0.0, 0.0);
initval(phincr_a,v14);
if (phincr_a != 0) xmtrphase(v14);
if (tpwrsf_a < 4095.0) { obspwrf(tpwrsf_a); obspower(tpwrs+6.0); }
else obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, t3, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_a < 4095.0) obspwrf(4095.0);
txphase(zero); if (phincr_a != 0) xmtrphase(zero);
zgradpulse(gzlvl4,gt4);
delay(taua -pwN -0.5*pw -gt4 -2.0*GRADIENT_DELAY -pwHs_dly); /* delay=1/4J(NH) */
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
dec2phase(t3);
zgradpulse(gzlvl4,gt4);
delay(taua -1.5*pwN -gt4 -2.0*GRADIENT_DELAY -pwHs_dly); /* delay=1/4J(NH) */
initval(phincr_d,v14);
txphase(two); if (phincr_d != 0) xmtrphase(v14);
if (tpwrsf_d < 4095.0) { obspwrf(tpwrsf_d); obspower(tpwrs+6.0); }
else obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, two, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_d < 4095.0) obspwrf(4095.0);
txphase(zero); if (phincr_d != 0) xmtrphase(zero);
sim3pulse(pw, 0.0, pwN, zero, zero, t3, rof1, rof1);
dec2phase(zero);
zgradpulse(gzlvl5,gt5);
delay(taua -1.5*pwN -wtg_dly -gt5 -2.0*GRADIENT_DELAY);
if(wtg3919[0] == 'y') /* 3919 watergate */
{
txphase(v11);
rgpulse(pw*0.231,v11,rof1,rof1);
delay(d3919);
rgpulse(pw*0.692,v11,rof1,rof1);
delay(d3919);
rgpulse(pw*1.462,v11,rof1,rof1);
delay(d3919/2.0-pwN);
dec2rgpulse(2.0*pwN, zero, rof1, rof1);
txphase(v12);
delay(d3919/2.0-pwN);
rgpulse(pw*1.462,v12,rof1,rof1);
delay(d3919);
rgpulse(pw*0.692,v12,rof1,rof1);
delay(d3919);
rgpulse(pw*0.231,v12,rof1,rof1);
}
else /* soft pulse watergate */
{
initval(phincr_d,v14);
txphase(two); if (phincr_d != 0) xmtrphase(v14);
if (tpwrsf_d < 4095.0) { obspwrf(tpwrsf_d); obspower(tpwrs+6.0); }
obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, two, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_d < 4095.0) obspwrf(4095.0);
txphase(zero); if (phincr_d != 0) xmtrphase(zero);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
initval(phincr_u,v14);
txphase(two); if (phincr_u != 0) xmtrphase(v14);
if (tpwrsf_u < 4095.0) { obspwrf(tpwrsf_u); obspower(tpwrs+6.0); }
obspower(tpwrs);
shaped_pulse("H2Osinc", pwHs, two, 2.0e-6, 0.0);
obspower(tpwr);
if (tpwrsf_u < 4095.0) obspwrf(4095.0);
txphase(zero); if (phincr_u != 0) xmtrphase(zero);
}
zgradpulse(gzlvl5,gt5);
delay(taua -1.5*pwN -wtg_dly -gt5 -2.0*GRADIENT_DELAY);
dec2rgpulse(pwN,zero,0.0,0.0);
/* acquire data */
rcvron();
status(C);
setreceiver(t14);
}
pulsesequence()
{
/* menu variables */
double slice_str,pe_length,read_str,power,angle,TR,TIR,slice_coffset;
double trim_read,trim_slice,freqir,encode_on,read_on,ir_on,sel_crush;
/* internal variables */
double pe_length_eff,GPmin,GPstep;
double aq_time,area_readout,read_rephase_str,GRR,GRead,freqreadout;
double slice_rephase_str,area_slice,GSR,GSS,GCR2,grad_factor;
double time[5],cycle_time,start_cycle[20],relaxation,finish_time;
double powir,powexcite,sel_length,pe_step,pe_min;
double slice_offset[128],GCR1,ir_str;
double B1_90,B1_excite,extra_TE;
double rf_max,ir_len,cur_angle,ramp_lenr,ramp_lens;
int a;
read_str = getval("Read_Str");
slice_str = getval("Slice_Str");
pe_length = getval("PE_length");
ir_str = getval("IR_Grad_Str");
sel_crush = getval("Sel_Crush");
ramp_lenr = getval("ramp_lenr");
ramp_lens = getval("ramp_lens");
extra_TE = getval("extra_TE");
TIR = getval("TIR");
TR = getval("TR");
power=getval("Power");
angle = getval("angle");
trim_slice = getval("Slice_Trim");
trim_read = getval("Read_Trim");
freqreadout = getval("Read_Offset");
freqir = getval("IR_Offset");
encode_on=getval("encode_on");
read_on=getval("read_on");
ir_on=getval("ir_on");
/* rf_max = getval("rf_max"); */
ir_len = getval("ir_len");
cur_angle = getval("cur_angle");
/* rf length calculation and offset lists #0*/
sel_length = 0.003*(1000.0/(slice_str*thk));
for (a=0;a<ns;a++)
{
slice_offset[a] = pss[a]* 10.0 * slice_str;
}
GCR2 = sel_crush * HZ_TO_GAUSS;
GSS = slice_str * HZ_TO_GAUSS;
/* phase encoding */
pe_length_eff = (2.0/3.14159)*pe_length;
pe_step = 1.0/(lpe*10.0*pe_length_eff);
pe_min = pe_step*(nv/2);
GPmin = pe_min * HZ_TO_GAUSS;
GPstep = -pe_step * HZ_TO_GAUSS;
/* rephase for readout */
aq_time = at;
grad_factor = sw/((double)read_str*lro*10.0);
area_readout = (0.001 + (ramp_lenr*0.001/2.0) + (aq_time/2)) * read_str*grad_factor;
read_rephase_str = -1.0*area_readout/pe_length_eff;
GRR = read_rephase_str * HZ_TO_GAUSS * trim_read;
GRead = read_str * HZ_TO_GAUSS*grad_factor;
/* rephase the slice */
area_slice = ((sel_length/2) + (ramp_lens*0.001/2.0))*slice_str;
slice_rephase_str = -1.0*area_slice/pe_length_eff;
GSR = slice_rephase_str * HZ_TO_GAUSS*trim_slice;
/* calculate the rf levels */
B1_90 = (slice_str*thk/1000.0)* B1_SINC3S;
B1_excite = B1_90*(cur_angle/90.0);
powexcite = (B1_excite/1000.0)*4096.0;
powir = 4096.0;
/* calculate the timing */
if (ir_on==1)
time[0] = 0.011 + ir_len*0.001 + 0.0001;
else
time[0] = 0.0001;
/* ir */
time[1] = sel_length + (2*ramp_lens*0.001) + 0.001; /* slice select */
time[2] = extra_TE+ pe_length; /* phase encoding etc. */
time[3] = aq_time + (2*ramp_lenr*0.001)+0.001; /* acquisition window */
time[4] = pe_length; /* rewind */
cycle_time = time[1]+time[2]+time[3]+time[4];
/* printf("\nCycle Time = %f",cycle_time); */
create_offset_list(slice_offset,ns,OBSch,0);
/*
for (a=0;a<ns;a++)
printf("\nOffset %d = %f",a,slice_offset[a]);
*/
GCR1 = ir_str * HZ_TO_GAUSS;
if (ir_on==1)
start_cycle[0] = 0.011 + TIR;
else
start_cycle[0] = 0.0001;
finish_time = start_cycle[0] + (ns*ne*cycle_time);
/* printf("\n Finish Time = %f",finish_time); */
relaxation = TR - finish_time;
/* START THE PULSE SEQUENCE */
assign(v10,zero);
assign(v11,zero);
initval(ne,v7);
status(A);
obspower(power);
/* begin phase encode loop */
peloop(seqcon[2],nv,v1,v2);
delay(relaxation);
/* ir */
obspwrf(powir);
obsoffset(freqir);
if (ir_on==1)
{
shaped_pulse("HYPSEC4",ir_len*0.001,v10,rof1,rof2);
obl_shapedgradient("","CRUSH","",0.011,0,GCR1,0,1,WAIT);
zero_all_gradients();
delay(TIR-0.011);
}
delay(0.0001);
loop(v7,v8); /* loop over T1 times measured */
msloop(seqcon[1],ns,v5,v6); /* loop over slices */
/* slice selection readout */
obspwrf(powexcite);
voffset(0,v6);
obl_shapedgradient("","","RAMPUP",ramp_lens*0.001,0,0,GSS,1,WAIT);
obl_shapedgradient("","","CONST",sel_length+0.001,0,0,GSS,1,NOWAIT);
delay(0.001);
shaped_pulse("SINC3S",sel_length,v11,rof1,rof2);
obl_shapedgradient("","","RAMPDN",ramp_lens*0.001,0,0,GSS,1,WAIT);
zero_all_gradients();
delay(extra_TE);
/* encode and rephasing */
if ((read_on==1)&&(encode_on==1))
pe3_shapedgradient("SINUSOID",pe_length,GRR,GPmin,GSR,0,GPstep,0,zero,v2,zero);
if ((read_on!=1)&&(encode_on==1))
pe3_shapedgradient("SINUSOID",pe_length,0,GPmin,GSR,0,GPstep,0,zero,v2,zero);
if ((read_on!=1)&&(encode_on!=1))
pe3_shapedgradient("SINUSOID",pe_length,0,0,GSR,0,0,0,zero,zero,zero);
if ((read_on==1)&&(encode_on!=1))
pe3_shapedgradient("SINUSOID",pe_length,GRR,0,GSR,0,0,0,zero,zero,zero);
zero_all_gradients();
/* readout */
obsoffset(freqreadout);
if (read_on==1)
{
obl_shapedgradient("RAMPUP","","",ramp_lenr*0.001,GRead,0,0,1,WAIT);
obl_shapedgradient("CONST","","",at+0.001,GRead,0,0,1,NOWAIT);
delay(0.001);
acquire(np,1.0/(sw));
obl_shapedgradient("RAMPDN","","",ramp_lenr*0.001,GRead,0,0,1,WAIT);
zero_all_gradients();
}
else
{
delay(0.001);
acquire(np,1.0/(sw));
}
/* rewind and crush */
if (encode_on==1)
{
pe3_shapedgradient("SINUSOID",pe_length,0,-GPmin,GCR2,0,-GPstep,0,zero,v2,zero);
zero_all_gradients();
}
else delay(pe_length);
endmsloop(seqcon[1],v6);
endloop(v8);
endpeloop(seqcon[2],v2);
}
pulsesequence() {
// Define Variables and Objects and Get Parameter Values
double aXfam2 = getval("aXfam2");
double pw1Xfam2 = getval("pw1Xfam2");
double pw2Xfam2 = getval("pw2Xfam2");
double pw3Xfam2 = getval("pw3Xfam2");
double pw4Xfam2 = getval("pw4Xfam2");
double nXfam2 = getval("nXfam2");
initval(nXfam2,v4);
putCmd("pw2Xmqmas=pwXfam1"); // Sequence uses pwXfam1 and sets pw2Xmqmas
double d2init = getval("d2"); // Define the Split d2 in the Pulse Sequence
double ival = getval("ival");
double d20 = 1.0;
double d21 = 0.0;
double d22 = 0.0;
if (ival == 1.5) {
d20 = 9.0*d2init/16.0;
d21 = 7.0*d2init/16.0;
d22 = 0.0;
}
else if (ival == 2.5) {
d20 = 12.0*d2init/31.0;
d21 = 0.0*d2init/31.0;
d22 = 19.0*d2init/31.0;
}
else {
d20 = 1.0*d2init;
d21 = 0.0*d2init;
d22 = 0.0*d2init;
}
double tXechselinit = getval("tXechsel"); // Adjust the selective echo delay for the
double tXechsel = tXechselinit - 3.0e-6; // attenuator switch time.
if (tXechsel < 0.0) tXechsel = 0.0;
DSEQ dec = getdseq("H");
strncpy(dec.t.ch,"dec",3);
putCmd("chHtppm='dec'\n");
strncpy(dec.s.ch,"dec",3);
putCmd("chHspinal='dec'\n");
// Set Constant-time Period for d2.
if (d2_index == 0) d2_init = getval("d2");
double d2_ = (ni - 1)/sw1 + d2_init;
putCmd("d2acqret = %f\n",roundoff(d2_,12.5e-9));
putCmd("d2dwret = %f\n",roundoff(1.0/sw1,12.5e-9));
//--------------------------------------
// Copy Current Parameters to Processed
//-------------------------------------
putCmd("groupcopy('current','processed','acquisition')");
// Dutycycle Protection
DUTY d = init_dutycycle();
d.dutyon = getval("pw1Xmqmas") + nXfam2*(pw1Xfam2 + pw2Xfam2 + pw3Xfam2 +pw4Xfam2) +
getval("pwXechsel");
d.dutyoff = d1 + 4.0e-6;
d.c1 = d.c1 + (!strcmp(dec.seq,"tppm"));
d.c1 = d.c1 + ((!strcmp(dec.seq,"tppm")) && (dec.t.a > 0.0));
d.t1 = d2_ + tXechselinit + getval("rd") + getval("ad") + at;
d.c2 = d.c2 + (!strcmp(dec.seq,"spinal"));
d.c2 = d.c2 + ((!strcmp(dec.seq,"spinal")) && (dec.s.a > 0.0));
d.t2 = d2_ + tXechselinit + getval("rd") + getval("ad") + at;
d = update_dutycycle(d);
abort_dutycycle(d,10.0);
// Set Phase Tables
if (phase1 == 0) {
settable(phf1Xmqmas,12,table1);
settable(ph1Xfam2,6,table2);
settable(ph2Xfam2,6,table3);
settable(phfXechsel,96,table4);
settable(phRec,48,table5);
}
else {
settable(phf1Xmqmas,6,table6);
settable(ph1Xfam2,6,table7);
settable(ph2Xfam2,6,table8);
settable(phfXechsel,48,table9);
settable(phRec,24,table10);
if (phase1 == 2) {
tsadd(phf1Xmqmas,30,360);
}
}
setreceiver(phRec);
obsstepsize(1.0);
// Begin Sequence
xmtrphase(phf1Xmqmas); decphase(zero);
obspower(getval("tpwr"));
obspwrf(getval("aXmqmas"));
obsunblank(); decunblank(); _unblank34();
delay(d1);
sp1on(); delay(2.0e-6); sp1off(); delay(2.0e-6);
// H Decoupler on Before MQMAS
_dseqon(dec);
// Two-Pulse MQMAS with DFS Conversion
rgpulse(getval("pw1Xmqmas"),zero,0.0,0.0);
xmtrphase(zero); txphase(ph1Xfam2);
obspwrf(aXfam2);
delay(d20);
// X FAM2 Pulse
loop(v4,v5);
xmtron();
delay(pw1Xfam2);
xmtroff();
txphase(ph2Xfam2);
delay(pw2Xfam2);
xmtron();
delay(pw3Xfam2);
xmtroff();
txphase(ph2Xfam2);
delay(pw4Xfam2);
endloop(v5);
// Tau Delay and Second Selective Echo Pulse
xmtrphase(phfXechsel);
obsblank();
obspower(getval("dbXechsel"));
obspwrf(getval("aXechsel"));
delay(3.0e-6);
obsunblank();
delay(d21 + tXechsel);
rgpulse(getval("pwXechsel"),zero,0.0,0.0);
delay(d22);
// Begin Acquisition
obsblank(); _blank34();
delay(getval("rd"));
startacq(getval("ad"));
acquire(np, 1/sw);
endacq();
_dseqoff(dec);
obsunblank(); decunblank(); _unblank34();
}
void pulsesequence()
{
/* DECLARE VARIABLES */
char C13refoc[MAXSTR],comp_flg[MAXSTR],fsat[MAXSTR],f1180[MAXSTR];
int phase,t1_counter;
double pwClvl = getval("pwClvl"), /* coarse power for C13 pulse */
pwC = getval("pwC"), /* C13 90 degree pulse length at pwClvl */
rf0, /* maximum fine power when using pwC pulses */
rfst, /* fine power for the stCall pulse */
compC = getval("compC"), /* adjustment for C13 amplifier compression */
tau1, /* t1 delay */
taua, /* < 1 / 4J(NH) 2.25 ms */
taub, /* 1 / 4J(NH) in NH : 2.68 ms */
pwn, /* PW90 for N-nuc */
pwN, /* N15 pw90 for BioPack */
pwNlvl, /* N15 power for BioPack */
pwn_cp, /* PW90 for N CPMG */
pwHs, /* BioPack selective PW90 for water excitation */
compH, /* amplifier compression factor*/
compN, /* amplifier compression factor*/
phase_sl,
tsatpwr, /* low power level for presat */
tpwrsf_u, /* fine power adjustment on flip-up sel 90 */
tpwrsf_d, /* fine power adjustment on flip-down sel 90 */
tpwrsl, /* low power level for sel 90 */
dhpwr2, /* power level for N hard pulses */
dpwr2_comp, /* power level for CPMG compensation */
dpwr2_cp, /* power level for N CPMG */
tauCPMG, /* CPMG delay */
ncyc, /* number of times to loop */
ncyc_max, /* max number of times to loop */
time_T2, /* total time for T2 measuring */
tofps, /* water freq */
sw1,
pwr_delay, /* POWER_DELAY recalculated*/
timeC,
gt1,
gt2,
gt3,
gt4,
gt5,
gt6,
gstab, /* stabilization delay */
BPpwrlimits, /* =0 for no limit, =1 for limit */
gzlvl1,
gzlvl2,
gzlvl3,
gzlvl4,
gzlvl5,
gzlvl6;
P_getreal(GLOBAL,"BPpwrlimits",&BPpwrlimits,1);
/* LOAD VARIABLES */
getstr("C13refoc", C13refoc);
/* taub = 1/(8*93.0); */
taua = getval("taua");
taub = getval("taub");
pwNlvl = getval("pwNlvl");
pwN = getval("pwN");
pwn = getval("pwn");
pwn_cp = getval("pwn_cp");
pwHs = getval("pwHs");
compH = getval("compH");
compN = getval("compN");
phase_sl = getval("phase_sl");
tsatpwr = getval("tsatpwr");
tpwrsf_u = getval("tpwrsf_u");
tpwrsf_d = getval("tpwrsf_d");
tpwrsl = getval("tpwrsl");
dhpwr2 = getval("dhpwr2");
dpwr2_comp = getval("dpwr2_comp");
dpwr2_cp = getval("dpwr2_cp");
ncyc = getval("ncyc");
ncyc_max = getval("ncyc_max");
time_T2 = getval("time_T2");
phase = (int) (getval("phase") + 0.5);
sw1 = getval("sw1");
tofps = getval("tofps");
gt1 = getval("gt1");
gt2 = getval("gt2");
gt3 = getval("gt3");
gt4 = getval("gt4");
gt5 = getval("gt5");
gt6 = getval("gt6");
gstab = getval("gstab");
gzlvl1 = getval("gzlvl1");
gzlvl2 = getval("gzlvl2");
gzlvl3 = getval("gzlvl3");
gzlvl4 = getval("gzlvl4");
gzlvl5 = getval("gzlvl5");
gzlvl6 = getval("gzlvl6");
getstr("fsat",fsat);
getstr("comp_flg",comp_flg);
getstr("f1180",f1180);
setautocal(); /* activate auto-calibration flags */
if (autocal[0] == 'n')
{
