pulsesequence()
{
/* Internal variable declarations *************************/
/*timing*/
double tr_delay;
double te_d1,te_d2,te_d3; /* delays */
double tau1,tau2,tau3;
/*voxel crusher multipliers */
double fx,fy,fz;
/*localization parameters*/
double freq1,freq2,freq3;
double vox1_cr,vox2_cr, vox3_cr;
int nDim;
double rprof,pprof,sprof;
char profile_vox[MAXSTR],profile_ovs[MAXSTR];
double restol, resto_local, csd_ppm;
/*phase cycle****/
int counter,noph;
char autoph[MAXSTR], pcflag[MAXSTR];
int rf1_phase[64] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3};
int rf2_phase[64] = {0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,
0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3,0,0,0,0,2,2,2,2,1,1,1,1,3,3,3,3};
int rf3_phase[64] = {0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,
0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3,0,2,1,3};
/* Initialize paramaters **********************************/
init_mri(); //this gets all the parameters that are defined in acqparms.h, etc
get_wsparameters();
get_ovsparameters();
rprof = getval("rprof");
pprof = getval("pprof");
sprof = getval("sprof");
//read the crusher factors that are designed to create grad on the same axis without refoc
fx=getval("fx");
fy=getval("fy");
fz=getval("fz");
getstr("profile_vox",profile_vox);
getstr("profile_ovs",profile_ovs);
/*set voxel sizes for butterfly crushers to 10^6 to set the slice portion to zero ***/
vox1_cr=1000000;
vox2_cr=1000000;
vox3_cr=1000000;
/***** RF power initialize *****/
init_rf(&p1_rf,p1pat,p1,flip1,rof1,rof2);
init_rf(&p2_rf,p2pat,p2,flip2,rof1,rof2);
/***** Initialize gradient structs *****/
trampfixed=trise; //rise time =trise
tcrush=granularity(tcrush,GRADIENT_RES); //this is to avoid the granularity errors
//if trampfixed is used, rise time needs to be checked
if (trise*2>tcrush){
abort_message("tcrush too short. Minimum tcrush = %fms \n",1000*trise*2);
}
if (gcrush>gmax){
abort_message("gcrush too large. Max gcrush = %f \n",gmax*0.95);
}
init_slice_butterfly(&vox1_grad,"vox1",vox1,gcrush,tcrush);
init_slice_butterfly(&vox2_grad,"vox2",vox2,gcrush,tcrush);
init_slice_butterfly(&vox3_grad,"vox3",vox3,gcrush,tcrush);
init_slice_butterfly(&vox1_crush,"vox1_crush",vox1_cr,gcrush,tcrush);
init_slice_butterfly(&vox2_crush,"vox2_crush",vox2_cr,gcrush,tcrush);
init_slice_butterfly(&vox3_crush,"vox3_crush",vox3_cr,gcrush,tcrush);
if (profile_vox[0] == 'y') {
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
}
/***** RF and Gradient calculations *****/
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
calc_slice(&vox1_grad,&p2_rf,WRITE,"gvox1");
calc_slice(&vox2_grad,&p2_rf,WRITE,"gvox2");
calc_slice(&vox3_grad,&p2_rf,WRITE,"gvox3");
calc_slice(&vox1_crush,&p2_rf,WRITE,"vox1_crush");
calc_slice(&vox2_crush,&p2_rf,WRITE,"vox2_crush");
calc_slice(&vox3_crush,&p2_rf,WRITE,"vox3_crush");
if (profile_vox[0] == 'y') {
calc_readout(&ro_grad,WRITE,"gro","sw","at");
putvalue("gro",ro_grad.roamp); // RO grad
calc_readout_refocus(&ror_grad,&ro_grad,WRITE,"gror");
putvalue("tror",ror_grad.duration); // ROR duration