/* selective H20 one-lobe sinc pulse */
if (pwHs > 0.0)
tpwrsl = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /*needs 1.69 times more*/
else tpwrsl = 0.0;
tpwrsl = (int) (tpwrsl); /*power than a square pulse */
}
else /* if autocal = 'y'(yes), 'q'(quiet), r(read), or 's'(semi) */
{
if(FIRST_FID) /* call Pbox */
{
H2OsincA = pbox_Rsh("H2OsincA", "sinc90", pwHs, 0.0, compH*pw, tpwr);
ofs_check(H1ofs, C13ofs, N15ofs, H2ofs);
}
pwHs = H2OsincA.pw; tpwrsl = H2OsincA.pwr-1.0; /* 1dB correction applied */
pwn = pwN; dhpwr2 = pwNlvl;
}
if (tpwrsf_u < 4095.0)
{
tpwrsl = tpwrsl + 6.0;
pwr_delay = POWER_DELAY + PWRF_DELAY;
}
else pwr_delay = POWER_DELAY;
/* maximum fine power for pwC pulses (and initialize rfst) */
rf0 = 4095.0; rfst=0.0;
/* 180 degree adiabatic C13 pulse from 0 to 200 ppm */
if (C13refoc[A]=='y')
{rfst = (compC*4095.0*pwC*4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35));
rfst = (int) (rfst + 0.5);
if ( 1.0/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35)) < pwC )
{ text_error( " Not enough C13 RF. pwC must be %f usec or less.\n",
(1.0e6/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35))) ); psg_abort(1); }}
/* check validity of parameter range */
if(dm[A] == 'y' || dm[B] == 'y' || dm[C] == 'y')
{
printf("incorrect Dec1 decoupler flags! Should be nnn ");
psg_abort(1);
}
if(dm2[A] == 'y' || dm2[B] == 'y' || dm2[C] == 'y' )
{
printf("incorrect Dec2 decoupler flags! Should be nnn ");
psg_abort(1);
}
if( tsatpwr > 8 )
{
printf("tsatpwr too large !!! ");
psg_abort(1);
}
if( dpwr2_cp > 61 )
{
printf("don't fry the probe, dpwr2_cp too large for cpmg !");
psg_abort(1);
}
if( ncyc > 100)
{
printf("ncyc exceeds 100. May be too much \n");
psg_abort(1);
}
if( time_T2 > 0.090 )
{
printf("total T2 recovery time exceeds 90 msec. May be too long \n");
psg_abort(1);
}
if( ncyc > 0)
{
tauCPMG = time_T2/(4*ncyc) - pwn_cp;
if( ix == 1 )
printf("nuCPMG for current experiment is (Hz): %5.3f \n",1/(4*(tauCPMG+pwn_cp)) );
}
else
{
tauCPMG = time_T2/4 - pwn_cp;
if( ix == 1 )
printf("nuCPMG for current experiment is (Hz): not applicable \n");
}
ncyc_max = time_T2/1e-3;
if( tauCPMG + pwn_cp < 0.000250)
{
printf("WARNING: value of tauCPMG must be larger than or equal to 250 us\n");
printf("maximum value of ncyc allowed for current time_T2 is: %5.2f \n",ncyc_max);
psg_abort(1);
}
if(gt1 > 3e-3 || gt2 > 3e-3 || gt3 > 3e-3|| gt4 > 3e-3
|| gt5 > 3e-3 || gt6 > 3e-3 )
{
printf("gti must be less than 3e-3\n");
psg_abort(1);
}
/* LOAD VARIABLES */
settable(t1, 2, phi1);
settable(t2, 8, phi2);
settable(t3, 8, phi3);
settable(t4, 1, phi4);
settable(t5, 1, phi5);
settable(t6, 1, phi6);
settable(t7, 8, rec);
/* Phase incrementation for hypercomplex 2D data */
if (phase == 2) {
tsadd(t4,2,4);
tsadd(t5,2,4);
tsadd(t6,2,4);
tsadd(t7,2,4);
}
/* Set up f1180 */
tau1 = d2;
if(f1180[A] == 'y')
tau1 += ( 1.0 / (2.0*sw1) - (pw + pwN*2.0/3.1415));
else
tau1 = tau1 - pw;
if(tau1 < 0.2e-6) tau1 = 0.2e-6;
tau1 = tau1/2.0;
/* Calculate modifications to phases for States-TPPI acquisition */
if( ix == 1 ) d2_init = d2;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5 );
if( t1_counter %2 ) {
tsadd(t2,2,4);
tsadd(t3,2,4);
tsadd(t7,2,4);
}
/* BEGIN ACTUAL PULSE SEQUENCE */
status(A);
decpower(dpwr); /* Set decoupler1 power to dpwr */
decpower(pwClvl);
decpwrf(rfst);
decoffset(dof);
dec2power(dhpwr2); /* Set decoupler2 power to dhpwr2 */
/* Presaturation Period */
if(fsat[0] == 'y')
{
obspower(tsatpwr); /* Set power for presaturation */
obsoffset(tofps); /* move H carrier to the water */
rgpulse(d1,zero,rof1,rof1); /* presat. with transmitter */
obspower(tpwr); /* Set power for hard pulses */
}
else
{
obspower(tpwr); /* Set power for hard pulses */
delay(d1);
}
obsoffset(tof);
status(B);
/* apply the compensation 15N pulses if desired */
if(comp_flg[A] == 'y') {
dec2power(dpwr2_comp); /* Set decoupler2 compensation power */
timeC = time_T2*(ncyc_max-ncyc)/ncyc_max;
dec2rgpulse(timeC,zero,0.0,0.0);
dec2power(dhpwr2);
}
rcvroff();
delay(20.0e-6);
/* shaped pulse on water */
obspower(tpwrsl);
if (tpwrsf_d<4095.0) obspwrf(tpwrsf_d);
if (autocal[A] == 'y')
shaped_pulse("H2OsincA",pwHs,three,rof1,0.0);
else
shaped_pulse("H2Osinc_d",pwHs,three,rof1,0.0);
if (tpwrsf_d<4095.0) obspwrf(4095.0);
obspower(tpwr);
/* shaped pulse on water */
rgpulse(pw,two,rof1,0.0);
txphase(zero);
dec2phase(zero);
delay(2.0e-6);
zgradpulse(gzlvl1,gt1);
delay(gstab);
delay(taua - gt1 - gstab -2.0e-6); /* delay < 1/4J(XH) */
sim3pulse(2*pw,0.0e-6,2*pwn,zero,zero,zero,0.0,0.0);
txphase(one);
dec2phase(t1);
delay(taua - gt1 - gstab -2.0e-6);
delay(2.0e-6);
zgradpulse(gzlvl1,gt1);
delay(gstab);
rgpulse(pw,one,0.0,0.0);
delay(2.0e-6);
zgradpulse(gzlvl2,gt2);
delay(gstab);
if (BPpwrlimits > 0.5)
{
dec2power(dpwr2_cp -3.0); /* reduce for probe protection */
pwn_cp=pwn_cp*compN*1.4;
}
else
dec2power(dpwr2_cp); /* Set decoupler2 power to dpwr2_cp for CPMG period */
dec2rgpulse(pwn_cp,t1,rof1,2.0e-6);
dec2phase(zero);
/* start of the CPMG train for first period time_T2/2 on Ny(1-2Hz) */
if(ncyc > 0)
{
delay(tauCPMG - (2/PI)*pwn_cp - 2.0e-6);
dec2rgpulse(2*pwn_cp,one,0.0,0.0);
delay(tauCPMG);
}
if(ncyc > 1)
{
initval(ncyc-1,v4);
loop(v4,v5);
delay(tauCPMG);
dec2rgpulse(2*pwn_cp,one,0.0,0.0);
delay(tauCPMG);
endloop(v5);
}
/* eliminate cross-relaxation */
delay(2.0e-6);
zgradpulse(gzlvl3,gt3);
delay(gstab);
delay(taub - gt3 - gstab -2.0e-6 - pwn_cp);
/* composite 1H 90y-180x-90y on top of 15N 180x */
dec2rgpulse(pwn_cp-2*pw,zero,0.0e-6,0.0);
sim3pulse(pw,0.0e-6,pw,one,zero,zero,0.0,0.0);
sim3pulse(2*pw,0.0e-6,2*pw,zero,zero,zero,0.0,0.0);
sim3pulse(pw,0.0e-6,pw,one,zero,zero,0.0,0.0);
dec2rgpulse(pwn_cp-2*pw,zero,0.0,0.0e-6);
/* composite 1H 90y-180x-90y on top of 15N 180x */
delay(taub - gt3 - gstab -2.0e-6 - pwn_cp - 4.0*pw);
delay(2.0e-6);
zgradpulse(gzlvl3,gt3);
delay(gstab);
rgpulse(pw,one,0.0,0.0);
rgpulse(2.0*pw,zero,0.0,0.0);
rgpulse(pw,one,0.0,0.0);
/* start of the CPMG train for second period time_T2/2 on Nx(1-2Iz) */
if(ncyc > 1)
{
initval(ncyc-1,v4);
loop(v4,v5);
delay(tauCPMG);
dec2rgpulse(2*pwn_cp,zero,0.0,0.0);
delay(tauCPMG);
endloop(v5);
}
if(ncyc > 0)
{
delay(tauCPMG);
dec2rgpulse(2*pwn_cp,zero,0.0,0.0);
delay(tauCPMG - (2/PI)*pwn_cp - 2.0e-6);
}
dec2phase(one);
dec2rgpulse(pwn_cp,one,2.0e-6,0.0);
delay(rof1);
dec2power(dhpwr2); /* Set decoupler2 power back to dhpwr2 */
dec2phase(t3);
delay(2.0e-6);
zgradpulse(gzlvl4,gt4);
delay(gstab);
if(phase==1)
dec2rgpulse(pwn,t2,rof1,0.0);
if(phase==2)
dec2rgpulse(pwn,t3,rof1,0.0);
txphase(t4);
decphase(one);
dec2phase(zero);
/* 15N chemical shift labeling with optional 13C decoupling of Ca & C'*/
if ( (C13refoc[A]=='y') && (tau1 > 0.5e-3 + WFG2_START_DELAY) )
{delay(tau1 - 0.5e-3 - WFG2_START_DELAY); /* WFG2_START_DELAY */
decshaped_pulse("stC200", 1.0e-3, zero, 0.0, 0.0);
delay(tau1 - 0.5e-3);}
else delay(2.0*tau1);
/* finish of 15N shift labeling*/
rgpulse(pw,t4,0.0,0.0);
/* shaped pulse on water */
obspower(tpwrsl);
if (tpwrsf_u<4095.0) obspwrf(tpwrsf_u);
if (autocal[A] == 'y')
shaped_pulse("H2OsincA",pwHs,t5,rof1,0.0);
else
shaped_pulse("H2Osinc_u",pwHs,t5,rof1,0.0);
if (tpwrsf_u<4095.0) obspwrf(4095.0);
obspower(tpwr);
/* shaped pulse on water */
delay(2.0e-6);
zgradpulse(gzlvl5,gt5);
delay(gstab/2.0);
delay(taua - pwr_delay - rof1 - WFG_START_DELAY
- pwHs - WFG_STOP_DELAY - pwr_delay
- gt5 - gstab/2.0 -2.0e-6);
sim3pulse(2.0*pw,0.0,2.0*pwn,zero,zero,zero,0.0,0.0);
delay(2.0e-6);
zgradpulse(gzlvl5,gt5);
delay(gstab/2.0);
delay(taua
- gt5 - 2.0e-6 -gstab
- pwr_delay - rof1 - WFG_START_DELAY
- pwHs - WFG_STOP_DELAY - pwr_delay - 2.0e-6);
/* shaped pulse on water */
obspower(tpwrsl);
if (tpwrsf_u<4095.0) obspwrf(tpwrsf_u);
if (autocal[A] == 'y')
shaped_pulse("H2OsincA",pwHs,zero,rof1,0.0);
else
shaped_pulse("H2Osinc_u",pwHs,zero,rof1,0.0);
if (tpwrsf_u<4095.0) obspwrf(4095.0);
obspower(tpwr);
/* shaped pulse on water */
sim3pulse(pw,0.0e-6,pwn,zero,zero,t6,2.0e-6,0.0);
txphase(zero);
dec2phase(zero);
delay(2.0e-6);
zgradpulse(gzlvl6,gt6);
delay(gstab/2.0);
delay(taua - gt6 - gstab/2.0 -2.0e-6 - pwr_delay
- pwHs);
initval(1.0,v3);
obsstepsize(phase_sl);
xmtrphase(v3);
obspower(tpwrsl);
if (tpwrsf_d<4095.0) obspwrf(tpwrsf_d);
if (autocal[A] == 'y')
shaped_pulse("H2OsincA",pwHs,two,rof1,0.0);
else
shaped_pulse("H2Osinc_d",pwHs,two,rof1,0.0);
if (tpwrsf_d<4095.0) obspwrf(4095.0);
obspower(tpwr);
xmtrphase(zero);
sim3pulse(2*pw,0.0e-6,2*pwn,zero,zero,zero,rof1,rof1);
initval(1.0,v3);
obsstepsize(phase_sl);
xmtrphase(v3);
obspower(tpwrsl);
if (tpwrsf_u<4095.0) obspwrf(tpwrsf_u);
if (autocal[A] == 'y')
shaped_pulse("H2OsincA",pwHs,two,rof1,0.0);
else
shaped_pulse("H2Osinc_u",pwHs,two,rof1,0.0);
if (tpwrsf_u<4095.0) obspwrf(4095.0);
obspower(tpwr);
xmtrphase(zero);
delay(2.0e-6);
zgradpulse(gzlvl6,gt6);
delay(gstab/2.0);
delay(taua - pwHs - gt6 - gstab/2.0 -2.0e-6
+ 2.0*pw/PI - pwn
- 2.0*POWER_DELAY);
dec2rgpulse(pwn,zero,0.0,0.0);
decpower(dpwr); /* lower power on dec */
dec2power(dpwr2); /* lower power on dec2 */
/* acquire data */
status(C);
setreceiver(t7);
}
pulsesequence() {
/* Acquisition variables */
double dw; /* nominal dwell time, = 1/sw */
double aqtm = getval("aqtm");
/* Delay variables */
double tref,
te_delay1, te_delay2, tr_delay, ti_delay,
del1, del2, del3, del4, del5, /* before and after diffusion gradients */
busy1, busy2, /* time spent on rf pulses etc. in TE periods */
seqtime, invTime;
int use_minte;
/* RF and receiver frequency variables */
double freq90[MAXNSLICE],freq180[MAXNSLICE],freqIR[MAXNSLICE]; /* frequencies for multi-slice */
int shape90=0, shape180=0, shapeIR=0; /* List ID for RF shapes */
double roff1, roff2, roffn; /* Receiver offsets when FOV is offset along readout */
/* Gradient amplitudes, may vary depending on "image" parameter */
double peramp, perinc, peamp, roamp, roramp;
/* diffusion variables */
#define MAXDIR 1024 /* Will anybody do more than 1024 directions or b-values? */
int diff_in_one = 0;
double tmp, tmp_ss2;
double roarr[MAXDIR], pearr[MAXDIR], slarr[MAXDIR];
int nbval, /* Total number of bvalues*directions */
nbro, nbpe, nbsl; /* bvalues*directions along RO, PE, and SL */
double bro[MAXDIR], bpe[MAXDIR], bsl[MAXDIR], /* b-values along RO, PE, SL */
brs[MAXDIR], brp[MAXDIR], bsp[MAXDIR], /* the cross-terms */
btrace[MAXDIR], /* and the trace */
max_bval=0,
dcrush, dgss2, /* "delta" for crusher and gss2 gradients */
Dro, Dcrush, Dgss2; /* "DELTA" for readout, crusher and gss2 gradients */
/* loop variable */
int i;
/* Real-time variables used in this sequence **************/
int vms_slices = v3; // Number of slices
int vms_ctr = v4; // Slice loop counter
int vnseg = v5; // Number of segments
int vnseg_ctr = v6; // Segment loop counter
int vetl = v7; // Number of choes in readout train
int vetl_ctr = v8; // etl loop counter
int vblip = v9; // Sign on blips in multi-shot experiment
int vssepi = v10; // Number of Gradient Steady States lobes
int vssepi_ctr = v11; // Steady State counter
int vacquire = v12; // Argument for setacqvar, to skip steady states
/******************************************************/
/* VARIABLE INITIALIZATIONS ***************************/
/******************************************************/
get_parameters();
euler_test();
if (tep < 0) { // adjust by reducing gpropdelay by that amount
gpropdelay += tep;
tep = 0;
}
setacqmode(WACQ|NZ); // Necessary for variable rate sampling
use_minte = (minte[0] == 'y');
/******************************************************/
/* CALCULATIONS ***************************************/
/******************************************************/
if (ix == 1) {
/* Calculate RF pulse */
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
/* Calculate gradients: */
init_slice(&ss_grad,"ss",thk);
calc_slice(&ss_grad, &p1_rf,WRITE,"gss");
init_slice_refocus(&ssr_grad,"ssr");
calc_slice_refocus(&ssr_grad, &ss_grad, WRITE,"gssr");
if (spinecho[0] == 'y') {
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof1);
calc_rf(&p2_rf,"tpwr2","tpwr2f");
init_slice_butterfly(&ss2_grad,"ss2",thk,gcrush,tcrush);
calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2");
}
else ss2_grad.duration = 0; /* used for diffusion calculations */
init_readout(&epiro_grad,"epiro",lro,np,sw);
init_readout_refocus(&ror_grad,"ror");
init_phase(&epipe_grad, "epipe",lpe,nv);
init_phase(&per_grad,"per",lpe,nv);
init_readout(&nav_grad,"nav",lro,np,sw);
init_epi(&epi_grad);
if (!strcmp(orient,"oblique")) {
if ((phi != 90) || (psi != 90) || (theta != 90)) {
/* oblique slice - this should take care of most cases */
epiro_grad.slewRate /= 3; /* = gmax/trise */
epipe_grad.slewRate /= 3;
}
}
calc_epi(&epi_grad,&epiro_grad,&epipe_grad,&ror_grad,&per_grad,&nav_grad,NOWRITE);
/* Make sure the slice refocus, readout refocus,
and phase dephaser fit in the same duration */
tref = calc_sim_gradient(&ror_grad, &per_grad, &null_grad, getval("tpe"), WRITE);
if (sgldisplay) displayEPI(&epi_grad);
/* calc_sim_gradient recalculates per_grad, so reset its
base amplitude for centric ordering or fractional k-space*/
switch(ky_order[0]) {
case 'l':
per_grad.amp *= (fract_ky/(epipe_grad.steps/2));
break;
case 'c':
per_grad.amp = (nseg/2-1)*per_grad.increment;
break;
}
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof1,rof1);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrush,tcrush);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
}
if (fsat[0] == 'y') {
create_fatsat();
}
if (diff[0] == 'y') {
init_generic(&diff_grad,"diff",gdiff,tdelta);
diff_grad.maxGrad = gmax;
calc_generic(&diff_grad,NOWRITE,"","");
/* adjust duration, so tdelta is from start ramp up to start ramp down */
if (ix == 1) {
diff_grad.duration += diff_grad.tramp;
calc_generic(&diff_grad,WRITE,"","");
}
}
/* Acquire top-down or bottom-up ? */
if (ky_order[1] == 'r') {
epipe_grad.amp *= -1;
per_grad.amp *= -1;