}
//set all gradients along a particular direction to zero if profile is needed
if (profile_ovs[0]=='y'){
if (rprof==1) {
vox1_grad.amp=0; //set slice selection in read direction to none
vox3_crush.amp=0; // set corresponding crusher gradients to none
}
else if(pprof==1) {
vox2_grad.amp=0;
vox1_crush.amp=0;
}
else if(sprof==1) {
vox3_grad.amp=0;
vox2_crush.amp=0;
}
}
/* Optional OVS and Water Suppression */
if (ovs[0] == 'y') create_ovsbands();
if (sat[0] == 'y') create_satbands();
if (ws[0] == 'y') create_watersuppress();
//Read in parameters not defined in acqparms.h and sglHelper
nDim=getval("nDim");
restol=getval("restol"); //local frequency offset
roff=getval("roff"); //receiver offset
csd_ppm=getval("csd_ppm"); //chemical shift displacement factor
noph=getval("noph");
getstr("autoph",autoph);
getstr("pcflag",pcflag);
settable(t3,noph,rf1_phase);
settable(t2,noph,rf2_phase);
settable(t1,noph,rf3_phase);
/* tau1, tau2 and tau3 are sums of all events in TE*/
tau1 = vox1_grad.rfCenterFront+GDELAY+rof2;
tau2 = vox1_grad.rfCenterBack + vox1_grad.rfCenterFront+2*(GDELAY+rof2);
tau3 = vox3_grad.rfCenterBack+GDELAY+rof2;
temin = tau1+5.0*tau2+tau3;
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
if (te < temin) {
abort_message("te too short. Minimum te = %.2f ms\n",temin*1000);
}
/***** Calculate TE delays *****/
te_d1 = te/12.0 - tau1+GDELAY;
te_d2 = te/6.0 - tau2+2*(GDELAY+rof2);
te_d3 = te/12.0 - tau3+GDELAY+rof2;
//Calculate delta from resto to include local frequency line+ chemical shift offset
resto_local=resto-restol;
/***** Min TR *****/
trmin = GDELAY + p1 + te + at+rof1+rof2;
if (ws[0] == 'y') trmin += wsTime;
if (ovs[0] == 'y') trmin += ovsTime;
if (sat[0] == 'y') trmin += satTime;
if (profile_vox[0] == 'y') trmin += ror_grad.duration + ro_grad.duration - at;
if (mintr[0] == 'y') {
tr = trmin; // ensure at least 4us between gradient events
putvalue("tr",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("TR too short. Minimum TR= %.2fms\n",trmin*1000);
}
/***** Calculate TR delay *****/
tr_delay = tr - trmin;
/* Frequency offsets */
freq1 = poffset(pos1,vox1_grad.ssamp); // First RF pulse
freq2 = poffset(pos2,vox2_grad.ssamp); // Second RF pulse
freq3 = poffset(pos3,vox3_grad.ssamp); // Third RF pulse
freq1=freq1-csd_ppm*sfrq;
freq2=freq2-csd_ppm*sfrq;
freq3=freq3-csd_ppm*sfrq;
/* Frequency offsets */
if (profile_vox[0] == 'y') {
/* Shift DDR for pro ************************************/
roff = -poffset(pro,ro_grad.roamp);
}
/* Put gradient information back into VnmrJ parameters */
putvalue("gvox1",vox1_grad.ssamp);
putvalue("gvox2",vox2_grad.ssamp);
putvalue("gvox3",vox3_grad.ssamp);
putvalue("rgvox1",vox1_grad.tramp);
putvalue("rgvox2",vox2_grad.tramp);
putvalue("rgvox3",vox3_grad.tramp);
sgl_error_check(sglerror);
if (ss<0) g_setExpTime(tr*(nt-ss)*arraydim);
else g_setExpTime(tr*(nt*arraydim+ss));
/**[2.7] PHASE CYCLING ******************************************************/
assign(zero, oph);
counter=(double)nt*(ix-1);
if (autoph[0] == 'n') counter=0.0; //only goes through nt, if 'y' goes through nt*array