per_grad.increment *= -1;
}
} /* end gradient setup if ix == 1 */
/* Load table used to determine multi-shot direction */
settable(t2,(int) nseg,epi_grad.table2);
/* What is happening in the 2 TE/2 periods (except for diffusion)? */
busy1 = ss_grad.rfCenterBack + ssr_grad.duration;
busy2 = tep + nav_grad.duration*(epi_grad.center_echo + 0.5);
if (navigator[0] == 'y')
busy2 += (tep + nav_grad.duration + per_grad.duration);
/* How much extra time do we have in each TE/2 period? */
if (spinecho[0] == 'y') {
busy1 += (GDELAY + ss2_grad.rfCenterFront);
busy2 += ss2_grad.rfCenterBack;
temin = MAX(busy1,busy2)*2;
if (use_minte) te = temin;
te_delay1 = te/2 - busy1;
te_delay2 = te/2 - busy2;
if (temin > te) { /* Use min TE and try and catch further violations of min TE */
te_delay1 = temin/2 - busy1;
te_delay2 = temin/2 - busy2;
}
}
else { /* Gradient echo */
temin = (busy1 + busy2);
if (use_minte) te = temin;
te_delay1 = te - temin;
te_delay2 = 0;
if (temin > te) te_delay1 = 0;
}
/* Now fill in the diffusion delays:
del1 = between 90 and 1st diffusion gradient
del2 = after 1st diffusion gradient
del3 = before 2nd diffusion gradient when both in same TE/2 period
del4 = before 2nd diffusion gradient when in different TE/2 period
del5 = before acquisition
Ie, the order is:
90 - del1 - diff - del2 - (diff - del3) - 180 - (del4 - diff) - del5 - acq
where one and only one of the two options (diff - del3) or (del4 - diff) is used
*/
if (diff[0] == 'y') {
tmp_ss2 = GDELAY + ss2_grad.duration; /* ss2 grad + 4us delay */
del1 = del2 = del3 = del4 = del5 = 0;
if (tDELTA < (diff_grad.duration + tmp_ss2)) /* Minimum DELTA */
abort_message("ERROR %s: tDELTA is too short, minimum is %.2fms\n",
seqfil,(diff_grad.duration + tmp_ss2)*1000+0.005);
if (tDELTA + diff_grad.duration > te_delay1 + tmp_ss2 + te_delay2) {
if (!use_minte) {
abort_message("ERROR %s: Maximum tDELTA is %.2fms",
seqfil,te_delay1 + ss2_grad.duration + te_delay2 - diff_grad.duration);
}
else {
tmp = (tDELTA + diff_grad.duration) - (te_delay1 + tmp_ss2 + te_delay2);
if (spinecho[0] == 'y') {
te_delay1 += (tmp/2);
te_delay2 += (tmp/2);
}
else
te_delay1 += tmp;
temin += tmp;
}
}
if (spinecho[0] == 'y') {
if (te_delay1 >= (tDELTA + diff_grad.duration)) { /* Put them both in 1st TE/2 period, */
diff_in_one = (diff[0] == 'y'); /* no need to increase temin */
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = te_delay1 - (tDELTA+diff_grad.duration); /* time after diffusion gradients */
del5 = te_delay2; /* delay in second TE/2 period */
}
else { /* put them on each side of the 180 */
diff_in_one = 0;
busy1 += diff_grad.duration;
busy2 += diff_grad.duration;
temin = 2*MAX(busy1,busy2);
/* Optimally, the 2nd diff grad is right after the 180 */
del2 = tDELTA - diff_grad.duration - tmp_ss2; /* This is always > 0, or we would have aborted above */
del1 = te_delay1 - (diff_grad.duration + del2);
if (del1 < 0) {
del1 = 0; /* Place the 1st right after the 90 and push the 2nd out */
del4 = tDELTA - te_delay1 - ss2_grad.duration;
}
del5 = te_delay2 - (del4 + diff_grad.duration);
/* del5 could still be < 0, when te_delay2 < diff_grad.duration */
if (del5 < 0) {
del1 += fabs(del5); /* Increase each TE/2 period by abs(del5) */
del5 = 0;
}
}
}
else { /* gradient echo */
diff_in_one = (diff[0] == 'y');
del1 = 0;
del2 = tDELTA - diff_grad.duration; /* time between diffusion gradients */
del3 = 0;
del4 = 0;
if (!use_minte) /* user defined TE */
del5 = te_delay1 - (tDELTA + diff_grad.duration);
}
} /* End of Diffusion block */
else {
del1 = te_delay1;
del5 = te_delay2;
del2 = del3 = del4 = 0;
}
if (sgldisplay) {
text_message("busy1/2, temin = %f, %f, %f",busy1*1e3, busy2*1e3, temin*1e3);
text_message("te_delay1/2 = %f, %f",te_delay1*1e3, te_delay2*1e3);
text_message("delays 1-5: %.2f, %.2f, %.2f, %.2f, %.2fms\n",del1*1000,del2*1000,del3*1000,del4*1000,del5*1000);
}
/* Check if TE is long enough */
temin = ceil(temin*1e6)/1e6; /* round to nearest us */
if (use_minte) {
te = temin;
putvalue("te",te);
}
else if (temin > te) {
abort_message("TE too short, minimum is %.2f ms\n",temin*1000);
}
if (ir[0] == 'y') {
ti_delay = ti - (pi*ssi_grad.rfFraction + rof2 + ssi_grad.rfDelayBack)
- (ss_grad.rfDelayFront + rof1 + p1*(1-ss_grad.rfFraction));
if (ti_delay < 0) {
abort_message("TI too short, minimum is %.2f ms\n",(ti-ti_delay)*1000);
}
}
else ti_delay = 0;
invTime = GDELAY + ssi_grad.duration + ti_delay;
/* Minimum TR per slice, w/o options */
seqtime = GDELAY + ss_grad.rfCenterFront // Before TE
+ te
+ (epiro_grad.duration - nav_grad.duration*(epi_grad.center_echo+0.5)); // After TE
/* Add in time for options outside of TE */
if (ir[0] == 'y') seqtime += invTime;
if (fsat[0] == 'y') seqtime += fsatTime;
trmin = seqtime + 4e-6; /* ensure a minimum of 4us in tr_delay */
trmin *= ns;
if (tr - trmin < 0.0) {
abort_message("%s: Requested tr too short. Min tr = %.2f ms\n",
seqfil,ceil(trmin*100000)/100.00);
}
/* spread out multi-slice acquisition over total TR */
tr_delay = (tr - ns*seqtime)/ns;
/******************************************************/
/* Return gradient values to VnmrJ interface */
/******************************************************/
putvalue("etl",epi_grad.etl+2*ssepi);
putvalue("gro",epiro_grad.amp);
putvalue("rgro",epiro_grad.tramp);
putvalue("gror",ror_grad.amp);
putvalue("tror",ror_grad.duration);
putvalue("rgror",ror_grad.tramp);
putvalue("gpe",epipe_grad.amp);
putvalue("rgpe",epipe_grad.tramp);
putvalue("gped",per_grad.amp);
putvalue("tped",per_grad.duration);
putvalue("rgped",per_grad.tramp);
putvalue("gss",ss_grad.amp);
putvalue("gss2",ss2_grad.ssamp);
putvalue("rgss",ss_grad.tramp);
putvalue("gssr",ssr_grad.amp);
putvalue("tssr",ssr_grad.duration);
putvalue("rgssr",ssr_grad.tramp);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
putvalue("rgssi",ssi_grad.crusher1RampToSsDuration);
putvalue("rgcrush",ssi_grad.crusher1RampToCrusherDuration);
putvalue("at_full",epi_grad.duration);
putvalue("at_one",nav_grad.duration);
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("np_ramp",epi_grad.np_ramp);
putvalue("np_flat",epi_grad.np_flat);
if (diff[0] == 'y') { /* CALCULATE B VALUES */
/* Get multiplication factors and make sure they have same # elements */
/* All this is only necessary because putCmd only work for ix==1 */
nbro = (int) getarray("dro",roarr); nbval = nbro;
nbpe = (int) getarray("dpe",pearr); if (nbpe > nbval) nbval = nbpe;
nbsl = (int) getarray("dsl",slarr); if (nbsl > nbval) nbval = nbsl;
if ((nbro != nbval) && (nbro != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (readout)",seqfil);
if ((nbpe != nbval) && (nbpe != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (phase)",seqfil);
if ((nbsl != nbval) && (nbsl != 1))
abort_message("%s: Number of directions/b-values must be the same for all axes (slice)",seqfil);
if (nbro == 1) for (i = 1; i < nbval; i++) roarr[i] = roarr[0];
if (nbpe == 1) for (i = 1; i < nbval; i++) pearr[i] = pearr[0];
if (nbsl == 1) for (i = 1; i < nbval; i++) slarr[i] = slarr[0];
}
else {
nbval = 1;
roarr[0] = 0;
pearr[0] = 0;
slarr[0] = 0;
}
for (i = 0; i < nbval; i++) {
/* We need to worry about slice gradients & crushers for slice gradients */
/* Everything else is outside diffusion gradients, and thus constant */
/* for all b-values/directions */
/* Readout */
bro[i] = bval(gdiff*roarr[i],tdelta,tDELTA);
/* Phase */
bpe[i] = bval(gdiff*pearr[i],tdelta,tDELTA);
/* Slice */
dgss2 = p2/2; Dgss2 = dgss2;
dcrush = tcrush; Dcrush = dcrush + p2;
bsl[i] = bval(gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2);
bsl[i] += bval(gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gcrush,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2);
}
if (!diff_in_one) {
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsl[i] += bval_nested(gdiff*slarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Readout/Slice Cross-terms */
brs[i] = bval2(gdiff*roarr[i],gdiff*slarr[i],tdelta,tDELTA);
if (spinecho[0] == 'y') {
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
brs[i] += bval_cross(gdiff*roarr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
}
/* Readout/Phase Cross-terms */
brp[i] = bval2(gdiff*roarr[i],gdiff*pearr[i],tdelta,tDELTA);
/* Slice/Phase Cross-terms */
bsp[i] = bval2(gdiff*slarr[i],gdiff*pearr[i],tdelta,tDELTA);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,gcrush,dcrush,Dcrush);
bsp[i] += bval_cross(gdiff*pearr[i],tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2);
btrace[i] = (bro[i]+bsl[i]+bpe[i]);
if (max_bval < btrace[i]) {
max_bval = (bro[i]+bsl[i]+bpe[i]);
}
} /* End for-all-directions */
putarray("bvalrr",bro,nbval);
putarray("bvalpp",bpe,nbval);
putarray("bvalss",bsl,nbval);
putarray("bvalrp",brp,nbval);
putarray("bvalrs",brs,nbval);
putarray("bvalsp",bsp,nbval);
putarray("bvalue",btrace,nbval);
putvalue("max_bval",max_bval);
/* Set all gradients depending on whether we do */
/* Use separate variables, because we only initialize & calculate gradients for ix==1 */
peamp = epipe_grad.amp;
perinc = per_grad.increment;
peramp = per_grad.amp;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
switch ((int)image) {
case 1: /* Real image scan, don't change anything */
break;
case 0: /* Normal reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = epiro_grad.amp;
roramp = ror_grad.amp;
break;
case -1: /* Inverted image scan */
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
case -2: /* Inverted reference scan */
peamp = 0;
perinc = 0;
peramp = 0;
roamp = -epiro_grad.amp;
roramp = -ror_grad.amp;
break;
default: break;
}
/* Generate phase-ramped pulses: 90, 180, and IR */
offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]);
shape90 = shapelist(p1pat,ss_grad.rfDuration,freq90,ns,0,seqcon[1]);
if (spinecho[0] == 'y') {
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shape180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
}
if (ir[0] == 'y') {
offsetlist(pss,ssi_grad.ssamp,0,freqIR,ns,seqcon[1]);
shapeIR = shapelist(pipat,ssi_grad.rfDuration,freqIR,ns,0,seqcon[1]);
}
sgl_error_check(sglerror);
roff1 = -poffset(pro,epi_grad.amppos);
roff2 = -poffset(pro,epi_grad.ampneg);
roffn = -poffset(pro,nav_grad.amp);
roff1 = -poffset(pro,epi_grad.amppos*roamp/epiro_grad.amp);
roff2 = -poffset(pro,epi_grad.ampneg*roamp/epiro_grad.amp);
roffn = -poffset(pro,nav_grad.amp);
dw = granularity(1/sw,1/epi_grad.ddrsr);
/* Total Scan Time */
g_setExpTime(tr*nt*nseg*arraydim);
/******************************************************/
/* PULSE SEQUENCE *************************************/
/******************************************************/
rotate();
F_initval(epi_grad.etl/2, vetl);
/* vetl is the loop counter in the acquisition loop */
/* that includes both a positive and negative readout lobe */
F_initval(nseg, vnseg);
/* NB. F_initval(-ssepi,vssepi); currently gives errors */
initval(-ssepi,vssepi); /* gradient steady state lobes */
obsoffset(resto); delay(GDELAY);
ifzero(rtonce); grad_advance(gpropdelay); endif(rtonce);
loop(vnseg,vnseg_ctr); /* Loop through segments in segmented EPI */
msloop(seqcon[1],ns,vms_slices,vms_ctr); /* Multislice loop */
assign(vssepi,vssepi_ctr);
sp1on(); delay(4e-6); sp1off(); /* Output trigger to look at scope */
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
getelem(t2,vnseg_ctr,vblip); /* vblip = t2[vnseg_ctr]; either 1 or -1 for pos/neg blip */
/* Optional FAT SAT */
if (fsat[0] == 'y') {
fatsat();
}
/* Optional IR + TI delay */
if (ir[0] == 'y') {
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0.0,0.0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayBack);
shapedpulselist(shapeIR,ssi_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(ti_delay);
}
/* 90 ss degree pulse */
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0.0,0.0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shape90,p1_rf.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus */
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT);
delay(del1);
if (diff[0] == 'y')
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del2);
if (diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
-diff_grad.amp*dro,-diff_grad.amp*dpe,-diff_grad.amp*dsl,WAIT);
delay(del3);
/* Optional 180 ss degree pulse with crushers */
if (spinecho[0] == 'y') {
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(GDELAY);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0.0,0.0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shape180,ss2_grad.rfDuration,oph,rof1,rof1,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
}
delay(del4);
if ((diff[0] == 'y') && !diff_in_one)
obl_shapedgradient(diff_grad.name,diff_grad.duration,
diff_grad.amp*dro,diff_grad.amp*dpe,diff_grad.amp*dsl,WAIT);
delay(del5);
/* Optional navigator echo */
if (navigator[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,roramp,0,0,WAIT);
obl_shapedgradient(nav_grad.name,nav_grad.duration,
-nav_grad.amp,0,0,NOWAIT);
delay(tep);
roff = roffn; /* Set receiver offset for navigator gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
/* Phase encode dephaser here if navigator echo was acquired */
var_shapedgradient(per_grad.name,per_grad.duration,0,-peramp,0,perinc,vnseg_ctr,WAIT);
}
else {
var_shapedgradient(per_grad.name,per_grad.duration,
-roramp,-peramp,0,perinc,vnseg_ctr,WAIT);
}
/* Start readout and phase encode gradient waveforms, NOWAIT */
/* If alternating ky-ordering, get polarity on blips from table */
var_shaped3gradient(epiro_grad.name,epipe_grad.name,"", /* patterns */
epiro_grad.duration, /* duration */
roamp,0,0, /* amplitudes */
peamp,vblip, /* step and multiplier */
NOWAIT); /* Don't wait */
delay(tep);
/* Acquisition loop */
assign(one,vacquire); // real-time acquire flag
nowait_loop(epi_grad.etl/2 + ssepi,vetl,vetl_ctr);
ifzero(vssepi_ctr); //vssepi_ctr = -ssepi, -ssepi+1, ..., 0, 1,2,...