initval(counter,v1);
initval(noph,v3);
add(v1,ct,v2);
modn(v2,v3,v2);
/* Full phase cycling requires 64 steps*/
if (pcflag[0] == 'n') {
assign(zero,v2);
getelem(t1,v2,v10);
getelem(t2,v2,v11);
getelem(t3,v2,v12);
}
else
{
getelem(t1,v2,v10);
getelem(t2,v2,v11);
getelem(t3,v2,v12);
}
/*Start of the sequence*/
obsoffset(resto_local); // need it here for water suppression to work
delay(GDELAY);
rot_angle(vpsi,vphi,vtheta);
if (ticks) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
/* TTL scope trigger **********************************/
//sp1on(); delay(4e-6); sp1off();
/* Saturation bands ***********************************/
if (ovs[0] == 'y') ovsbands();
if (sat[0] == 'y') satbands();
/* Water suppression **********************************/
if (ws[0] == 'y') watersuppress();
/* Slice selective 90 degree RF pulse *****/
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(GDELAY);
shaped_pulse(p1pat,p1,zero,rof1,rof2);
/* start localization */
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
if (nDim > 2.5) {
delay(te_d1); //this is at least GDELAY == 4 us
obl_shaped3gradient(vox1_grad.name,vox1_crush.name,"",vox1_grad.duration,vox1_grad.amp,fy*vox1_crush.amp,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
shapedpulseoffset(p2_rf.pulseName,vox1_grad.rfDuration,v12,rof1,rof2,freq1);
delay(vox1_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient (vox1_grad.name,vox1_crush.name,"",vox1_grad.duration,vox1_grad.amp,fy*0.777*vox1_crush.amp,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
shapedpulseoffset(p2_rf.pulseName,vox1_grad.rfDuration,v12,rof1,rof2,freq1);
delay(vox1_grad.rfDelayBack);
delay(te_d2);
}
if (nDim > 1.5) { //this is 2nd slice selection
obl_shaped3gradient("",vox2_grad.name,vox2_crush.name,vox2_grad.duration,0,vox2_grad.amp,fz*vox2_crush.amp,NOWAIT);
delay(vox2_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
shapedpulseoffset(p2_rf.pulseName,vox2_grad.rfDuration,v11,rof1,rof2,freq2);
delay(vox2_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient("",vox2_grad.name,vox2_crush.name,vox2_grad.duration,0,vox2_grad.amp,fz*0.777*vox2_crush.amp,NOWAIT);
delay(vox2_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
shapedpulseoffset(p2_rf.pulseName,vox2_grad.rfDuration,v11,rof1,rof2,freq2);
delay(vox2_grad.rfDelayBack);
delay(te_d2);
}
if (nDim > 0.5){ //this is 3rd slice selection
obl_shaped3gradient(vox3_crush.name,"",vox3_grad.name,vox3_grad.duration,fx*vox3_crush.amp,0,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
shapedpulseoffset(p2_rf.pulseName,vox3_grad.rfDuration,v10,rof1,rof2,freq3);
delay(vox3_grad.rfDelayBack);
delay(te_d2);
obl_shaped3gradient(vox3_crush.name,"",vox3_grad.name,vox3_grad.duration,fx*vox3_crush.amp,0,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
shapedpulseoffset(p2_rf.pulseName,vox3_grad.rfDuration,v10,rof1,rof2,freq3);
delay(vox3_grad.rfDelayBack);
delay(te_d3);
}
if (profile_vox[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,
-rprof*ror_grad.amp,-pprof*ror_grad.amp,-sprof*ror_grad.amp,WAIT);