assign(zero,vacquire); // turn on acquisition after all ss lobes
endif(vssepi_ctr);
incr(vssepi_ctr);
setacqvar(vacquire); // Set acquire flag
roff = roff1; /* Set receiver offset for positive gradient */
delay(epi_grad.skip-alfa); /* ramp up */
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw); //dw = 1/sw
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
roff = roff2; /* Set receiver offset for negative gradient */
delay(epi_grad.skip-alfa);
startacq(alfa);
for(i=0;i<np/2;i++){
sample(dw);
delay((epi_grad.dwell[i] - dw));
}
if (aqtm > at) sample(aqtm-at);
endacq();
delay(epi_grad.skip - dw - (aqtm-at));
nowait_endloop(vetl_ctr);
delay(tr_delay);
endmsloop(seqcon[1],vms_ctr); /* end multislice loop */
endloop(vnseg_ctr); /* end segments loop */
} /* end pulsesequence */
pulsesequence()
{
/* DECLARE AND LOAD VARIABLES */
void makeHHdec(), makeCdec(); /* utility functions */
char f1180[MAXSTR], /* Flag to start t1 @ halfdwell */
mag_flg[MAXSTR], /* magic-angle coherence transfer gradients */
C13refoc[MAXSTR], /* C13 sech/tanh pulse in middle of t1*/
NH2only[MAXSTR], /* spectrum of only NH2 groups */
T1[MAXSTR], /* insert T1 relaxation delay */
T1rho[MAXSTR], /* insert T1rho relaxation delay */
T2[MAXSTR], /* insert T2 relaxation delay */
TROSY[MAXSTR], /* do TROSY on N15 and H1 */
Hdecflg[MAXSTR], /* HH-h**o decoupling flag */
Cdecflg[MAXSTR]; /* low power C-13 decoupling flag */
int icosel, /* used to get n and p type */
ihh=1, /* used in HH decouling to improve water suppression */
t1_counter, /* used for states tppi in t1 */
rTnum, /* number of relaxation times, relaxT */
rTcounter; /* to obtain maximum relaxT, ie relaxTmax */
double tau1, /* t1 delay */
lambda = 0.91/(4.0*getval("JNH")), /* 1/4J H1 evolution delay */
tNH = 1.0/(4.0*getval("JNH")), /* 1/4J N15 evolution delay */
relaxT = getval("relaxT"), /* total relaxation time */
rTarray[1000], /* to obtain maximum relaxT, ie relaxTmax */
maxrelaxT = getval("maxrelaxT"), /* maximum relaxT in all exps */
ncyc, /* number of pulsed cycles in relaxT */
pwr_dly, /* power delay */
/* the sech/tanh pulse is automatically calculated by the macro "proteincal", */
/* and is called directly from your shapelib. */
pwClvl = getval("pwClvl"), /* coarse power for C13 pulse */
pwC = getval("pwC"), /* C13 90 degree pulse length at pwClvl */
rf0, /* maximum fine power when using pwC pulses */
rfst, /* fine power for the stCall pulse */
compH = getval("compH"), /* adjustment for H1 amplifier compression */
compN = getval("compN"), /* adjustment for N15 amplifier compression */
compC = getval("compC"), /* adjustment for C13 amplifier compression */
calH = getval("calH"), /* multiplier on a pw pulse for H1 calibration */
tpwrsf = getval("tpwrsf"), /* fine power adustment for soft pulse */
pwHs = getval("pwHs"), /* H1 90 degree pulse length at tpwrs */
pwHH = 0.0, /* pwHH = pwHs for HH h**o-decoupling */
tpwrs, /* power for the pwHs ("H2Osinc") pulse */
pwNlvl = getval("pwNlvl"), /* power for N15 pulses */
pwN = getval("pwN"), /* N15 90 degree pulse length at pwNlvl */
calN = getval("calN"), /* multiplier on a pwN pulse for calibration */
slNlvl, /* power for N15 spin lock */
slNrf = 1500.0, /* RF field in Hz for N15 spin lock at 600 MHz */
sw1 = getval("sw1"),
gt1 = getval("gt1"), /* coherence pathway gradients */
gzcal = getval("gzcal"), /* dac to G/cm conversion */
gzlvl1 = getval("gzlvl1"),
gzlvl2 = getval("gzlvl2"),
BPpwrlimits, /* =0 for no limit, =1 for limit */
gt0 = getval("gt0"), /* other gradients */
gt3 = getval("gt3"),
gt4 = getval("gt4"),
gt5 = getval("gt5"),
gstab = getval("gstab"),
gzlvl0 = getval("gzlvl0"),
gzlvl3 = getval("gzlvl3"),
gzlvl4 = getval("gzlvl4"),
gzlvl5 = getval("gzlvl5");
P_getreal(GLOBAL,"BPpwrlimits",&BPpwrlimits,1);
getstr("f1180",f1180);
getstr("mag_flg",mag_flg);
getstr("C13refoc",C13refoc);
getstr("NH2only",NH2only);
getstr("T1",T1);
getstr("T1rho",T1rho);
getstr("T2",T2);
getstr("TROSY",TROSY);
getstr("Hdecflg", Hdecflg);
getstr("Cdecflg", Cdecflg);
/* LOAD PHASE TABLE */
settable(t3,2,phi3);
settable(t4,1,phx);
if (TROSY[A]=='y')
{settable(t1,1,ph_x);
settable(t9,1,phx);
settable(t10,1,phy);
settable(t11,1,phx);
settable(t12,2,recT);}
else
{settable(t1,1,phx);
settable(t9,8,phi9);
settable(t10,1,phx);
settable(t11,1,phy);
settable(t12,4,rec);}
/* INITIALIZE VARIABLES */
/* maximum fine power for pwC pulses (and initialize rfst) */
rf0 = 4095.0; rfst=0.0;
/* 180 degree adiabatic C13 pulse from 0 to 200 ppm */
if (C13refoc[A]=='y')
{rfst = (compC*4095.0*pwC*4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35));
rfst = (int) (rfst + 0.5);
if ( 1.0/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35)) < pwC )
{ text_error( " Not enough C13 RF. pwC must be %f usec or less.\n",
(1.0e6/(4000.0*sqrt((30.0*sfrq/600.0+7.0)/0.35))) ); psg_abort(1); }}
/* selective H20 one-lobe sinc pulse */
if(pwHs > 1e-6)
tpwrs = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /* needs 1.69 times more */
else /* power than a square pulse */
tpwrs = 0.0;
tpwrs = (int) (tpwrs);
if (tpwrsf<4095.0) tpwrs = tpwrs + 6.0;
if (tpwrsf < 4095.0)
{
tpwrs = tpwrs + 6.0;
pwr_dly = POWER_DELAY + PWRF_DELAY;
}
else pwr_dly = POWER_DELAY;
/* power level for N15 spinlock (90 degree pulse length calculated first) */
slNlvl = 1/(4.0*slNrf*sfrq/600.0) ;
slNlvl = pwNlvl - 20.0*log10(slNlvl/(pwN*compN));
slNlvl = (int) (slNlvl + 0.5);
/* use 1/8J times for relaxation measurements of NH2 groups */
if ( (NH2only[A]=='y') && ((T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y')) )
{ tNH = tNH/2.0; }
/* reset calH and calN for 2D if inadvertently left at 2.0 */
if (ni>1.0) {calH=1.0; calN=1.0;}
/* make shapes and set up parameters for HH h**o-decoupling */
if(Cdecflg[0] == 'y') makeCdec();
if(Hdecflg[0] == 'y') makeHHdec();
if(Hdecflg[0] != 'n')
{
pwHH = pwHs;
pwHs = 0.0;
}
/* CHECK VALIDITY OF PARAMETER RANGES */
if ((TROSY[A]=='y') && (gt1 < -2.0e-4 + pwHs + 1.0e-4 + 2.0*POWER_DELAY))
{ text_error( " gt1 is too small. Make gt1 equal to %f or more.\n",
(-2.0e-4 + pwHs + 1.0e-4 + 2.0*POWER_DELAY) ); psg_abort(1); }
if((dm[A] == 'y' || dm[B] == 'y' || dm[C] == 'y' ))
{ text_error("incorrect dec1 decoupler flags! Should be 'nnn' "); psg_abort(1); }
if((dm2[A] == 'y' || dm2[B] == 'y'))
{ text_error("incorrect dec2 decoupler flags! Should be 'nny' "); psg_abort(1); }
if( dpwr2 > 50 )
{ text_error("don't fry the probe, DPWR2 too large! "); psg_abort(1); }
if( pw > 50.0e-6 )
{ text_error("dont fry the probe, pw too high ! "); psg_abort(1); }
if( pwN > 100.0e-6 )
{ text_error("dont fry the probe, pwN too high ! "); psg_abort(1); }
/* RELAXATION TIMES AND FLAGS */
/* evaluate maximum relaxT, relaxTmax chosen by the user */
rTnum = getarray("relaxT", rTarray);
relaxTmax = rTarray[0];
for (rTcounter=1; rTcounter<rTnum; rTcounter++)
if (relaxTmax < rTarray[rTcounter]) relaxTmax = rTarray[rTcounter];
/* compare relaxTmax with maxrelaxT */
if (maxrelaxT > relaxTmax) relaxTmax = maxrelaxT;
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > d1) )
{ text_error("Maximum relaxation time, relaxT, is greater than d1 ! "); psg_abort(1);}
if ( ((T1[A]=='y') && (T1rho[A]=='y')) || ((T1[A]=='y') && (T2[A]=='y')) ||
((T1rho[A]=='y') && (T2[A]=='y')) )
{ text_error("Choose only one relaxation measurement ! "); psg_abort(1); }
if ( ((T1[A]=='y') || (T1rho[A]=='y')) &&
((relaxT*100.0 - (int)(relaxT*100.0+1.0e-4)) > 1.0e-6) )
{ text_error("Relaxation time, relaxT, must be zero or multiple of 10msec"); psg_abort(1);}
if ( (T2[A]=='y') &&
(((relaxT+0.01)*50.0 - (int)((relaxT+0.01)*50.0+1.0e-4)) > 1.0e-6) )
{ text_error("Relaxation time, relaxT, must be odd multiple of 10msec"); psg_abort(1);}
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > 0.25) && (ix==1) )
{ printf("WARNING, sample heating will result for relaxT>0.25sec"); }
if ( ((T1rho[A]=='y') || (T2[A]=='y')) && (relaxTmax > 0.5) )
{ text_error("relaxT greater than 0.5 seconds will heat sample"); psg_abort(1);}
if ( ((NH2only[A]=='y') || (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y'))
&& (TROSY[A]=='y') )
{ text_error("TROSY not implemented with NH2 spectrum, or relaxation exps."); psg_abort(1);}
if ((TROSY[A]=='y') && (dm2[C] == 'y'))
{ text_error("Choose either TROSY='n' or dm2='n' ! "); psg_abort(1); }
/* PHASES AND INCREMENTED TIMES */
/* Phase incrementation for hypercomplex 2D data, States-Haberkorn element */
if (TROSY[A]=='y')
{ if (phase1 == 2) icosel = -1;
else { tsadd(t4,2,4); tsadd(t10,2,4); icosel = +1; }
}
else { if (phase1 == 2) {tsadd(t10,2,4); icosel = +1;}
else icosel = -1;
}
if(Hdecflg[0] != 'n') ihh = icosel;
/* Set up f1180 */
tau1 = d2;
if((f1180[A] == 'y') && (ni > 1.0))
{ tau1 += ( 1.0 / (2.0*sw1) ); if(tau1 < 0.2e-6) tau1 = 0.0; }
tau1 = tau1/2.0;
/* Calculate modifications to phases for States-TPPI acquisition */
if( ix == 1) d2_init = d2;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5 );
if(t1_counter % 2)
{ tsadd(t3,2,4); tsadd(t12,2,4); }
/* Correct inverted signals for NH2 only spectra */
if ((NH2only[A]=='y') && (T1[A]=='n') && (T1rho[A]=='n') && (T2[A]=='n'))
{ tsadd(t3,2,4); }
/* BEGIN PULSE SEQUENCE */
status(A);
obspower(tpwr);
decpower(pwClvl);
decpwrf(rf0);
dec2power(pwNlvl);
txphase(zero);
decphase(zero);
dec2phase(zero);
if(Hdecflg[0] != 'n')
{
delay(5.0e-5);
rgpulse(pw,zero,rof1,0.0);
rgpulse(pw,one,0.0,rof1);
zgradpulse(1.5*gzlvl0, 0.5e-3);
delay(5.0e-4);
rgpulse(pw,zero,rof1,0.0);
rgpulse(pw,one,0.0,rof1);
zgradpulse(-gzlvl0, 0.5e-3);
}
delay(d1);
/* xxxxxxxxxxxxxxxxx CONSTANT SAMPLE HEATING FROM N15 RF xxxxxxxxxxxxxxxxx */
if (T1rho[A]=='y')
{dec2power(slNlvl);
dec2rgpulse(relaxTmax-relaxT, zero, 0.0, 0.0);
dec2power(pwNlvl);}
if (T2[A]=='y')
{ncyc = 8.0*100.0*(relaxTmax - relaxT);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl-3.0); /* reduce for probe protection */
pwN=pwN*compN*1.4;
}
if (ncyc > 0)
{initval(ncyc,v1);
loop(v1,v2);
delay(0.625e-3 - pwN);
dec2rgpulse(2*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v2);}
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl); /* restore normal value */
pwN=getval("pwN");
}
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
rcvroff();
if (TROSY[A]=='n')
dec2rgpulse(pwN, zero, 0.0, 0.0); /*destroy N15 magnetization*/
zgradpulse(gzlvl0, 0.5e-3);
delay(1.0e-4);
if (TROSY[A]=='n') dec2rgpulse(pwN, one, 0.0, 0.0);
zgradpulse(0.7*gzlvl0, 0.5e-3);
decpwrf(rfst);
txphase(t1);
delay(5.0e-4);
if ( dm3[B] == 'y' ) /* begins optional 2H decoupling */
{
lk_hold();
dec3rgpulse(1/dmf3,one,10.0e-6,2.0e-6);
dec3unblank();
dec3phase(zero);
delay(2.0e-6);
setstatus(DEC3ch, TRUE, 'w', FALSE, dmf3);
}
rgpulse(calH*pw,t1,0.0,0.0); /* 1H pulse excitation */
txphase(zero);
dec2phase(zero);
zgradpulse(gzlvl0, gt0);
delay(lambda - gt0 - pwHH);
if(Hdecflg[0] != 'n')
{
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHH, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHH, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
}
else
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
txphase(one);
zgradpulse(gzlvl0, gt0);
delay(lambda - gt0 - pwHH);
rgpulse(pw, one, 0.0, 0.0);
txphase(two);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHs, two, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
if (TROSY[A]=='y')
zgradpulse(ihh*gzlvl3, gt3);
else
zgradpulse(-ihh*gzlvl3, gt3);
dec2phase(t3);
delay(2.0e-4);
dec2rgpulse(calN*pwN, t3, 0.0, 0.0);
txphase(zero);
decphase(zero);
/* xxxxxxxxxxxxxxxxxx OPTIONS FOR N15 RELAXATION xxxxxxxxxxxxxxxxxxxx */
if ( (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y') )
{
dec2phase(one);
zgradpulse(gzlvl4, gt4); /* 2.0*GRADIENT_DELAY */
delay(tNH - gt4 - 2.0*GRADIENT_DELAY);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, one, 0.0, 0.0);
zgradpulse(gzlvl4, gt4); /* 2.0*GRADIENT_DELAY */
delay(tNH - gt4 - 2.0*GRADIENT_DELAY);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (T1[A]=='y')
{
dec2rgpulse(pwN, one, 0.0, 0.0);
dec2phase(three);
zgradpulse(gzlvl0, gt0); /* 2.0*GRADIENT_DELAY */
delay(2.5e-3 - gt0 - 2.0*GRADIENT_DELAY - pw);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(2.5e-3 - pw);
ncyc = (100.0*relaxT);
initval(ncyc,v4);
if (ncyc > 0)
{loop(v4,v5);
delay(2.5e-3 - pw);
rgpulse(2.0*pw, two, 0.0, 0.0);
delay(2.5e-3 - pw);
delay(2.5e-3 - pw);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(2.5e-3 - pw);
endloop(v5);}
dec2rgpulse(pwN, three, 0.0, 0.0);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
/* Theory suggests 8.0 is better than 2PI as RF */
/* field multiplier and experiment confirms this.*/
if (T1rho[A]=='y') /* Shift evolution of 2.0*pwN/PI for one pulse */
{ /* at end left unrefocused as for normal sequence*/
delay(1.0/(8.0*slNrf) - pwN);
decrgpulse(pwN, zero, 0.0, 0.0);
dec2power(slNlvl);
/* minimum 5ms spinlock to dephase */
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0); /* spins not locked */
sim3pulse(2.0*pw, 0.0, 2.0*pw, zero, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
ncyc = 100.0*relaxT;
initval(ncyc,v4); if (ncyc > 0)
{loop(v4,v5);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
sim3pulse(2.0*pw, 0.0, 2.0*pw, two, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
sim3pulse(2.0*pw, 0.0, 2.0*pw, zero, zero, zero, 0.0, 0.0);
dec2rgpulse((2.5e-3-pw), zero, 0.0, 0.0);
endloop(v5);}
dec2power(pwNlvl);
decrgpulse(pwN, zero, 0.0, 0.0);
delay(1.0/(8.0*slNrf) + 2.0*pwN/PI - pwN);
}
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (T2[A]=='y')
{
dec2phase(zero);
initval(0.0,v3); initval(180.0,v4);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl-3.0); /* reduce for probe protection */
pwN=pwN*compN*1.4;
}
ncyc = 100.0*relaxT;
initval(ncyc,v5);
loop(v5,v6);
initval(3.0,v7);
loop(v7,v8);
delay(0.625e-3 - pwN);
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v8);
delay(0.625e-3 - pwN - SAPS_DELAY);
add(v4,v3,v3); obsstepsize(1.0); xmtrphase(v3); /* SAPS_DELAY */
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN - pw);
rgpulse(2*pw, zero, 0.0, 0.0);
delay(0.625e-3 - pwN - pw );
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
xmtrphase(zero); /* SAPS_DELAY */
delay(0.625e-3 - pwN - SAPS_DELAY);
initval(3.0,v9);
loop(v9,v10);
delay(0.625e-3 - pwN);
dec2rgpulse(2.0*pwN, zero, 0.0, 0.0);
delay(0.625e-3 - pwN);
endloop(v10);
endloop(v6);
if (BPpwrlimits > 0.5)
{
dec2power(pwNlvl); /* restore normal value */
pwN=getval("pwN");
}
}
/* xxxxxxxxxxxxxxxxxx OPTIONS FOR N15 EVOLUTION xxxxxxxxxxxxxxxxxxxxx */
txphase(zero);
dec2phase(t9);
if ( (NH2only[A]=='y') || (T1[A]=='y') || (T1rho[A]=='y') || (T2[A]=='y') )
{
delay(tau1);
/* optional sech/tanh pulse in middle of t1 */
if (C13refoc[A]=='y') /* WFG_START_DELAY */
{decshaped_pulse("stC200", 1.0e-3, zero, 0.0, 0.0);
delay(tNH - 1.0e-3 - WFG_START_DELAY - 2.0*pw);}
else
{delay(tNH - 2.0*pw);}
rgpulse(2.0*pw, zero, 0.0, 0.0);
if (tNH < gt1 + 1.99e-4) delay(gt1 + 1.99e-4 - tNH);
delay(tau1);
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
txphase(t4);
dec2phase(t10);
if (tNH > gt1 + 1.99e-4) delay(tNH - gt1 - 2.0*GRADIENT_DELAY);
else delay(1.99e-4 - 2.0*GRADIENT_DELAY);
}
else if (TROSY[A]=='y')
{
if ( (C13refoc[A]=='y') && (tau1 > 0.5e-3 + WFG2_START_DELAY) )
{delay(tau1 - 0.5e-3 - WFG2_START_DELAY); /* WFG2_START_DELAY */
decshaped_pulse("stC200", 1.0e-3, zero, 0.0, 0.0);
delay(tau1 - 0.5e-3);}
else delay(2.0*tau1);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
delay(2.0e-4 - 2.0*GRADIENT_DELAY);
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
txphase(three);
delay(gt1 + 2.0e-4 - pwHs - 1.0e-4 - 2.0*pwr_dly);
obspower(tpwrs);
if (tpwrsf<4095.0) obspwrf(tpwrsf);
shaped_pulse("H2Osinc", pwHs, three, 5.0e-5, 0.0);
obspower(tpwr);
if (tpwrsf<4095.0) obspwrf(4095.0);
txphase(t4);
delay(5.0e-5);
}
else
{ /* fully-coupled spectrum */
if (dm2[C]=='n') {rgpulse(2.0*pw, zero, 0.0, 0.0); pw=0.0;}
if ( (C13refoc[A]=='y') && (tau1 > 0.5e-3 + WFG2_START_DELAY) )
{delay(tau1 - 0.5e-3 - WFG2_START_DELAY); /* WFG2_START_DELAY */
simshaped_pulse("", "stC200", 2.0*pw, 1.0e-3, zero, zero, 0.0, 0.0);
delay(tau1 - 0.5e-3);
delay(gt1 + 2.0e-4);}
else
{delay(tau1);
rgpulse(2.0*pw, zero, 0.0, 0.0);
delay(gt1 + 2.0e-4 - 2.0*pw);
delay(tau1);}
pw=getval("pw");
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
if (mag_flg[A] == 'y') magradpulse(gzcal*gzlvl1, gt1);
else zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
txphase(t4);
dec2phase(t10);
delay(2.0e-4 - 2.0*GRADIENT_DELAY);
}
if (T1rho[A]=='y') delay(POWER_DELAY);
/* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
if (TROSY[A]=='y') rgpulse(pw, t4, 0.0, 0.0);
else sim3pulse(pw, 0.0, pwN, t4, zero, t10, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
zgradpulse(gzlvl5, gt5);
if (TROSY[A]=='y') delay(lambda - 0.65*(pw + pwN) - gt5);
else delay(lambda - 1.3*pwN - gt5);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
zgradpulse(gzlvl5, gt5);
txphase(one);
dec2phase(t11);
delay(lambda - 1.3*pwN - gt5);
sim3pulse(pw, 0.0, pwN, one, zero, t11, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
zgradpulse(1.5*gzlvl5, gt5);
delay(lambda - 1.3*pwN - gt5);
sim3pulse(2.0*pw, 0.0, 2.0*pwN, zero, zero, zero, 0.0, 0.0);
dec2phase(t10);
zgradpulse(1.5*gzlvl5, gt5);
if (TROSY[A]=='y') delay(lambda - 1.6*pwN - gt5);
else delay(lambda - 0.65*pwN - gt5);
if (TROSY[A]=='y') dec2rgpulse(pwN, t10, 0.0, 0.0);
else rgpulse(pw, zero, 0.0, 0.0);
delay((gt1/10.0) + 1.0e-4 +gstab - 0.65*pw + 2.0*GRADIENT_DELAY + POWER_DELAY);
if ( dm3[B] == 'y' ) /* turns off 2H decoupling */
{
setstatus(DEC3ch, FALSE, 'c', FALSE, dmf3);
dec3rgpulse(1/dmf3,three,2.0e-6,2.0e-6);
dec3blank();
lk_autotrig(); /* resumes lock pulsing */
}
rgpulse(2.0*pw, zero, 0.0, 0.0);
dec2power(dpwr2); /* POWER_DELAY */
if (mag_flg[A] == 'y') magradpulse(icosel*gzcal*gzlvl2, 0.1*gt1);
else zgradpulse(icosel*gzlvl2, 0.1*gt1); /* 2.0*GRADIENT_DELAY */
if(Cdecflg[0] == 'y')
{
delay(gstab-2.0*POWER_DELAY-PRG_START_DELAY+rof2);
rcvron();
statusdelay(C,1.0e-4);
if (dm3[B] == 'y')
{
delay(1/dmf3);
lk_sample();
}
setreceiver(t12);
pbox_decon(&Cdseq);
if(Hdecflg[0] == 'y')
homodec(&HHdseq);
}
else
{
delay(gstab+rof2);
rcvron();
statusdelay(C,1.0e-4);
if (dm3[B] == 'y')
{
delay(1/dmf3);
lk_sample();
}
setreceiver(t12);
if(Hdecflg[0] == 'y')
homodec(&HHdseq);
}
}
int main(int argc, char **argv) {
int simpleSocket = 0;
int simplePort = 0;
int returnStatus = 0;
char IP[255] = "";
char port[10] = "";
char line1mode[4] = "";
char line2mode[4] = "";
char sign_addr[4] = "";
char line1color[10] = "";
char line1text[1024] = "";
char line2color[10] = "";
char line2text[1024] = "";
char time_var[3] = "";
int timearray[2] ;
int datearray[2];
char buffer[1024] = "";
struct sockaddr_in simpleServer;
struct hostent *server;
int LOL1;
char LOL[256];
int temp;
char stringtemp[1024];
int c;
if (1 == argc)
exit(1);
while (1)
{
static struct option long_options[] =
{
/* These options set a flag. */
{"debug", no_argument, &DEBUG, 1},
/* These options don't set a flag.