delay(GDELAY);
obl_shapedgradient(ro_grad.name,ro_grad.duration,
rprof*ro_grad.amp,pprof*ro_grad.amp,sprof*ro_grad.amp,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
} else {
startacq(alfa);
acquire(np,1.0/sw);
endacq();
}
delay(tr_delay);
pulsesequence()
{
/***** Internal variable declarations *****/
int shapelist1,shapelist2,shapelist3; /* pulse shapes (lists) */
double freq1,freq2,freq3,ws_delta;
double rprof,pprof,sprof;
double restol, resto_local,csd_ppm;
char profile_ovs[MAXSTR];
char profile_vox[MAXSTR];
int wsfirst; //wsfirst makes ws unit to be exececuted first
int isis;
int counter,noph;
char autoph[MAXSTR],pcflag[MAXSTR];
/* sequence timing variables */
double te_delay1, te_delay2, newdelay,tr_delay, tm_delay;
double tau1=0, tau2=0;
/* Extra crushers */
double gcrushtm,tcrushtm;
double ky;
double vox3_cr, vox3r_cr;
double gcrush_end, tcrush_end;
/*extra ws pulse flag*/
char ws_tm[MAXSTR];
double wsflipftm;
double tmwstpwr,tmwstpwrf;
init_mri();
noph=(int)getval("noph");
isis=(int)getval("isis");
int inv1[32]= {0, 0, 0, 0, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3};//excitation pulse
int inv2[32]= {0, 0, 1, 1, 2, 2, 3, 3, 0, 0, 1, 1, 2, 2, 3, 3, 1, 1, 2, 2, 3, 3, 0, 0, 1, 1, 2, 2, 3, 3, 0, 0}; //refocusing pulse
int inv3[32]= {0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3};//inversion pulse
int phrec[32]= {0, 2, 2, 0, 2, 0, 0, 2, 0, 2, 2, 0, 2, 0, 0, 2, 1, 3, 3, 1, 3, 1, 1, 3, 1, 3, 3, 1, 3, 1, 1, 3};// rec phase
int phrec0[32]= {0, 0, 2, 2, 2, 2, 0, 0, 0, 0, 2, 2, 2, 2, 0, 0, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1};// rec phase for non-isis
/***** Real-time variables used in this sequence *****/
int vinv1 = v1; // on/off flag first inversion pulse
int vms = v5; // dummy shapedpulselist slice counter (= one)
get_ovsparameters();
get_wsparameters();
rprof = getval("rprof");
pprof = getval("pprof");
sprof = getval("sprof");
ky=getval("ky");
getstr("autoph",autoph);
getstr("pcflag",pcflag);
getstr("profile_ovs",profile_ovs);
getstr("profile_vox",profile_vox);
wsfirst=(int)getval("wsfirst");
restol=getval("restol"); //local frequency offset
roff=getval("roff"); //receiver offset
csd_ppm=getval("csd_ppm"); //chemical shift displacement factor
gcrushtm = getval("gcrushtm");
tcrushtm = getval("tcrushtm");
wsflipftm = getval("wsflipftm");
getstr("ws_tm",ws_tm);
ws_delta=getval("ws_delta");
vox3_cr=1000000;
/***** RF power calculations *****/
shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2);
shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2);
shape_rf(&p3_rf,"p3",p3pat,p3,flip3,rof1,rof2);
shape_rf(&p4_rf,"p4",p4pat,p4,flip4,rof1,rof2);
p4_rf.flipmult=wsflipftm;
calc_rf(&p1_rf,"tpwr1","tpwr1f");
calc_rf(&p2_rf,"tpwr2","tpwr2f");
calc_rf(&p3_rf,"tpwr3","tpwr3f");
calc_rf(&p4_rf,"tpwr4","tpwr4f");
// wsfpwrtm=p4_rf.powerFine*wsflipftm; /* ws fine RF power */
trampfixed=trise; //rise time =trise
tcrush=granularity(tcrush,GRADIENT_RES); //this is to avoid the granularity errors
//if trampfixed is used, rise time needs to be checked
if (trise*2>tcrush){