We distinguish them by their indices. */
{"server", required_argument, 0, 'a'},
{"port", required_argument, 0, 'b'},
{"sign", required_argument, 0, 'c'},
{"line1color", required_argument, 0, 'd'},
{"line1text", required_argument, 0, 'e'},
{"line2color", required_argument, 0, 'f'},
{"line2text", required_argument, 0, 'g'},
{"time", required_argument, 0, 'h'},
{"line1mode", required_argument, 0, 'i'},
{"line2mode", required_argument, 0, 'j'},
{"date", required_argument, 0, 'k'},
{"help", no_argument, 0, '?'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
c = getopt_long (argc, argv, "?", long_options, &option_index);
if (c == -1)
break;
switch (c)
{
case 'a':
if (DEBUG == 1)
printf("--server is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >254){
fprintf(stderr,"IP too long\n\n");
exit(1);
}
strncpy(IP, optarg, temp); //IP = optarg;
break;
case 'b':
if (DEBUG == 1)
printf("--port is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >9){
fprintf(stderr,"Port too long\n\n");
exit(1);
}
strncpy(port, optarg, temp); //port = optarg
break;
case 'c':
if (DEBUG == 1)
printf("--sign is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >1){
fprintf(stderr,"sign Addr is too long\n\n");
exit(1);
}
strncpy(sign_addr, optarg, temp); //sign_addr = optarg;
break;
case 'd':
if (DEBUG == 1)
printf("--line1color is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >9){
fprintf(stderr,"Color to long\n\n");
exit(1);
}
strncpy(line1color, optarg, temp); //line1color = optarg;
break;
case 'e':
if (DEBUG == 1)
printf("--line1text is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >1023){
fprintf(stderr,"Text too long\n\n");
exit(1);
}
strncpy(line1text, optarg, temp); //line1text = optarg;
break;
case 'f':
if (DEBUG == 1)
printf("--line2color is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >9){
fprintf(stderr,"Color2 too long\n\n");
exit(1);
}
strncpy(line2color, optarg, temp); //line2color = optarg;
break;
case 'g':
if (DEBUG == 1)
printf("--line2text is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >1023){
fprintf(stderr,"Text2 too long\n\n");
exit(1);
}
strncpy(line2text, optarg, temp); //line2text = optarg;
break;
case 'h':
if (DEBUG == 1)
printf("--time is %s\n\n", optarg);
temp=strlen(optarg);
strncpy(time_var, optarg, temp); //time_var = optarg;
temp = atoi(time_var);
if (temp == 1){
timearray[0] = 1;
} else if (temp == 2){
timearray[1] = 1 ;
}else {
printf("TIME VAR IS WRONG :( (OUT OF RANGE)\n");
exit(1);
}
break;
case 'i':
if (DEBUG == 1)
printf("--line1mode is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >3){
fprintf(stderr,"line1mode too long\n\n");
exit(1);
}
strncpy(line1mode, optarg, temp); //line1mode = optarg;
break;
case 'j':
if (DEBUG == 1)
printf("--line2mode is %s\n\n", optarg);
temp=strlen(optarg);
if (temp >3){
fprintf(stderr,"line2mode too long\n\n");
exit(1);
}
strncpy(line2mode, optarg, temp); //line2mode = optarg;
break;
case 'k':
if (DEBUG == 1)
printf("--date is %s\n\n", optarg);
temp=strlen(optarg);
strncpy(time_var, optarg, temp); //time_var = optarg;
temp = atoi(time_var);
if (temp == 1){
datearray[0] = 1;
} else if (temp == 2){
datearray[1] = 1 ;
}else {
printf("DATEVAR IS WRONG :( (OUT OF RANGE)\n");
exit(1);
}
break;
case '?':
fprintf(stderr, "Welcome to %s ! this program will display two lines of text on a 4120c led sign add --time <line num> to add time at the end of line \n",argv[0]);
// 0 1 2 3 4 5 6 7
fprintf(stderr, "Usage: %s --server <ip> --port <port> --sign <addr> --line1color <color> --line1mode <mode letter> --line1text \"line 1\" --line2mode <mode letter> --line2color <color> --line2text \"line 2\"\n", argv[0]);
exit(1);
break;
}
}
/* create a streaming socket */
simpleSocket = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP);
if (simpleSocket == -1) {
fprintf(stderr, "Could not create a socket!\n");
exit(1);
}
else {
fprintf(stderr, "Socket created!\n");
}
/* retrieve the port number for connecting */
simplePort = atoi(port);
// server = gethostbyname(argv[1]); is the magical dns lookup
server = gethostbyname(IP);
/* setup the address structure */
/* use the IP address sent as an argument for the server address */
bzero(&simpleServer, sizeof(simpleServer));
simpleServer.sin_family = AF_INET;
//inet_addr(server, &simpleServer.sin_addr.s_addr); is outdated
bcopy((char *)server->h_addr,
(char *)&simpleServer.sin_addr.s_addr,
server->h_length);
simpleServer.sin_port = htons(simplePort);
/* connect to the address and port with our socket */
returnStatus = connect(simpleSocket, (struct sockaddr *)&simpleServer, sizeof(simpleServer));
if (returnStatus == 0) {
if (DEBUG ==1 ){
fprintf(stderr, "Connect successful!\n");
}
}
else {
fprintf(stderr, "Could not connect to address!\n");
close(simpleSocket);
exit(1);
}
/* get the mode sign mode sane */
if(strcmp(line1mode,"")==0){
strncpy(line1mode, "b", 1);
}
if(strcmp(line2mode,"")==0){
strncpy(line2mode, "t", 1);
}
/* get the message to the server */
temp=sprintf(stringtemp,"AZ%s",sign_addr); //Start building the message here
if (DEBUG == 1){
printf("DEBUG: %s \n",stringtemp);
}
temp=write(simpleSocket,stringtemp,temp); //shove it out the door
read(simpleSocket, buffer, sizeof(buffer));
if (DEBUG == 1){
printf("DEBUG FROM SERVER: %s \n",buffer);
}
temp=sprintf(stringtemp,"AA");
temp=write(simpleSocket,stringtemp,temp);
temp=sprintf(stringtemp,"%c%c%s %c%c",smf,topline,line1mode,fontmode,normalsmallfont); //Set the sign to hold on top line
// and normal small font in to buffer
temp=write(simpleSocket,stringtemp,temp); //write buffer to socket
if (strcmp(line1color,"red")==0){ //line 1 color anyone?
if (DEBUG == 1){
printf("DEBUG: red argv[4] \n");
}
temp=sprintf(stringtemp,"%c%c",cc,red);// set the color code
temp=write(simpleSocket,stringtemp,temp); //and shove it out the door
}else if (strcmp(line1color,"green")==0){
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: green argv[4] \n");
}
}else if (strcmp(line1color,"amber")==0){
temp=sprintf(stringtemp,"%c%c",cc,amb);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: Amber argv[4] \n");
}
}else
{
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: WRONG INPUT --line1color \n");
}
}
temp=strlen(line1text); //count the line1text which should be a string
temp=write(simpleSocket,line1text,temp); // and shove x chars out the door
if (timearray[0] == 1){ //time at the end of the line
temp=sprintf(stringtemp," %c",timeLED);
temp=write(simpleSocket,stringtemp,temp);
}
if (datearray[0] == 1){ //date at the end of the line
temp=sprintf(stringtemp," %c%c",date,datemmddyy);
temp=write(simpleSocket,stringtemp,temp);
}
//Now for the Bot line
temp=sprintf(stringtemp,"%c%c%s %c%c",smf,botline,line2mode,fontmode,normalsmallfont); //Set the sign to scroll on bot line
// and normal small font in to buffer
temp=write(simpleSocket,stringtemp,temp); //write buffer to mainfd (which should be the serial port see signfp.c)
if (strcmp(line2color,"red")==0){ //line2color anyone?
if (DEBUG == 1){
printf("DEBUG: red argv[6] \n");
}
temp=sprintf(stringtemp,"%c%c",cc,red);// set the color code
temp=write(simpleSocket,stringtemp,temp); //and shove it out the door
}else if (strcmp(line2color,"green")==0){
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: green --line2color \n");
}
}else if (strcmp(line2color,"amber")==0){
temp=sprintf(stringtemp,"%c%c",cc,amb);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: amb --line2color \n");
}
}else
{
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
if (DEBUG == 1){
printf("DEBUG: WRONG INPUT --line2color \n");
}
}
temp=strlen(line2text); //count the argv5 which should be a string
temp=write(simpleSocket,line2text,temp); // and shove x chars out the door
if (DEBUG == 1){
printf("DEBUG line2text: %s \n",line2text);
}
if (timearray[1] == 1){ //then line 2 time is added
temp=sprintf(stringtemp," %c",timeLED);
temp=write(simpleSocket,stringtemp,temp);
}
if (datearray[1] == 1){ //date at the end of the line
temp=sprintf(stringtemp," %c%c",date,datemmddyy);
temp=write(simpleSocket,stringtemp,temp);
}
temp=sprintf(stringtemp," %c",end); // tell the sign were done
temp=write(simpleSocket,stringtemp,temp); // output it
if (DEBUG == 1){
printf("DEBUG: End sent \n");
}
usleep(250);
endloop(simpleSocket);
returnStatus = read(simpleSocket, buffer, sizeof(buffer));
if ( returnStatus > 0 ) {
printf("%d: %s", returnStatus, buffer);
} else {
fprintf(stderr, "Return Status = %d \n", returnStatus);
}
close(simpleSocket);
return 0;
}
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 *************************/
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);
}
pulsesequence() {
// Define Variables and Objects and Get Parameter Values
double aXxyxy8 = getval("aXxyxy8");
double aYxyxy8 = getval("aYxyxy8");
double pwXxyxy8 = getval("pwXxyxy8");
double pwYxyxy8 = getval("pwYxyxy8");
double nXYxy8 = getval("nXYxy8");
int counter = nXYxy8;
initval(nXYxy8,v8);
double fXYxy8 = getval("fXYxy8");
double onYxyxy8 = getval("onYxyxy8");
double srate = getval("srate");
DSEQ dec = getdseq("H");
strncpy(dec.t.ch,"dec",3);
putCmd("chHtppm='dec'\n");
strncpy(dec.s.ch,"dec",3);
putCmd("chHspinal='dec'\n");
DSEQ mix = getdseq("Hmix");
strncpy(mix.t.ch,"dec",3);
putCmd("chHmixtppm='dec'\n");
strncpy(dec.s.ch,"dec",3);
putCmd("chHmixspinal='dec'\n");
//--------------------------------------
// Copy Current Parameters to Processed
//-------------------------------------
putCmd("groupcopy('current','processed','acquisition')");
// Dutycycle Protection
DUTY d = init_dutycycle();
d.dutyon = getval("pwX90") + nXYxy8*(pwXxyxy8 + pwYxyxy8);
d.dutyoff = d1 + 4.0e-6;
d.c1 = d.c1 + (!strcmp(dec.seq,"tppm"));
d.c1 = d.c1 + ((!strcmp(dec.seq,"tppm")) && (dec.t.a > 0.0));
d.t1 = getval("rd") + getval("ad") + at;
d.c2 = d.c2 + (!strcmp(dec.seq,"spinal"));
d.c2 = d.c2 + ((!strcmp(dec.seq,"spinal")) && (dec.s.a > 0.0));
d.t2 = getval("rd") + getval("ad") + at;
d.c3 = d.c3 + (!strcmp(mix.seq,"tppm"));
d.c3 = d.c3 + ((!strcmp(mix.seq,"tppm")) && (mix.t.a > 0.0));
d.t3 = nXYxy8*(1.0/srate - pwXxyxy8 - pwYxyxy8);
d.c4 = d.c4 + (!strcmp(mix.seq,"spinal"));
d.c4 = d.c4 + ((!strcmp(mix.seq,"spinal")) && (mix.s.a > 0.0));
d.t4 = nXYxy8*(1.0/srate - pwXxyxy8 - pwYxyxy8);
d = update_dutycycle(d);
abort_dutycycle(d,10.0);
// Set Phase Tables
settable(phX90,4,table1);
settable(phXYxy8,8,table2);
settable(phXxyxy8,4,table3);
settable(phYxyxy8,4,table4);
settable(phRec,4,table5);
settable(ph1Rec,4,table6);
settable(ph2Rec,4,table7);
settable(ph3Rec,4,table8);
int tix = counter%8;
if ((tix == 1) || (tix == 7)) ttadd(phRec,ph1Rec,4);
if ((tix == 2) || (tix == 6)) ttadd(phRec,ph2Rec,4);
if ((tix == 3) || (tix == 5)) ttadd(phRec,ph3Rec,4);
setreceiver(phRec);
// Begin Sequence
txphase(phX90); decphase(zero);
obspwrf(getval("aX90"));
obsunblank(); decunblank(); _unblank34();
delay(d1);
sp1on(); delay(2.0e-6); sp1off(); delay(2.0e-6);
// X Direct Polarization
rgpulse(getval("pwX90"),phX90,0.0,0.0);
// xy8XY Period
if (counter > 0) {
_dseqon(mix);
delay(pwXxyxy8/2.0);
obspwrf(aXxyxy8); dec2pwrf(aYxyxy8);
sub(v1,v1,v1);
if (counter >= 1) {
loop(v8,v9);
getelem(phXYxy8,v1,v4);
incr(v1);
getelem(phXxyxy8,ct,v2);
getelem(phYxyxy8,ct,v3);
add(v4,v2,v2);
add(v4,v3,v3);
txphase(v2); dec2phase(v3);
delay((1.0 - fXYxy8)/srate - pwYxyxy8/2.0 - pwXxyxy8/2.0);
if (onYxyxy8 == 2)
dec2rgpulse(pwYxyxy8,v3,0.0,0.0);
else
delay(pwYxyxy8);
delay(fXYxy8/srate - pwYxyxy8/2.0 - pwXxyxy8/2.0);
rgpulse(pwXxyxy8,v2,0.0,0.0);
endloop(v9);
delay(1.0/srate - pwXxyxy8/2.0);
}
_dseqoff(mix);
}
// Begin Acquisition
_dseqon(dec);
obsblank(); _blank34();
delay(getval("rd"));
startacq(getval("ad"));
acquire(np, 1/sw);
endacq();
_dseqoff(dec);
obsunblank(); decunblank(); _unblank34();
}
pulsesequence() {
/* Internal variable declarations *************************/
int shapelist90,shapelist180;
int table = 0;
double tau1,tau2,tau3,te1_delay,te2_delay,te3_delay,tr_delay;
double freq90[MAXNSLICE],freq180[MAXNSLICE];
double thk2fact,crush_step,neby2,crush_ind;
int suppressSTE,*crushtab;
char crushmod[MAXSTR];
int i;
/* Real-time variables used in this sequence **************/
int vpe_steps = v1; // Number of PE steps
int vpe_ctr = v2; // PE loop counter
int vpe_mult = v3; // PE multiplier, ranges from -PE/2 to PE/2
int vpe_offset = v4; // PE/2 for non-table offset
int vms_slices = v5; // Number of slices
int vms_ctr = v6; // Slice loop counter
int vne = v7; // Number of echoes
int vne_ctr = v8; // Echo loop counter
int vssc = v9; // Compressed steady-states
int vtrimage = v10; // Counts down from nt, trimage delay when 0
int vacquire = v11; // Argument for setacqvar, to skip steady state acquires
int vphase90 = v12; // Phase of 90 degree excitation pulse
int vphase180 = v13; // Phase of 180 degree refocusing pulse
int vphindex = v14; // Phase cycle index
int vneindex = v15; // Echo index, odd or even
int vcrush = v16; // Crusher modulation
int vtrigblock = v17; // Number of slices per trigger block
/* Initialize paramaters **********************************/
init_mri();
getstr("crushmod",crushmod);
suppressSTE=getval("suppressSTE");
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
table = 1;
}
/* RF Power & Bandwidth Calculations **********************/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Calculate thk2fact to ensure gss=gss2 for the choice of p1 and p2
so that the sequence remains robust in the absence of correct
balancing of slice select and slice refocus gradients */
thk2fact=p2_rf.bandwidth/p1_rf.bandwidth;
putvalue("thk2fact",thk2fact);
/* Initialize gradient structures *************************/
init_readout(&ro_grad,"ro",lro,np,sw);
ro_grad.pad1=alfa; ro_grad.pad2=alfa;
init_readout_refocus(&ror_grad,"ror");
init_phase(&pe_grad,"pe",lpe,nv);
init_slice(&ss_grad,"ss",thk);
init_slice(&ss2_grad,"ss2",thk*thk2fact);
init_slice_refocus(&ssr_grad,"ssr");
init_generic(&crush_grad,"crush",gcrush,tcrush);