abort_message("tcrush too short. Minimum tcrush = %fms \n",1000*trise*2);
}
if (gcrush>gmax){
abort_message("gcrush too large. Max gcrush = %f \n",gmax*0.95);
}
init_slice(&vox1_grad,"vox1",vox1);
init_slice(&vox2_grad,"vox2",vox2);
init_slice_butterfly(&vox3_crush,"vox3_crush",vox3_cr,gcrush,tcrush);
init_slice_butterfly(&vox3r_crush,"vox3r_crush",vox3_cr,gcrush,tcrush);
init_slice_butterfly(&vox3_grad,"vox3",vox3,gcrush,tcrush);
init_generic(&tmcrush_grad,"tmcrush",gcrushtm,tcrushtm); //crusher grad during tm
if (profile_vox[0] == 'y') {
init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro);
init_readout_refocus(&ror_grad,"ror");
}
/***** Gradient calculations *****/
calc_slice(&vox1_grad,&p1_rf,WRITE,"vox1_grad");
calc_slice(&vox2_grad,&p2_rf,WRITE,"vox2_grad");
calc_slice(&vox3_grad,&p3_rf,NOWRITE,"");
calc_slice(&vox3_crush,&p3_rf,WRITE,"vox3_crush");
calc_slice(&vox3r_crush,&p3_rf,NOWRITE,"");
vox3r_crush.crusher1Moment0 -= vox2_grad.m0ref; //only now can re-calculate the moment
vox3r_crush.crusher1CalcFlag=AMPLITUDE_FROM_MOMENT_DURATION_RAMP;
calc_slice(&vox3r_crush,&p3_rf,WRITE,"vox3r_crush");
vox3_grad.crusher2Moment0 *= vox3_grad.m0def/vox3_grad.m0ref*ky; //only now can re-calculate the moment
vox3_grad.crusher2CalcFlag=AMPLITUDE_FROM_MOMENT_DURATION_RAMP;
calc_slice(&vox3_grad,&p3_rf,WRITE,"vox3_grad");
calc_generic(&tmcrush_grad,WRITE,"","");
if (profile_vox[0] == 'y') {
calc_readout(&ro_grad,WRITE,"gro","sw","at");
putvalue("gro",ro_grad.roamp); // RO grad
calc_readout_refocus(&ror_grad,&ro_grad,WRITE,"gror");
putvalue("tror",ror_grad.duration); // ROR duration
}
if (profile_ovs[0]=='y'){
if (rprof==1) {
vox1_grad.amp=0;
}
else if(pprof==1) {
vox2_grad.amp=0;
}
else if(sprof==1) {
vox3_grad.amp=0;
}
}
/***** Check nt is a multiple of 2 *****/
if (ix == 1) {
if ((int)nt%2 != 0)
text_message("WARNING: SPECIAL requires 2 steps. Set nt as a multiple of 2\n");
}
/* Optional Outer Volume Suppression */
if (ovs[0] == 'y') create_ovsbands();
if (sat[0] == 'y') create_satbands();
/* Optional Water Suppression */
if (ws[0] == 'y') create_watersuppress();
/***** Set up frequency offset pulse shape list *****/
offsetlist(&pos1,vox1_grad.ssamp,0,&freq1,1,'s');
offsetlist(&pos2,vox2_grad.ssamp,0,&freq2,1,'s');
offsetlist(&pos3,vox3_grad.ssamp,0,&freq3,1,'s');
if (profile_ovs[0]=='y'&& sprof==1) freq3=0.0;
if (profile_ovs[0]=='y'&& pprof==1) freq2=0.0;
if (profile_ovs[0]=='y'&& rprof==1) freq1=0.0;
freq1=freq1-csd_ppm*sfrq;
freq2=freq2-csd_ppm*sfrq;
freq3=freq3-csd_ppm*sfrq;
shapelist1 = shapelist(p1_rf.pulseName,vox1_grad.rfDuration,&freq1,1,vox1_grad.rfFraction,'s');
shapelist2 = shapelist(p2_rf.pulseName,vox2_grad.rfDuration,&freq2,1,vox2_grad.rfFraction,'s');
shapelist3 = shapelist(p3_rf.pulseName,vox3_grad.rfDuration,&freq3,1,vox3_grad.rfFraction,'s');
/* Calculate delta from resto to include local frequency line + chemical shift offset */
resto_local=resto-restol;
/* Frequency offsets */
if (profile_vox[0] == 'y') {
/* Shift DDR for pro ************************************/
roff = -poffset(pro,ro_grad.roamp);
}
/* Set tables */
/* Real time variables for inversion pulses */
settable(t1,noph,inv1);
settable(t2,noph,inv2);
settable(t3,noph,inv3);
/* Phase cycle for excitation pulse and receiver */
if (isis!=1) settable(t4,noph,phrec0);
else settable(t4,noph,phrec);
/* shapedpulselist variable */
assign(one,vms);
/* Put gradient information back into VnmrJ parameters */
putvalue("gvox1",vox1_grad.ssamp);
putvalue("gvox2",vox2_grad.ssamp);
putvalue("gvox3",vox3_grad.ssamp);
putvalue("rgvox1",vox1_grad.tramp);
putvalue("rgvox2",vox2_grad.tramp);
putvalue("rgvox3",vox3_grad.tramp);
sgl_error_check(sglerror);
if (ss<0) g_setExpTime(trmean*(nt-ss)*arraydim);
else g_setExpTime(tr*(ntmean*arraydim+ss));
/* PULSE SEQUENCE *************************************/
/* Real time variables for inversion pulses */
counter=(double)nt*(ix-1);
if (autoph[0] == 'n') counter=0.0;
initval(counter,v11);
initval(noph,v13); //v13=number of phase cycling steps
add(v11,ctss,v12); //v12=counter
modn(v12,v13,v12); //v12 runs from 1:v13
getelem(t1,v12,v8); /* 90 DEG. SPIN ECHO PULSE */
getelem(t2,v12,v9); /* 180 DEG. SPIN ECHO P. */
getelem(t3,v12,v10); /* ISIS 180 DEG. ADIAB. PULSE */
getelem(t4,v12,oph); /*RCVR PHASE*/
mod2(v12,vinv1); // this controls 1D isis on, off, on, of... up to noph(=32)
/****************************************************/
/* Sequence Timing **********************************/
/****************************************************/
/* Min TE ******************************************/
tau1 = vox2_grad.rfCenterBack + vox3_grad.rfCenterFront;
tau2 = vox3_grad.rfCenterBack+alfa;
temin = 2*(MAX(tau1,tau2) + 4e-6); /* have at least 4us between gradient events */
if (minte[0] == 'y') {
te = temin;
putvalue("te",te);
}
else if (te < temin) {
abort_message("TE too short. Minimum TE = %.2fms\n",temin*1000);
}
te_delay1 = te/2 - tau1;
te_delay2 = te/2 - tau2;
printf("te delay1 is %f", te_delay1);
printf("te delay2 is %f", te_delay2);
/***************************************************/
/* Min TM ******************************************/
if (ws_tm[0] == 'y') {
tau1 = vox1_grad.rfCenterBack + rof1+rof2+p4_rf.rfDuration+tmcrush_grad.duration + 4e-6 + vox2_grad.rfCenterFront;
}
else tau1 = vox1_grad.rfCenterBack + rof2+tmcrush_grad.duration + 4e-6 + vox2_grad.rfCenterFront;
tmmin = tau1 + 4e-6; /* have at least 4us between gradient events */
if (mintm[0] == 'y') {
tm = tmmin;
putvalue("tm",tm);
}
else if (tm < tmmin) {
abort_message("TM too short. Minimum TM = %.2fms\n",tmmin*1000);
}
tm_delay = (tm - tau1);
/* Relaxation delay ***********************************/
/***** Min TR *****/
trmin = vox1_grad.rfCenterFront + tm + te+alfa + at + 20e-6;
if (profile_vox[0] == 'y') trmin += ror_grad.duration + ro_grad.duration - at;
if (ws[0] == 'y') trmin += wsTime;
if (ovs[0] == 'y') trmin += ovsTime;
if (sat[0] == 'y') trmin += satTime;
if (mintr[0] == 'y') {
tr = trmin;
putCmd("setvalue('tr',%f,'current')\n",tr);
}
if ((trmin-tr) > 12.5e-9) {
abort_message("tr too short. Minimum tr = %.2f ms\n",(trmin)*1000);
}
/***** Calculate TR delay *****/