/* Gradient calculations **********************************/
calc_readout(&ro_grad,WRITE,"gro","sw","at");
calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror");
calc_phase(&pe_grad,WRITE,"gpe","tpe");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p2_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
calc_generic(&crush_grad,WRITE,"","");
/* Equalize slice refocus and PE gradient durations *******/
calc_sim_gradient(&ror_grad,&null_grad,&ssr_grad,0.0,WRITE);
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') create_inversion_recovery();
sgl_error_check(sglerror);
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.amp,0,freq90,ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
shapelist90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]);
shapelist180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]);
/* To ensure proper overlap spin and stimulated echoes ensure that the
middle of the refocusing RF pulse is the centre of the pulse and that
echoes are formed in the centre of the acquisition window */
if (ss2_grad.rfFraction != 0.5)
abort_message("ERROR %s: Refocusing RF pulse must be symmetric (RF fraction = %.2f)",
seqfil,ss2_grad.rfFraction);
if (ro_grad.echoFraction != 1)
abort_message("ERROR %s: Echo Fraction must be 1",seqfil);
/* Find sum of all events in each half-echo period ********/
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + pe_grad.duration + crush_grad.duration + ro_grad.timeToEcho;
tau3 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(MAX(tau1,tau2),tau3); // Minimum echo spacing
espmin += 2*GRADIENT_RES; // Ensure that each delay is at least GRADIENT_RES
te = granularity(te,2*GRADIENT_RES);
if (minesp[0] == 'y') {
te = espmin;
putvalue("te",te);
}
if (FP_LT(te,espmin)) {
abort_message("ERROR %s: Echo time too small, minimum is %.3fms\n",seqfil,espmin*1000);
}
te1_delay = te/2.0 - tau1; // Intra-esp delays
te2_delay = te/2.0 - tau2;
te3_delay = te/2.0 - tau3;
/* Now set the TE processing array accordingly */
putCmd("TE = 0"); /* Re-initialize TE */
for (i=0;i<ne;i++) putCmd("TE[%d] = %f",i+1,te*1000*(i+1));
/* Check nsblock, the number of slices blocked together
(used for triggering and/or inversion recovery) */
check_nsblock();
/* Minimum TR **************************************/
trmin = ss_grad.rfCenterFront + ne*te + ro_grad.timeFromEcho + pe_grad.duration + te3_delay + 2*GRADIENT_RES;
/* Increase TR if any options are selected *********/
if (sat[0] == 'y') trmin += satTime;
if (fsat[0] == 'y') trmin += fsatTime;
if (mt[0] == 'y') trmin += mtTime;
if (ticks > 0) trmin += GRADIENT_RES;
/* Adjust for all slices ***************************/
trmin *= ns;
/* Inversion recovery *********************************/
if (ir[0] == 'y') {
/* tauti is the additional time beyond IR component to be included in ti */
/* satTime, fsatTime and mtTime all included as those modules will be after IR */
tauti = satTime + fsatTime + mtTime + GRADIENT_RES + ss_grad.rfCenterFront;
/* calc_irTime checks ti and returns the time of all IR components */
trmin += calc_irTime(tauti,trmin,mintr[0],tr,&trtype);
}
if (mintr[0] == 'y') {
tr = trmin;
putvalue("tr",tr);
}
if (FP_LT(tr,trmin)) {
abort_message("ERROR %s: TR too short, minimum TR is %.3fms\n",seqfil,trmin*1000);
}
/* Calculate tr delay */
tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES);
/* Set pe_steps for profile or full image **********/
pe_steps = prep_profile(profile[0],nv,&pe_grad,&per_grad);
F_initval(pe_steps/2.0,vpe_offset);
/* Shift DDR for pro ************************************/
roff = -poffset(pro,ro_grad.roamp);
/* Adjust experiment time for VnmrJ *********************/
if (ssc<0) {
if (seqcon[2] == 'c') g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*arraydim));
else g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*pe_steps*arraydim));
}
else g_setExpTime(trmean*ntmean*pe_steps*arraydim + tr*ssc);
/* Set phase cycle tables */
if (suppressSTE) {
if ((int)nt%2 == 1)
abort_message("STE suppression requires a 2 step phase cycle. Set nt as a multiple of 2\n");
settable(t2,4,phref1s);
settable(t3,4,phref2s);
settable(t4,4,phrec1s);
settable(t5,4,phrec2s);
} else {
settable(t2,4,phref1);
settable(t3,4,phref2);
settable(t4,4,phrec1);
settable(t5,4,phrec2);
}
/* Set crusher table */
crushtab=malloc((int)ne*sizeof(int));
neby2=ceil(ne/2.0 - US); // US to handle precision errors
crush_step=gcrush/neby2;
for (i=0; i<ne; i++) {
crush_ind = (1.0-2.0*(i%2))*(neby2-floor(i/2));
crushtab[i] = (int)(crush_ind);
}
settable(t6,(int)ne,crushtab);
/* PULSE SEQUENCE ***************************************/
status(A);
rotate();
triggerSelect(trigger); // Select trigger input 1/2/3
obsoffset(resto);
delay(GRADIENT_RES);
initval(fabs(ssc),vssc); // Compressed steady-state counter
if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop
assign(one,vacquire); // real-time acquire flag
setacqvar(vacquire); // Turn on acquire when vacquire is zero
/* Phase for excitation pulse */
assign(zero,vphase90);
/* trigger */
if (ticks > 0) F_initval((double)nsblock,vtrigblock);
/* Begin phase-encode loop ****************************/
peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr);
if (trtype) delay(ns*tr_delay); // relaxation delay
/* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */
if ((ix > 1) && (ssc > 0))
assign(zero,vssc);
sub(vpe_ctr,vssc,vpe_ctr); // vpe_ctr counts up from -ssc
assign(zero,vssc);
if (seqcon[2] == 's')
assign(zero,vacquire); // Always acquire for non-compressed loop
else {
ifzero(vpe_ctr);
assign(zero,vacquire); // Start acquiring when vpe_ctr reaches zero
endif(vpe_ctr);
}
/* Read external kspace table if set ******************/
if (table)
getelem(t1,vpe_ctr,vpe_mult);
else {
ifzero(vacquire);
sub(vpe_ctr,vpe_offset,vpe_mult);
elsenz(vacquire);
sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states
endif(vacquire);
}
msloop(seqcon[1],ns,vms_slices,vms_ctr);
if (!trtype) delay(tr_delay); // Relaxation delay
if (ticks > 0) {
modn(vms_ctr,vtrigblock,vtest);
ifzero(vtest); // if the beginning of an trigger block
xgate(ticks);
grad_advance(gpropdelay);
delay(GRADIENT_RES);
elsenz(vtest);
delay(GRADIENT_RES);
endif(vtest);
}
sp1on(); delay(GRADIENT_RES); sp1off(); // Scope trigger
/* Prepulse options ***********************************/
if (ir[0] == 'y') inversion_recovery();
if (sat[0] == 'y') satbands();
if (fsat[0] == 'y') fatsat();
if (mt[0] == 'y') mtc();
/* 90 degree pulse ************************************/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GRADIENT_RES);
obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT);
delay(ss_grad.rfDelayFront);
shapedpulselist(shapelist90,ss_grad.rfDuration,vphase90,rof1,rof2,seqcon[1],vms_ctr);
delay(ss_grad.rfDelayBack);
/* Slice refocus **************************************/
obl_shapedgradient(ssr_grad.name,ssr_grad.duration,ror_grad.amp,0.0,-ssr_grad.amp,WAIT);
/* First half-TE delay ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(te1_delay);
F_initval(ne,vne);
loop(vne,vne_ctr);
/* Phase cycle for refocusing pulse and receiver */
mod4(ct,vphindex);
mod2(vne_ctr,vneindex);
ifzero(vneindex);
getelem(t2,vphindex,vphase180);
getelem(t4,vphindex,oph);
elsenz(vneindex);
getelem(t3,vphindex,vphase180);
getelem(t5,vphindex,oph);
endif(vneindex);
/* Crusher gradient modulation */
assign(one,vcrush);
if (crushmod[0] == 'y') {
assign(zero,vcrush);
ifzero(vneindex);
add(vcrush,one,vcrush);
elsenz(vneindex);
sub(vcrush,one,vcrush);
endif(vneindex);
}
if (crushmod[0] == 'p') {
getelem(t6,vne_ctr,vcrush);
crush_grad.amp=crush_step;
}
/* 180 degree pulse *******************************/
if (crushmod[0] == 'y' || crushmod[0] == 'p')
var3_shapedgradient(crush_grad.name,crush_grad.duration,0.0,0.0,0.0,0.0,0.0,crush_grad.amp,zero,zero,vcrush,WAIT);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0,crush_grad.amp,WAIT);
obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT);
delay(ss2_grad.rfDelayFront);
shapedpulselist(shapelist180,ss2_grad.rfDuration,vphase180,rof1,rof2,seqcon[1],vms_ctr);
delay(ss2_grad.rfDelayBack);
if (crushmod[0] == 'y' || crushmod[0] == 'p')
var3_shapedgradient(crush_grad.name,crush_grad.duration,0.0,0.0,0.0,0.0,0.0,crush_grad.amp,zero,zero,vcrush,WAIT);
else
obl_shapedgradient(crush_grad.name,crush_grad.duration,crush_grad.amp,0,crush_grad.amp,WAIT);
/* Second half-TE period ******************************/
delay(te2_delay);
/* Phase-encode gradient ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,-pe_grad.increment,vpe_mult,WAIT);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.roamp,0,0,NOWAIT);
delay(ro_grad.atDelayFront-alfa);
/* Acquire data ****************************************/
startacq(alfa);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ********************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT);
/* Second half-TE delay *******************************/
delay(te3_delay);
endloop(vne_ctr);
endmsloop(seqcon[1],vms_ctr);
endpeloop(seqcon[2],vpe_ctr);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence()
{
/* DECLARE VARIABLES */
char fsat[MAXSTR],
fscuba[MAXSTR],
f1180[MAXSTR], /* Flag to start t1 @ halfdwell */
sh_reb[MAXSTR],
codec[MAXSTR],
MQ_flg[MAXSTR],
filter_flg[MAXSTR];
int phase,
t1_counter; /* used for states tppi in t1 */
double tau1, /* t1 delay */
taua, /* set to exactly 1/4JCH */
tsatpwr, /* low level 1H trans.power for presat */
sw1, /* sweep width in f1 */
tpwr_cp, /* power level for 1H CPMG */
pw_cp, /* 1H pw for CPMG */
ncyc_cp, /* number of CPMG cycles */
time_T2, /* total time for CPMG trains */
tau_cpmg,
dhpwr,
pwc,
dmf_co,
dpwr_co,
dresco,
gt0,
gt1,
gt2,
gt3,
gt4,
gt5,
gt6,
gzlvl0,
gzlvl1,
gzlvl2,
gzlvl3,
gzlvl4,
gzlvl5,
gzlvl6,
tpwr,
pw,
d_reb,
pwc_reb,
dpwr3_D,
pwd,
pwd1,
tau_eq,
pwn,
dhpwr2;
/* LOAD VARIABLES */
getstr("fsat",fsat);
getstr("f1180",f1180);
getstr("fscuba",fscuba);
getstr("sh_reb",sh_reb);
getstr("codec",codec);
getstr("MQ_flg",MQ_flg);
getstr("filter_flg",filter_flg);
taua = getval("taua");
tpwr = getval("tpwr");
tsatpwr = getval("tsatpwr");
dpwr = getval("dpwr");
phase = (int) ( getval("phase") + 0.5);
sw1 = getval("sw1");
tpwr_cp = getval("tpwr_cp");
pw_cp = getval("pw_cp");
ncyc_cp = getval("ncyc_cp");
time_T2 = getval("time_T2");
dhpwr = getval("dhpwr");
pwc = getval("pwc");
pwn = getval("pwn");
dhpwr2 = getval("dhpwr2");
dmf_co = getval("dmf_co");
dpwr_co = getval("dpwr_co");
dresco = getval("dresco");
gt0 = getval("gt0");
gt1 = getval("gt1");
gt2 = getval("gt2");
gt3 = getval("gt3");
gt4 = getval("gt4");
gt5 = getval("gt5");
gt6 = getval("gt6");
gzlvl0 = getval("gzlvl0");
gzlvl1 = getval("gzlvl1");
gzlvl2 = getval("gzlvl2");
gzlvl3 = getval("gzlvl3");
gzlvl4 = getval("gzlvl4");
gzlvl5 = getval("gzlvl5");
gzlvl6 = getval("gzlvl6");
tpwr = getval("tpwr");
pw = getval("pw");
d_reb = getval("d_reb");
pwc_reb = getval("pwc_reb");
dpwr3_D = getval("dpwr3_D");
pwd = getval("pwd");
pwd1 = getval("pwd1");
tau_eq = getval("tau_eq");
/* LOAD PHASE TABLE */
settable(t1,4,phi1);
settable(t2,2,phi2);
settable(t4,8,phi4);
settable(t5,4,rec);
/* CHECK VALIDITY OF PARAMETER RANGES */
if((dm[A] == 'y' || dm[B] == 'y' || dm[C] == 'y' ))
{
printf("incorrect dec1 decoupler flags! ");
abort(1);
}
if((dm2[A] == 'y' || dm2[B] == 'y' || dm2[C] == 'y' || dm2[D] == 'y'))
{
printf("incorrect dec2 decoupler flags! ");
abort(1);
}
if( tsatpwr > 6 )
{
printf("TSATPWR too large !!! ");
abort(1);
}
if( dpwr > 48 )
{
printf("don't fry the probe, DPWR too large! ");
abort(1);
}
if(tpwr_cp > 62)
{
printf("don't fry the probe, tpwr_cp too large: < 62! ");
abort(1);
}
if(pw_cp < 9.5e-6) {
printf("pw_cp is too low; > 9.5us\n");
abort(1);
}
if( dpwr2 > -16 )
{
printf("don't fry the probe, DPWR2 too large! ");
abort(1);
}
if( pw > 20.0e-6 )
{
printf("dont fry the probe, pw too high ! ");
abort(1);
}
if(gt1 > 3e-3 || gt2 > 3e-3 || gt3 > 3e-3 || gt4 > 3e-3
|| gt5 > 3e-3 || gt6 > 3e-3)
{
printf("gradients on for too long. Must be < 3e-3 \n");
abort(1);
}
if(ncyc_cp > 80) {
printf("ncyc_cp is too large; must be less than 81\n");
abort(1);
}
if(time_T2 > .080) {
printf("time_T2 is too large; must be less than 80 ms\n");
abort(1);
}
if(ncyc_cp > 0) {
tau_cpmg = time_T2/(4.0*ncyc_cp) - pw_cp;
if(ix==1)
printf("nuCPMG for curent experiment is (Hz): %5.3f\n",1/(4.0*(tau_cpmg+pw_cp)));
}
else {
tau_cpmg = time_T2/(4.0) - pw_cp;
if(ix==1)
printf("nuCPMG for curent experiment is (Hz): not applicable");
}
if(tau_cpmg + pw_cp < 125e-6) {
printf("tau_cpmg is too small; decrease ncyc_cp\n");
abort(1);
}
if(dpwr_co > 42) {
printf("dpwr_co is too high; < 42\n");
abort(1);
}
if(dpwr3_D > 51) {
printf("dpwr3_D is too high; < 52\n");
abort(1);
}
if(dpwr3 > 59) {
printf("dpwr3 is too high; < 60\n");
abort(1);
}
if(ix==1)
printf("If at 800 turn dpwr3=-16, pwd1=0\n");
/* Phase incrementation for hypercomplex 2D data */
if (phase == 2)
tsadd(t1,1,4);
/* Set up f1180 tau1 = t1 */
tau1 = d2;
if(MQ_flg[A] == 'n')
tau1 = tau1 - 4.0/PI*pwc - POWER_DELAY - PRG_START_DELAY
- 2.0*pw - 2.0*pwn - PRG_STOP_DELAY - POWER_DELAY
- 4.0e-6;
else
tau1 = tau1 - 4.0/PI*pwc - POWER_DELAY - PRG_START_DELAY
- 2.0*pw - 2.0*pwn - PRG_STOP_DELAY - POWER_DELAY
- 4.0e-6;
if(f1180[A] == 'y') {
tau1 += ( 1.0 / (2.0*sw1));
if(tau1 < 0.4e-6) tau1 = 0.4e-6;
}
if(tau1 < 0.4e-6)
tau1 = 0.4e-6;
tau1 = tau1/2.0;
/* Calculate modifications to phases for States-TPPI acquisition */
if( ix == 1) d2_init = d2 ;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5 );
if(t1_counter % 2) {
tsadd(t1,2,4);
tsadd(t5,2,4);
}
/* BEGIN ACTUAL PULSE SEQUENCE */
status(A);
rlpower(tsatpwr,TODEV); /* Set transmitter power for 1H presaturation */
rlpower(dhpwr,DODEV); /* Set Dec1 power for 13C pulses */
rlpower(dhpwr2,DO2DEV); /* Set Dec2 power for 15N pulses */
obsoffset(tof);
/* Presaturation Period */
status(B);
if (fsat[0] == 'y')
{
delay(2.0e-5);
rgpulse(d1,zero,2.0e-6,2.0e-6); /* presaturation */