tr_delay = tr - trmin;
/**Sequence Begin**/
status(A);
obsoffset(resto_local);
delay(4e-6);
set_rotation_matrix(vpsi,vphi,vtheta);
if (ticks > 0) {
xgate(ticks);
grad_advance(gpropdelay);
delay(4e-6);
}
/* TTL scope trigger **********************************/
sp1on(); delay(4e-6); sp1off();
/* Saturation bands ***********************************/
if (ovs[0] == 'y') ovsbands();
if (sat[0] == 'y') satbands();
/* Post OVS water suppression *************************/
if (ws[0] == 'y') watersuppress();
/* First inversion pulse *****/
if (isis >= 1){ /*for the ISIS pulse on,off,on,off... or on,on,on,on... */
obspower(p1_rf.powerCoarse);
obspwrf(p1_rf.powerFine);
delay(4e-6);
if (isis == 1) /* for ISIS on,off,on,off,... */{
ifzero(vinv1);
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
shapedpulselist(shapelist1,vox1_grad.rfDuration,v10,rof1,rof2,'s',vms);
delay(vox1_grad.rfDelayBack);
elsenz(vinv1);
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,WAIT);
endif(vinv1);
}
else { /* for ISIS on,on,on,on...*/
obl_shapedgradient(vox1_grad.name,vox1_grad.duration,vox1_grad.amp,0,0,NOWAIT);
delay(vox1_grad.rfDelayFront);
shapedpulselist(shapelist1,vox1_grad.rfDuration,v10,rof1,rof2,'s',vms);
delay(vox1_grad.rfDelayBack);
}
}
else delay(vox1_grad.duration); //this is for isis off,off,off,off
/* tm delay before excitation pulse *****/
/* Optional TM water suppression ***********************/
if (ws_tm[0] == 'y') {
if (wsrf[0]=='y') {
obspower(p4_rf.powerCoarse);
obspwrf(p4_rf.powerFine);
delay(4e-6);
shapedpulseoffset(p4_rf.pulseName,p4_rf.rfDuration,zero,rof1,rof2,ws_delta);
}
else delay(p4_rf.rfDuration+rof1+rof2);
} //end of ws_tm='y' condition
delay(tm_delay);
/* TM Gradient crusher ********************************/
obl_shapedgradient(tmcrush_grad.name,tmcrush_grad.duration,0,0,tmcrush_grad.amp,WAIT);
/* 90 degree excitation pulse *****/
obspower(p2_rf.powerCoarse);
obspwrf(p2_rf.powerFine);
delay(4e-6);
obl_shapedgradient(vox2_grad.name,vox2_grad.duration,0,vox2_grad.amp,0,NOWAIT);
delay(vox2_grad.rfDelayFront);
shapedpulselist(shapelist2,vox2_grad.rfDuration,v8,rof1,rof2,'s',vms);
delay(vox2_grad.rfDelayBack);
delay(te_delay1);
/* 180 degree pulse ********************************/
obspower(p3_rf.powerCoarse);
obspwrf(p3_rf.powerFine);
delay(4e-6);
obl_shaped3gradient (vox3_crush.name,vox3r_crush.name,vox3_grad.name,vox3_grad.duration,vox3_crush.amp,vox3r_crush.amp,vox3_grad.amp,NOWAIT);
delay(vox3_grad.rfDelayFront);
shapedpulselist(shapelist3,vox3_grad.rfDuration,v9,rof1,rof2,'s',vms);
delay(vox3_grad.rfDelayBack);
delay(te_delay2);
//acquisition starts
if (profile_vox[0] == 'y') {
obl_shapedgradient(ror_grad.name,ror_grad.duration,
-rprof*ror_grad.amp,-pprof*ror_grad.amp,-sprof*ror_grad.amp,WAIT);
delay(4e-6);
obl_shapedgradient(ro_grad.name,ro_grad.duration,
rprof*ro_grad.amp,pprof*ro_grad.amp,sprof*ro_grad.amp,NOWAIT);
delay(ro_grad.atDelayFront);
startacq(alfa);
acquire(np,1.0/sw);
delay(ro_grad.atDelayBack);
endacq();
} else {
startacq(alfa);
acquire(np,1.0/sw);
endacq();
}
delay(tr_delay);
}