rlpower(tpwr,TODEV); /* Set transmitter power for hard 1H pulses */
delay(2.0e-5);
if(fscuba[0] == 'y')
{
delay(2.2e-2);
rgpulse(pw,zero,2.0e-6,0.0);
rgpulse(2*pw,one,2.0e-6,0.0);
rgpulse(pw,zero,2.0e-6,0.0);
delay(2.2e-2);
}
}
else
{
delay(d1);
}
rlpower(tpwr,TODEV); /* Set transmitter power for 1H CPMG pulses */
txphase(zero);
dec2phase(zero);
decphase(zero);
delay(1.0e-5);
/* Begin Pulses */
status(C);
rcvroff();
delay(20.0e-6);
decrgpulse(pwc,zero,4.0e-6,0.0);
delay(2.0e-6);
rgradient('z',gzlvl1);
delay(gt1);
rgradient('z',0.0);
delay(250.0e-6);
rgpulse(pw,zero,0.0,0.0);
decpower(d_reb);
delay(2.0e-6);
rgradient('z',gzlvl2);
delay(gt2);
rgradient('z',0.0);
delay(150.0e-6);
if(filter_flg[A] == 'y')
delay(taua - POWER_DELAY - gt2 - 152e-6
- WFG2_START_DELAY - 0.5*pwc_reb - 4.0/PI*pw);
else
delay(taua - POWER_DELAY - gt2 - 152e-6
- WFG2_START_DELAY - 0.5*pwc_reb);
simshaped_pulse("hard",sh_reb,2.0*pw,pwc_reb,zero,zero,0.0,0.0);
txphase(one);
decpower(dhpwr);
decphase(t4);
delay(taua - 0.5*pwc_reb - WFG2_STOP_DELAY - POWER_DELAY - gt2 - 152e-6 );
delay(2.0e-6);
rgradient('z',gzlvl2);
delay(gt2);
rgradient('z',0.0);
delay(150.0e-6);
if(filter_flg[A] == 'n')
rgpulse(pw,one,0.0,0.0);
if(filter_flg[A] == 'y') {
decrgpulse(pwc,t4,0.,0.);
decpower(d_reb);
decphase(zero);
delay(2.0e-6);
rgradient('z',gzlvl0);
delay(gt0);
rgradient('z',0.0);
delay(150.0e-6);
delay(taua - POWER_DELAY - gt0 - 152e-6
- WFG2_START_DELAY - 0.5*pwc_reb);
simshaped_pulse("hard",sh_reb,2.0*pw,pwc_reb,zero,zero,0.0,0.0);
txphase(one);
decpower(dhpwr);
decphase(t4);
delay(taua - 0.5*pwc_reb - WFG2_STOP_DELAY - POWER_DELAY - gt0 - 152e-6 );
delay(2.0e-6);
rgradient('z',gzlvl0);
delay(gt0);
rgradient('z',0.0);
delay(150.0e-6);
decrgpulse(pwc,t4,0.0,0.0);
rgpulse(pw,one,0.0,0.0);
}
decphase(t1);
delay(2.0e-6);
rgradient('z',gzlvl3);
delay(gt3);
rgradient('z',0.0);
delay(250.0e-6);
/* turn on 2H decoupling */
dec3phase(one);
dec3power(dpwr3);
dec3rgpulse(pwd1,one,4.0e-6,0.0);
dec3phase(zero);
dec3unblank();
dec3power(dpwr3_D);
dec3prgon(dseq3,pwd,dres3);
dec3on();
/* turn on 2H decoupling */
if(MQ_flg[A] == 'y') {
rgpulse(pw,zero,2.0e-6,0.0);
delay(2.0*pwn - PRG_START_DELAY - PRG_STOP_DELAY);
}
decrgpulse(pwc,t1,4.0e-6,0.0);
decphase(zero);
/* 13CO decoupling on */
decpower(dpwr_co);
decprgon(codec,1.0/dmf_co,dresco);
decon();
/* 13CO decoupling on */
delay(tau1);
rgpulse(2.0*pw,zero,0.0,0.0);
dec2rgpulse(2.0*pwn,zero,0.0,0.0);
delay(tau1);
/* 13CO decoupling off */
decoff();
decprgoff();
/* 13CO decoupling off */
decpower(dhpwr);
decrgpulse(pwc,zero,4.0e-6,0.0);
if(MQ_flg[A] == 'y')
rgpulse(pw,zero,0.0,0.0);
/* turn off decoupling */
dec3off();
dec3prgoff();
dec3blank();
dec3phase(three);
dec3power(dpwr3);
dec3rgpulse(pwd1,three,4.0e-6,0.0);
/* turn off decoupling */
obspower(tpwr_cp);
if(MQ_flg[A] == 'n') {
delay(2.0e-6);
rgradient('z',gzlvl4);
delay(gt4);
rgradient('z',0.0);
delay(250.0e-6);
}
else {
delay(2.0e-6);
rgradient('z',-1.0*gzlvl4);
delay(gt4);
rgradient('z',0.0);
delay(250.0e-6);
}
/* now include a delay to allow the spin system to equilibrate */
delay(tau_eq);
rgpulse(pw_cp,t2,4.0e-6,0.0);
txphase(one);
/* start of the CPMG period 1 */
if(ncyc_cp == 1) {
delay(tau_cpmg - (2.0/PI)*pw_cp);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
}
if(ncyc_cp == 2) {
delay(tau_cpmg - (2.0/PI)*pw_cp);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
}
if(ncyc_cp > 2) {
delay(tau_cpmg - (2.0/PI)*pw_cp);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
initval(ncyc_cp-2,v4);
loop(v4,v5);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
endloop(v5);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
}
txphase(t4); decphase(zero);
rgpulse(2.0*pw_cp,t4,2.0e-6,2.0e-6);
txphase(one);
if(ncyc_cp == 1) {
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0); txphase(one);
delay(tau_cpmg - 2.0/PI*pw_cp);
}
if(ncyc_cp == 2) {
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0); txphase(one);
delay(tau_cpmg - 2.0/PI*pw_cp);
}
if(ncyc_cp > 2) {
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
initval(ncyc_cp-2,v4);
loop(v4,v5);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0);
delay(tau_cpmg);
endloop(v5);
delay(tau_cpmg);
rgpulse(2.0*pw_cp,one,0.0,0.0); txphase(one);
delay(tau_cpmg - 2.0/PI*pw_cp);
}
rgpulse(pw_cp,zero,0.0,0.0);
delay(2.0e-6);
rgradient('z',gzlvl5);
delay(gt5);
rgradient('z',0.0);
delay(250.0e-6);
obspower(tpwr);
rgpulse(pw,zero,4.0e-6,0.0);
decpower(d_reb);
delay(2.0e-6);
rgradient('z',gzlvl6);
delay(gt6);
rgradient('z',0.0);
delay(150.0e-6);
delay(taua - POWER_DELAY - gt6 - 152e-6
- WFG2_START_DELAY - 0.5*pwc_reb);
simshaped_pulse("hard",sh_reb,2.0*pw,pwc_reb,zero,zero,0.0,0.0);
delay(taua - 0.5*pwc_reb - WFG2_STOP_DELAY - 2.0*POWER_DELAY - gt6 - 152e-6);
rlpower(dpwr,DODEV); /* Set power for decoupling */
rlpower(dpwr2,DO2DEV); /* Set power for decoupling */
delay(2.0e-6);
rgradient('z',gzlvl6);
delay(gt6);
rgradient('z',0.0);
delay(150.0e-6);
rgpulse(pw,zero,0.0,0.0);
/* rcvron(); */ /* Turn on receiver to warm up before acq */
/* BEGIN ACQUISITION */
status(D);
setreceiver(t5);
}
pulsesequence()
{
/* DECLARE VARIABLES */
char imino[MAXSTR], /* Sets dof2 for imino region */
amino[MAXSTR], /* Sets dof2 for amino region */
f1180[MAXSTR]; /* Flag to start t1 @ halfdwell */
int icosel, /* used to get n and p type */
t1_counter;
double tau1, /* t1 delay */
lambdaN = 0.94/(4.0*getval("JNH")), /* 1/4J N-H INEPT delay */
lambdaN_int, /* interval in CPMG train */
pwClvl = getval("pwClvl"), /* coarse power for C13 pulse */
pwC = getval("pwC"), /* C13 90 degree pulse length at pwClvl */
pwNlvl = getval("pwNlvl"), /* power for N15 pulses */
pwN = getval("pwN"), /* N15 90 degree pulse length at pwNlvl */
dof2a, /* offset for imino/amino */
tpwr = getval("tpwr"), /* power for H1 pulses */
pw = getval("pw"), /* H1 90 degree pulse length at tpwr */
compH = getval("compH"),
ncyc = getval("ncyc"), /* number of cycles in CPMG train */
sw1 = getval("sw1"),
grecov = getval("grecov"),
pwHs = getval("pwHs"), /* H1 90 degree pulse length at tpwrs */
tpwrs, /* power for the pwHs ("rna_H2Osinc") pulse */
pwHs2 = getval("pwHs2"), /* H1 90 degree pulse length at tpwrs2 */
tpwrs2, /* power for the pwHs2 square pulse */
gt1 = getval("gt1"), /* coherence pathway gradients */
gzlvl1 = getval("gzlvl1"),
gzlvl2 = getval("gzlvl2"),
gzlvl0 = getval("gzlvl0"),
gzlvl3 = getval("gzlvl3"),
gt3 = getval("gt3");
getstr("imino",imino);
getstr("amino",amino);
getstr("f1180",f1180);
/* LOAD PHASE TABLE */
settable(t1,1,phi1);
settable(t2,2,phi2);
settable(t3,1,phi3);
settable(t9,8,phi9);
settable(t10,1,phi10);
settable(t11,1,phi11);
settable(t12,1,phi12);
settable(t13,1,phi13);
settable(t14,4,rec);
/* INITIALIZE VARIABLES */
/* IMINO-region setting of dof2 */
if (imino[A] == 'y')
dof2a = dof2 - 45*dfrq2;
/* AMINO-region setting of dof2 */
else if (amino[A] == 'y')
dof2a = dof2 - 115*dfrq2;
else
dof2a = dof;
/* selective H20 one-lobe sinc pulse */
tpwrs = tpwr - 20.0*log10(pwHs/(compH*pw*1.69)); /* needs 1.69 times more */
tpwrs = (int) (tpwrs); /* power than a square pulse */
/* selective H20 square pulse */
tpwrs2 = tpwr - 20.0*log10(pwHs2/(compH*pw));
tpwrs2 = (int) (tpwrs2);
/* number of cycles and mixing time */
ncyc = (int) (ncyc + 0.5);
/* PHASES AND INCREMENTED TIMES */
/* Phase incrementation for hypercomplex 2D data, States-Haberkorn element */
if (phase1 == 1)
{ tsadd(t10,2,4); icosel = 1; }
else icosel = -1;
/* Calculate modifications to phases for States-TPPI acquisition */
if( ix == 1) d2_init = d2;
t1_counter = (int) ( (d2-d2_init)*sw1 + 0.5 );
if(t1_counter % 2)
{ tsadd(t2,2,4); tsadd(t14,2,4); }
/* Set up f1180 */
tau1 = d2;
if((f1180[A] == 'y') && (ni > 1.0))
{ tau1 += ( 1.0 / (2.0*sw1) ); if(tau1 < 0.2e-6) tau1 = 0.0; }
tau1 = tau1/2.0;
/* CHECK VALIDITY OF PARAMETER RANGE */
if ( ((imino[A]=='y') && (amino[A]=='y')) )
{
printf(" Choose ONE of imino='y' OR amino='y' ");
psg_abort(1);
}
if((dm[A] == 'y' || dm[B] == 'y'))
{
printf("incorrect dec1 decoupler flag! Should be 'nny' or 'nnn' ");
psg_abort(1);
}
if((dm2[A] == 'y' || dm2[B] == 'y'))
{
printf("incorrect dec2 decoupler flags! Should be 'nnn' or 'nny' ");
psg_abort(1);
}
if( ((dm[C] == 'y') && (dm2[C] == 'y') && (at > 0.18)) )
{
text_error("check at time! Don't fry probe !! ");
psg_abort(1);
}
if( dpwr > 50 )
{
printf("don't fry the probe, DPWR too large! ");
psg_abort(1);
}
if( dpwr2 > 50 )
{
printf("don't fry the probe, DPWR2 too large! ");
psg_abort(1);
}
if( pw > 20.0e-6 )
{
printf("dont fry the probe, pw too high ! ");
psg_abort(1);
}
if( pwC > 40.0e-6 )
{
printf("dont fry the probe, pwC too high ! ");
psg_abort(1);
}
if( pwN > 100.0e-6 )
{
printf("dont fry the probe, pwN too high ! ");
psg_abort(1);
}
if (ncyc > 24)
{
printf("CPMG heating! Reduce no. of ncyc!! ");
}
/* BEGIN ACTUAL PULSE SEQUENCE */
status(A);
rcvroff();
obspower(tpwr);
decpower(pwClvl);
dec2power(pwNlvl);
obsoffset(tof); /* Set the proton frequency to H2O */
dec2offset(dof2a); /* Set the nitrogen frequency to Nh2 or Nh */
decoffset(dof); /* Set the carbon frequency for decoupling */
txphase(zero);
decphase(zero);
dec2phase(zero);
delay(d1);
dec2rgpulse(pwN, zero, 0.0, 0.0); /*destroy N15 magnetization*/
zgradpulse(gzlvl0, 0.5e-3);
delay(grecov/2);
dec2rgpulse(pwN, one, 0.0, 0.0);
zgradpulse(0.7*gzlvl0, 0.5e-3);
initval(ncyc,v1);
lambdaN_int = ((2.0*lambdaN)/(2*ncyc));
dec2phase(zero);
delay(5.0e-4);
rcvroff();
rgpulse(pw, zero, 50.0e-6, 0.0);
assign(zero,v5);
if ( ncyc > 0 )
{
loop(v1,v14);
assign(v5,v6); /* v6 = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9*/
hlv(v5,v7); /* v7 = 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, */
hlv(v7,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 2, 2 */
mod2(v6,v6); /* v6 = 0, 1, 0, 1, 0, 1, 0, 1, 0, 1 */
mod2(v8,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 0, 0 */
add(v6,v8,v9); /* v9 = 0, 1, 0, 1, 1, 2, 1, 2, 0, 1 */
mod2(v9,v9); /* v9 = 0, 1, 0, 1, 1, 0, 1, 0, 0, 1*/
hlv(v8,v10); /* v7 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 2, 2 */
mod2(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1)*/
dbl(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
2, 2, 2, 2, 2, 2, 2, 2)*/
add(v9,v10,v11); /* v11 = 0, 1, 0, 1, 1, 0, 1, 0,
2, 3, 2, 3, 3, 2, 3, 2)*/
incr(v5); /* increment v5 by 1 */
txphase(v11);
decphase(v11);
delay(lambdaN_int);
sim3pulse(2*pw,0.0,2.0*pwN,v11,zero,v11,0.0,0.0);
delay(lambdaN_int);
endloop(v14);
txphase(t1);
}
rgpulse(pw,t1,0.0, 0.0);
txphase(one);
dec2phase(t2);
obspower(tpwrs);
shaped_pulse("rna_H2Osinc", pwHs, one, 5.0e-4, 0.0);
txphase(t11);
obspower(tpwr);
zgradpulse(gzlvl3,gt3);
delay(grecov);
dec2rgpulse(pwN,t2,0.0,0.0);
dec2phase(t9);
delay(tau1);
rgpulse(2.0*pw, t11, 0.0, 0.0);
delay(tau1);
delay(gt1 + grecov - 2.0*pw - SAPS_DELAY);
dec2rgpulse(2.0*pwN, t9, 0.0, 0.0);
dec2phase(t10);
zgradpulse(gzlvl1, gt1); /* 2.0*GRADIENT_DELAY */
delay(grecov - 2.0*GRADIENT_DELAY);
sim3pulse(pw,0.0,pwN,zero,zero,t10,0.0,0.0);
assign(zero,v5);
if ( ncyc > 0 )
{
loop(v1,v14);
assign(v5,v6); /* v6 = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9*/
hlv(v5,v7); /* v7 = 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, */
hlv(v7,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 2, 2 */
mod2(v6,v6); /* v6 = 0, 1, 0, 1, 0, 1, 0, 1, 0, 1 */
mod2(v8,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 0, 0 */
add(v6,v8,v9); /* v9 = 0, 1, 0, 1, 1, 2, 1, 2, 0, 1 */
mod2(v9,v9); /* v9 = 0, 1, 0, 1, 1, 0, 1, 0, 0, 1*/
hlv(v8,v10); /* v7 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 2, 2 */
mod2(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1)*/
dbl(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
2, 2, 2, 2, 2, 2, 2, 2)*/
add(v9,v10,v11); /* v11 = 0, 1, 0, 1, 1, 0, 1, 0,
2, 3, 2, 3, 3, 2, 3, 2)*/
incr(v5); /* increment v5 by 1 */
txphase(v11);
decphase(v11);
delay(lambdaN_int);
sim3pulse(2*pw,0.0,2.0*pwN,v11,zero,v11,0.0,0.0);
delay(lambdaN_int);
endloop(v14);
}
txphase(t12);
dec2phase(t3);
sim3pulse(pw, 0.0, pwN, t12, zero, t3, 0.0, 0.0);
txphase(zero);
dec2phase(zero);
if ( ncyc > 0 )
{
loop(v1,v14);
assign(v5,v6); /* v6 = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9*/
hlv(v5,v7); /* v7 = 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, */
hlv(v7,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 2, 2 */
mod2(v6,v6); /* v6 = 0, 1, 0, 1, 0, 1, 0, 1, 0, 1 */
mod2(v8,v8); /* v7 = 0, 0, 0, 0, 1, 1, 1, 1, 0, 0 */
add(v6,v8,v9); /* v9 = 0, 1, 0, 1, 1, 2, 1, 2, 0, 1 */
mod2(v9,v9); /* v9 = 0, 1, 0, 1, 1, 0, 1, 0, 0, 1*/
hlv(v8,v10); /* v7 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 2, 2 */
mod2(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1)*/
dbl(v10,v10); /* v10 = 0, 0, 0, 0, 0, 0, 0, 0,
2, 2, 2, 2, 2, 2, 2, 2)*/
add(v9,v10,v11); /* v11 = 0, 1, 0, 1, 1, 0, 1, 0,
2, 3, 2, 3, 3, 2, 3, 2)*/
incr(v5); /* increment v5 by 1 */
txphase(v11);
decphase(v11);
delay(lambdaN_int);
sim3pulse(2*pw,0.0,2.0*pwN,v11,zero,v11,0.0,0.0);
delay(lambdaN_int);
endloop(v14);
}
rgpulse(pw, zero, 0.0, 0.0);
txphase(t13);
delay((gt1/10.0) + grecov/2 - 0.5*pw + 2.0*GRADIENT_DELAY - SAPS_DELAY + 2*POWER_DELAY);
rgpulse(2.0*pw, t13, 0.0, 0.0);
decpower(dpwr);
dec2power(dpwr2); /* POWER_DELAY */
zgradpulse(icosel*gzlvl2, gt1/10.0); /* 2.0*GRADIENT_DELAY */
delay(grecov/2);
status(C);
setreceiver(t14);
}
pulsesequence() {
/* Internal variable declarations *************************/
int shapelist90,shapelist180,shapelistIR;
double nseg;
double seqtime,tau1,tau2,tau3,
te1_delay,te2_delay,te3_delay,
iti_delay, ti_delay,
tr_delay;
double kzero;
double freq90[MAXNSLICE], freq180[MAXNSLICE], freqIR[MAXNSLICE];
/* 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 vssc = v10; // Compressed steady-states
int vtrimage = v11; // Counts down from nt, trimage delay when 0
int vacquire = v12; // Argument for setacqvar, to skip steady state acquires
int vphase180 = v13; // phase of 180 degree refocusing pulse
/* Initialize paramaters **********************************/
init_mri();
/* Load external PE table ********************************/
if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) {
loadtable(petable);
} else {
abort_message("petable undefined");
}
seqtime = 0.0;
espmin = 0.0;
kzero = getval("kzero");
/* RF Power & Bandwidth Calculations **********************/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
/* Initialize gradient structures *************************/
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_slice(&ss_grad,"ss",thk); /* NOTE assume same band widths for p1 and p2 */
init_slice_butterfly(&ss2_grad,"ss2",thk,gcrush,tcrush);
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,WRITE,"gpe","tpe");
calc_slice(&ss_grad,&p1_rf,WRITE,"gss");
calc_slice(&ss2_grad,&p1_rf,WRITE,"");
calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr");
/* Equalize refocus and PE gradient durations *************/
calc_sim_gradient(&ror_grad,&null_grad,&ssr_grad,0.0,WRITE);
/* Create optional prepulse events ************************/
if (sat[0] == 'y') create_satbands();
if (fsat[0] == 'y') create_fatsat();
if (mt[0] == 'y') create_mtc();
if (ir[0] == 'y') {
init_rf(&ir_rf,pipat,pi,flipir,rof1,rof2);
calc_rf(&ir_rf,"tpwri","tpwrif");
init_slice_butterfly(&ssi_grad,"ssi",thk,gcrushir,tcrushir);
calc_slice(&ssi_grad,&ir_rf,WRITE,"gssi");
}
/* Set up frequency offset pulse shape list ********/
offsetlist(pss,ss_grad.ssamp, 0,freq90, ns,seqcon[1]);
offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]);
offsetlist(pss,ssi_grad.ssamp,0,freqIR, ns,seqcon[1]);
shapelist90 = shapelist(p1pat,ss_grad.rfDuration, freq90, ns,0,seqcon[1]);
shapelist180 = shapelist(p2pat,ss2_grad.rfDuration,freq180,ns,0,seqcon[1]);
shapelistIR = shapelist(pipat,ssi_grad.rfDuration,freqIR, ns,0,seqcon[1]);
/* same slice selection gradient and RF pattern used */
if (ss_grad.rfFraction != 0.5)
abort_message("ERROR %s: RF pulse must be symmetric (RF fraction = %.2f)",
seqfil,ss_grad.rfFraction);
if (ro_grad.echoFraction != 1)
abort_message("ERROR %s: Echo Fraction must be 1",seqfil);
/* Find sum of all events in each half-echo period ********/
tau1 = ss_grad.rfCenterBack + ssr_grad.duration + ss2_grad.rfCenterFront;
tau2 = ss2_grad.rfCenterBack + pe_grad.duration + ro_grad.timeToEcho;
tau3 = ro_grad.timeFromEcho + pe_grad.duration + ss2_grad.rfCenterFront;
espmin = 2*MAX(MAX(tau1,tau2),tau3); // Minimum echo spacing
if (minesp[0] == 'y') {
esp = espmin + 8e-6; // ensure at least 4us delays in both TE periods
putvalue("esp",esp);
}
else if (((espmin+8e-6)-esp) > 12.5e-9) {
abort_message("ERROR %s: Echo spacing too small, minimum is %.2fms\n",seqfil,(espmin+8e-6)*1000);
}
te1_delay = esp/2.0 - tau1; // Intra-esp delays
te2_delay = esp/2.0 - tau2;
te3_delay = esp/2.0 - tau3;
te = kzero*esp; // Return effective TE
putvalue("te",te);
/* Minimum TR **************************************/
/* seqtime is total time per slice */
seqtime = 2*4e-6 + ss_grad.rfCenterFront + etl*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;
if (ir[0] == 'y') {
/* Inter-IR delay */
if (ns > 1)
iti_delay = seqtime - ssi_grad.duration;
/* it is probably safe to assume that seqtime is always > the pulse widths */
else
iti_delay = 0;
/* Inversion Recovery */
timin = ssi_grad.rfCenterBack + ss_grad.rfCenterFront;
timin += 8e-6; // from sp1on/off and after 90 pulse power setting
timin += seqtime*(ns-1) + iti_delay;
if (ti < timin + 4e-6) // ensure at least a 4us delay
abort_message("%s: ti too short, minimum is %.2fms",seqfil,timin*1000);
/* Delay after the last IR pulse */
ti_delay = ti - timin;
/* force all slices to be acquired back-to-back, with a single TR delay at end */
trtype = 1;
}
else {
iti_delay = ti_delay = 0;
}
trmin = ns*(seqtime + 4e-6);
if (ir[0] == 'y') {
trmin += (4e-6 + ssi_grad.rfCenterFront + ti);
}
if (mintr[0] == 'y'){
tr = trmin;
putvalue("tr",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("TR too short. Minimum TR = %.2fms\n",trmin*1000);
}
tr_delay = (tr - trmin)/ns;
/* Set number of segments for profile or full image **********/
nseg = prep_profile(profile[0],nv/etl,&pe_grad,&per_grad);
/* Shift DDR for pro *******************************/
roff = -poffset(pro,ro_grad.roamp);
/* Calculate total acquisition time */
g_setExpTime(tr*(nt*nseg*getval("arraydim") + ssc) + trimage*getval("arraydim"));
/* Return parameters to VnmrJ */
putvalue("rgss",ss_grad.tramp); //90 slice ramp
if (ss2_grad.enableButterfly) { //180 slice ramps
putvalue("rcrush",ss2_grad.crusher1RampToCrusherDuration);
putvalue("rgss2",ss2_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgss2",ss2_grad.tramp);
}
if (ro_grad.enableButterfly) {
putvalue("rgro",ro_grad.crusher1RampToSsDuration);
}
else {
putvalue("rgro",ro_grad.tramp); //RO ramp
}
putvalue("tror",ror_grad.duration); //ROR duration
putvalue("rgror",ror_grad.tramp); //ROR ramp
putvalue("gpe",pe_grad.peamp); //PE max amp
putvalue("gss",ss_grad.ssamp);
putvalue("gro",ro_grad.roamp);
/* PULSE SEQUENCE *************************************/
initval(fabs(ssc),vssc); // Compressed steady-state counter
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);
obsoffset(resto);
delay(4e-6);
initval(nseg,vseg);
loop(vseg,vseg_ctr);
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* 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);
setacqvar(vacquire); // Turn on acquire when vacquire is zero
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
if(ir[0] == 'y') { /* IR for all slices prior to data acquisition */
obspower(ir_rf.powerCoarse);
obspwrf(ir_rf.powerFine);
delay(4e-6);
msloop(seqcon[1],ns,vms_slices,vms_ctr);
obl_shapedgradient(ssi_grad.name,ssi_grad.duration,0,0,ssi_grad.amp,NOWAIT);
delay(ssi_grad.rfDelayFront);
shapedpulselist(shapelistIR,ssi_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr);
delay(ssi_grad.rfDelayBack);
delay(iti_delay);
endmsloop(seqcon[1],vms_ctr);
delay(ti_delay);
}
msloop(seqcon[1],ns,vms_slices,vms_ctr);
/* 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,ror_grad.amp,0.0,-ssr_grad.amp,WAIT);
/* First half-TE delay ********************************/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(te1_delay);
peloop(seqcon[2],etl,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 *******************************/
/* Note, ss2_grad.amp is max gradient for butterfly shape; flat top = _.ssamp */
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);
/* Phase-encode gradient ******************************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,-pe_grad.increment,vpe_mult,WAIT);
/* Second half-TE period ******************************/
delay(te2_delay);
/* Readout gradient ************************************/
obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT);
delay(ro_grad.atDelayFront);
/* Acquire data ****************************************/
startacq(alfa);
acquire(np,1.0/sw);
endacq();
delay(ro_grad.atDelayBack);
/* Rewinding phase-encode gradient ********************/
/* Phase encode, refocus, and dephase gradient ******************/
pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT);
/* Second half-TE delay *******************************/
delay(te3_delay);
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);
/* Inter-image delay **********************************/
sub(ntrt,ct,vtrimage);
decr(vtrimage);
ifzero(vtrimage);
delay(trimage);
endif(vtrimage);
}
pulsesequence()
{
double predelay,seqtime,glimit,gshimlim;
double gbasex,gbasey,gbasez,del;
double shimno;
double gdaclim,shimscale;
double delx,dely,delz;
del = getval("del");
gbasex = getval("gbasex");
gbasey = getval("gbasey");
gbasez = getval("gbasez");
shimno = getval("shimno");
shimscale = getval("shimscale");
gshimlim = getval("gshimlim"); /* shim dac limit */
gdaclim = gshimlim*shimscale; /* gradient dac limit */
// initparms_sis();
initval(1, v1); /* no of complex point segments to acquire */
seqtime = at+pw+rof1+rof2+te+(2*trise);
predelay = tr - seqtime; /* predelay based on tr */
if (predelay <= 0.0) {
abort_message("%s: TR too short. Min TR = %f ms",seqfil,seqtime*1e3);
}
/* check if shim limit is exceeded */
if(shimno > 0) {
glimit = abs(del)+abs(gbasex);
if((glimit > gshimlim) || (glimit >= 1600))
abort_message("X shim limit exceeded, %5.0f %5.0f %5.0f %5.3f", glimit,gshimlim,del,shimscale);
glimit = abs(del)+abs(gbasey);
if((glimit > gshimlim) || (glimit >= 1600))
abort_message("Y shim limit exceeded, %5.0f", glimit);
glimit = abs(del)+abs(gbasez);
if((glimit > gshimlim) || (glimit >= 1600))
abort_message("Z shim limit exceeded, %5.0f", glimit);
}
delx = 0; dely = 0; delz = 0;
if(shimno == 1) delx = del;
if(shimno == 2) dely = del;
if(shimno == 3) delz = del;
settable(t1,4,ph1); /* initialize phase tables and variables */
getelem(t1,ct,v7); /* 90 deg pulse phase */
settable(t4,4,phr);
getelem(t4,ct,oph); /* receiver phase */
initval(1,v3);
initval(1,v4);
initval(1,v5);
initval(ssc,v6);
assign(zero,v2);
status(A);
rotate();
obspower(tpwr);
delay(4e-6);
loop(v6,v8); /* steady state dummy scans */
delay(2*trise);
delay(predelay);
pulse(pw,v7);
delay(te);
delay(at);
endloop(v8);
loop(v1,v2); /* compressed acqn not used */
sub(v2,v3,v9); /* v9-v11 not used */
assign(zero,v10);
assign(zero,v11);
gradient('x',gbasex+delx);
gradient('y',gbasey+dely);
gradient('z',gbasez+delz);
delay(trise);
delay(predelay);
pulse(pw,v7);
delay(te);
startacq(alfa);
acquire(np,1.0/sw);
endacq();
endloop(v2);
delay(trise);
zero_all_gradients();
}
pulsesequence()
{
int i;
double df;
double f;
double *freqs;
double fstart;
double tunesw;
int ppfreq; /* Samples per frequency */
int nfreqs;
int chan;
int attn;
chan = 1;
if (find("tupwr") == -1){ /* Optional parameter "tupwr" sets tune pwr */
attn = 60;
}else{
attn = (int)getval("tupwr");
}
tunesw = getval( "tunesw" );
if (tunesw < 0.0)
tunesw = 1.0e7;
if (find("tuppf") == -1) { /* Optional "tuppf" sets Points Per Frequency */
ppfreq = 2;
} else {
ppfreq = getval( "tuppf" );
}
/*
* Start with a sweep of tunesw, centered on sfrq.
* sfrq is in units of MHz; freqs[] array must be in MHz.
* All other frequencies are in Hz.
*/
fstart = sfrq * 1e6 - tunesw / 2;
nfreqs = np / (2 * ppfreq);
freqs = (double *)malloc(sizeof(double) * nfreqs);
df = tunesw / (nfreqs - 1);
for (i=0, f=fstart; i<nfreqs; i++, f+=df){
freqs[i] = f * 1e-6;
}
create_freq_list(freqs, nfreqs, TODEV, 0);
free(freqs);
/* Begin pulse sequence */
initval((double)nfreqs, v1);
/* Start tune mode */
/*
putcode(TUNE_START);
putcode(chan);
putcode(attn);
delay(0.01);
*/
rcvron();
delay(0.02);
loop(v1, v2);{
vfreq(0, v2);
/* delay(0.0007); */
delay(0.0005);
/* Note: too short delay in acq gives "pts acquired 0 less than np" */
acquire((double)(2 * ppfreq), 0.0005);
/*acquire((double)(2 * ppfreq), 0.003);*/
}endloop(v2);
/* BEWARE: adding 1 ms delay here can delay sending data back by 2-3 sec!
/*delay(0.001);*/
}
int main(int argc, char *argv[]) {
int simpleSocket = 0;
int simplePort = 0;
int returnStatus = 0;
char buffer[256] = "";
struct sockaddr_in simpleServer;
struct hostent *server;
int LOL1;
char LOL[256];
int temp;
char stringtemp[1024];
if (6 != argc) {
fprintf(stderr, "Usage: %s <server> <port> <sign addr> <color> \"message\"\n", argv[0]);
exit(1);
}
/* create a streaming socket */
simpleSocket = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP);
if (simpleSocket == -1) {
fprintf(stderr, "Could not create a socket!\n");
exit(1);
}
else {
fprintf(stdout, "Socket created!\n");
}
/* retrieve the port number for connecting */
simplePort = atoi(argv[2]);
printf(" %s %s %s %s %s ",argv[1],argv[2],argv[3],argv[4],argv[5]);
// server = gethostbyname(argv[1]); is the magical dns lookup
server = gethostbyname(argv[1]);
/* setup the address structure */
/* use the IP address sent as an argument for the server address */
bzero(&simpleServer, sizeof(simpleServer));
simpleServer.sin_family = AF_INET;
//inet_addr(server, &simpleServer.sin_addr.s_addr); is outdated
bcopy((char *)server->h_addr,
(char *)&simpleServer.sin_addr.s_addr,
server->h_length);
simpleServer.sin_port = htons(simplePort);
/* connect to the address and port with our socket */
returnStatus = connect(simpleSocket, (struct sockaddr *)&simpleServer, sizeof(simpleServer));
if (returnStatus == 0) {
fprintf(stderr, "Connect successful!\n");
}
else {
fprintf(stderr, "Could not connect to address!\n");
close(simpleSocket);
exit(1);
}
/* get the message from the server */
temp=sprintf(stringtemp,"AZ%s",argv[3]);
printf("%s",stringtemp);
temp=write(simpleSocket,stringtemp,temp);
read(simpleSocket, buffer, sizeof(buffer));
printf("%s \n",buffer);
temp=sprintf(stringtemp,"AA");
temp=write(simpleSocket,stringtemp,temp);
temp=sprintf(stringtemp,"%c b %c%c",smf,fontmode,largetimesfont); //Set the sign to scroll on all lines
// and largetimes font in to buffer
temp=write(simpleSocket,stringtemp,temp); //write buffer to mainfd (which should be the serial port see signfp.c)
if (strcmp(argv[4],"red")==0){
temp=sprintf(stringtemp,"%c%c",cc,red);// set the color code
temp=write(simpleSocket,stringtemp,temp); //and shove it out the door
}else if (strcmp(argv[4],"green")==0){
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
}else if (strcmp(argv[4],"amber")==0){
temp=sprintf(stringtemp,"%c%c",cc,amb);
temp=write(simpleSocket,stringtemp,temp);
}else
{
temp=sprintf(stringtemp,"%c%c",cc,green);
temp=write(simpleSocket,stringtemp,temp);
}
temp=strlen(argv[5]); //count the argv2 which should be a string
temp=write(simpleSocket,argv[5],temp); // and shove x chars out the door
temp=sprintf(stringtemp," %c",end); // tell the sign were done
temp=write(simpleSocket,stringtemp,temp); // output it
usleep(250);
endloop(simpleSocket);
returnStatus = read(simpleSocket, buffer, sizeof(buffer));
if ( returnStatus > 0 ) {
printf("%d: %s", returnStatus, buffer);
} else {
fprintf(stderr, "Return Status = %d \n", returnStatus);
}
close(simpleSocket);
return 0;
}