pulsesequence() { /* declaration of SGL kernel structures */ SGL_KERNEL_INFO_T read, phase, slice, ss_pre, ss_post; /* declaration of internal variables */ double freqlist[MAXNSLICE]; double pe_steps; int shapelist1, table; double xtime, grad_duration, ror_pad,rod_pad; double temp_tr; double readAmp, phaseAmp, sliceAmp; double tepad, tepad2, temin2, htrmin, delayToRF, delayRFToAcq, delayAcqToRF; double rof_pad, delRof; double sliceRephTrim, sliceDephTrim; double readRephTrim, readDephTrim; int rfPhase[2] = {0,2}; /* declaration of realtime variables */ int vpe_steps = v1; int vpe_ctr = v2; int vms_slices = v3; int vms_ctr = v4; int vpe_offset = v5; int vpe_index = v6; int vss = v7; int vssc = v8; int vacquire = v9; int vphase = v10; settable(t2,2,rfPhase); /* setup phase encoding order */ table = set_pe_order(); init_mri(); if( (sliceRephTrim = getvalnwarn("sliceRephTrim")) == 0.0 ) { sliceRephTrim = 1.0; } if( (sliceDephTrim = getvalnwarn("sliceDephTrim")) == 0.0 ) { sliceDephTrim = 1.0; } if( (readRephTrim = getvalnwarn("readRephTrim")) == 0.0 ) { readRephTrim = 1.0; } if( (readDephTrim = getvalnwarn("readDephTrim")) == 0.0 ) { readDephTrim = 1.0; } shape_rf( &p1_rf, "p1", p1pat, p1, flip1, rof1, rof2 ); // excitation pulse init_slice( &ss_grad, "ss", thk ); // slice gradient init_slice_refocus( &ssr_grad, "ssr" ); // slice refocus init_slice_refocus( &ssd_grad, "ssd" ); // slice refocus init_readout( &ro_grad, "ro", lro, np, sw ); // read gradient init_readout_refocus( &ror_grad, "ror" ); // read dephase init_readout_refocus( &rod_grad, "ror" ); // read dephase init_phase( &pe_grad, "pe", lpe, nv ); // phase gradient ss_grad.maxGrad = gmax * 0.57; ssr_grad.maxGrad = gmax * 0.57; ssd_grad.maxGrad = gmax * 0.57; ro_grad.maxGrad = gmax * 0.57; ror_grad.maxGrad = gmax * 0.57; rod_grad.maxGrad = gmax * 0.57; pe_grad.maxGrad = glimpe < 0.57? gmax*glimpe : gmax * 0.57; /* calculate the RF pulses, gradient pulses and their interdependencies */ calc_rf( &p1_rf, "tpwr1", "tpwr1f" ); calc_slice( &ss_grad, &p1_rf, NOWRITE, "gss" ); ssr_grad.amp = ss_grad.amp; ssr_grad.gmult = sliceRephTrim; ssr_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE; calc_slice_refocus( &ssr_grad, &ss_grad, NOWRITE, "gssr" ); ssd_grad.amp = ss_grad.amp; ssd_grad.gmult = sliceDephTrim; ssd_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE; calc_slice_dephase( &ssd_grad, &ss_grad, NOWRITE, "gssd" ); calc_readout( &ro_grad, NOWRITE, "gro", "sw", "at" ); ror_grad.amp = ro_grad.amp; ror_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE; rod_grad.amp = ro_grad.amp; rod_grad.calcFlag = DURATION_FROM_MOMENT_AMPLITUDE; ror_grad.gmult = readRephTrim; calc_readout_refocus( &ror_grad, &ro_grad, NOWRITE, "gror" ); rod_grad.gmult = readDephTrim; calc_readout_rephase( &rod_grad, &ro_grad, NOWRITE, "grod" ); calc_phase( &pe_grad, NOWRITE, "gpe", "tpe" ); /* work out the position of the markers */ /* markerA */ /* ss_grad.rfDelayFront indicates the starting point of the RF pulse measured from the start of the slice gradient ( rof1:pulse length:rof2 ) */ double granulatedRFDelayFront = granularity( ss_grad.rfDelayFront, GRADIENT_RES ); if( granulatedRFDelayFront > ss_grad.rfDelayFront ) { granulatedRFDelayFront -= GRADIENT_RES; } /* ss_grad.rfDelayBack indicates the end point of the RF pulse measured to the end of the slice gradient ( rof1:pulse length:rof2 ) */ double granulatedRFDelayBack = granularity( ss_grad.rfDelayBack, GRADIENT_RES ); if( granulatedRFDelayBack > ss_grad.rfDelayBack ) { granulatedRFDelayBack -= GRADIENT_RES; } double granulatedRFDelay = granulatedRFDelayFront < granulatedRFDelayBack ? granulatedRFDelayFront : granulatedRFDelayBack; double markerADelay = granulatedRFDelay; /* read and phase gradients can overlap the start or end of the slice gradient by max of granulatedRFDElay */ double granulatedATDelayFront = granularity(ro_grad.atDelayFront, GRADIENT_RES); if( granulatedATDelayFront > ro_grad.atDelayFront ) { granulatedATDelayFront -= GRADIENT_RES; } double granulatedATDelayBack = granularity(ro_grad.atDelayBack, GRADIENT_RES); if( granulatedATDelayBack > ro_grad.atDelayBack ) { granulatedATDelayBack -= GRADIENT_RES; } double granulatedATDelay = granulatedATDelayFront < granulatedATDelayBack ? granulatedATDelayFront : granulatedATDelayBack; /* longest gradient between RF pulse and acquire dominates */ xtime = ssr_grad.duration + granulatedRFDelay; xtime = xtime > ssd_grad.duration + granulatedRFDelay ? xtime : ssd_grad.duration + granulatedRFDelay; xtime = xtime > ror_grad.duration + granulatedATDelay ? xtime : ror_grad.duration + granulatedATDelay; xtime = xtime > rod_grad.duration + granulatedATDelay ? xtime : rod_grad.duration + granulatedATDelay; xtime = xtime > pe_grad.duration ? xtime : pe_grad.duration; ror_pad = xtime - ror_grad.duration - granulatedATDelay; rod_pad = xtime - rod_grad.duration - granulatedATDelay; /* make a gradient list */ start_kernel( &sk ); add_gradient( (void*)&ss_grad, "slice", SLICE, START_TIME, "", 0.0, PRESERVE ); add_gradient( (void*)&ssr_grad, "sliceReph", SLICE, BEHIND, "slice", 0.0, INVERT ); add_gradient( (void*)&ror_grad, "readDeph", READ, BEHIND, "slice", -granulatedRFDelay + ror_pad, INVERT ); add_gradient( (void*)&ro_grad, "read", READ, BEHIND, "readDeph", 0.0, PRESERVE ); add_gradient( (void*)&pe_grad, "phase", PHASE, SAME_START, "readDeph", 0.0, PRESERVE ); add_gradient( (void*)&rod_grad, "readReph", READ, BEHIND, "read", 0.0, INVERT ); add_gradient( (void*)&pe_grad, "rewind", PHASE, SAME_END, "readReph", 0.0, INVERT ); add_gradient( (void*)&ss_grad, "nextSlice", SLICE, BEHIND, "readReph", rod_pad - granulatedRFDelay, PRESERVE ); add_gradient( (void*)&ssd_grad, "sliceDeph", SLICE, BEFORE, "nextSlice", 0, INVERT ); add_marker( "markerA", SAME_START, "slice", granulatedRFDelay ); add_marker( "markerB", SAME_START, "nextSlice", granulatedRFDelay ); /* get the minimum echo time */ temin = get_timing( FROM_RF_CENTER_OF, "slice", TO_ECHO_OF, "read" ); temin2 = get_timing( FROM_ECHO_OF, "read", TO_RF_CENTER_OF, "nextSlice" ); htrmin = MAX( temin, temin2 ); if( minte[0] == 'y' ){ te = htrmin; } tepad = granularity( te - temin, GRADIENT_RES ); tepad2 = granularity( te - temin2, GRADIENT_RES ); te = temin + tepad; putCmd("setvalue('te', %f, 'current')\n", te ); if( tepad>0.0 ) change_timing( "readDeph", tepad ); if( tepad2>0.0 ) change_timing( "nextSlice", tepad2 ); tr = get_timing( FROM_START_OF, "slice", TO_START_OF, "nextSlice" ); putvalue("tr", tr ); delayRFToAcq = get_timing( FROM_RF_PULSE_OF, "slice", TO_ACQ_OF, "read" ); delayAcqToRF = get_timing( FROM_ACQ_OF, "read", TO_RF_PULSE_OF, "nextSlice" ); set_comp_info( &ss_pre, "ss_pre" ); write_comp_grads_snippet( NULL, NULL, &ss_pre, "START_OF_KERNEL", "markerA" ); set_comp_info( &read, "ro" ); set_comp_info( &phase, "pe" ); set_comp_info( &slice, "ss" ); write_comp_grads_snippet( &read, &phase, &slice, "markerA", "markerB" ); set_comp_info( &ss_post, "ss_post" ); write_comp_grads_snippet( NULL, NULL, &ss_post, "markerB", "END_OF_KERNEL" ); /* Set up frequency offset pulse shape list ********/ offsetlist(pss,ss_grad.ssamp,0,freqlist,ns,seqcon[1]); shapelist1 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freqlist,ns,ss_grad.rfFraction, seqcon[1]); /* Set pe_steps for profile or full image **********/ pe_steps = prep_profile(profile[0],nv,&pe_grad,&pe_grad);/* profile[0] is n y or r */ F_initval(pe_steps/2.0,vpe_offset); g_setExpTime(trmean*(ntmean*pe_steps*arraydim + (1+fabs(ssc))*arraydim)); /* Shift DDR for pro *******************************/ roff = -poffset(pro,ro_grad.roamp); /* PULSE SEQUENCE */ status( A ); rotate(); triggerSelect(trigger); obsoffset( resto ); delay( GRADIENT_RES ); initval( 1+fabs( ssc ), vss ); obspower( p1_rf.powerCoarse ); obspwrf( p1_rf.powerFine ); delay( GRADIENT_RES ); assign(one,vacquire); // real-time acquire flag setacqvar(vacquire); // Turn on acquire when vacquire is zero obl_shapedgradient(ss_pre.name,ss_pre.dur,0,0,ss_pre.amp,NOWAIT); sp1on(); delay(GRADIENT_RES); sp1off(); delay(ss_pre.dur-GRADIENT_RES ); msloop( seqcon[1], ns, vms_slices, vms_ctr ); assign(vss,vssc); peloop( seqcon[2], pe_steps, vpe_steps, vpe_ctr ); 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); } if (table) getelem(t1,vpe_ctr,vpe_index); else { ifzero(vacquire); sub(vpe_ctr,vpe_offset,vpe_index); elsenz(vacquire); sub(zero,vpe_offset,vpe_index); endif(vacquire); } pe_shaped3gradient( read.name, phase.name, slice.name, read.dur, read.amp, 0, slice.amp, -pe_grad.increment, vpe_index, NOWAIT ); delay(ss_grad.rfDelayFront - granulatedRFDelay); shapedpulselist( shapelist1, ss_grad.rfDuration, oph, rof1, rof2, seqcon[1], vms_ctr ); delay( delayRFToAcq - alfa ); startacq(alfa); acquire( np, 1/ro_grad.bandwidth ); endacq(); delay( delayAcqToRF - ss_grad.rfDelayFront + granulatedRFDelay - GRADIENT_RES ); sp1on(); delay(GRADIENT_RES); sp1off(); endpeloop( seqcon[2], vpe_ctr ); endmsloop( seqcon[1], vms_ctr ); obl_shapedgradient(ss_post.name,ss_post.dur,0,0,ss_post.amp,WAIT); }
pulsesequence() { /* Internal variable declarations *********************/ double freq90[MAXNSLICE],freq180[MAXNSLICE]; double te_delay1,te_delay2,tr_delay,tau1,tau2,thk2fact,te_delay3=0.0,te_delay4=0.0,navTime=0.0; double crushm0,pem0,gcrushr,gcrushp,gcrushs,pecrush; double refsign=1,crushsign=1,navsign=1; int shape90,shape180,table=0,sepRefocus; char slprofile[MAXSTR]; /* sequence dependent diffusion variables */ double Gro,Gss; // "gdiff" for readout/readout refocus and slice/slice refocus double dgro,dgss; // "delta" for readout/readout refocus and slice/slice refocus double Dgro,Dgss; // "DELTA" for readout/readout refocus and slice/slice refocus double dcrush,dgss2; // "delta" for crusher and gss2 gradients double Dcrush,Dgss2; // "DELTA" for crusher and gss2 gradients int i; /* Real-time variables used in this sequence **********/ int vpe_steps = v1; // Number of PE steps int vpe_ctr = v2; // PE loop counter int vms_slices = v3; // Number of slices int vms_ctr = v4; // Slice loop counter int vpe_offset = v5; // PE/2 for non-table offset int vpe_mult = v6; // PE multiplier, ranges from -PE/2 to PE/2 int vph180 = v7; // Phase of 180 pulse int vph2 = v8; // alternate phase of 180 on odd transients int vssc = v9; // Compressed steady-states int vtrimage = v10; // Counts down from nt, trimage delay when 0 int vacquire = v11; // Argument for setacqvar, to skip steady state acquires int vtrigblock = v12; // Number of slices per trigger block /* Initialize paramaters *****************************/ init_mri(); thk2fact=getval("thk2fact"); pecrush=getval("pecrush"); sepRefocus=getvalnwarn("sepRefocus"); getstrnwarn("slprofile",slprofile); /* Check for external PE table ***********************/ init_tablepar("pelist"); // Initialize pelist parameter if (strcmp(petable,"n") && strcmp(petable,"N") && strcmp(petable,"")) { loadtable(petable); writetabletopar(t1,"pelist"); // Write t1 table to pelist parameter table = 1; } /* RF Power & Bandwidth Calculations ******************/ shape_rf(&p1_rf,"p1",p1pat,p1,flip1,rof1,rof2); shape_rf(&p2_rf,"p2",p2pat,p2,flip2,rof1,rof2); calc_rf(&p1_rf,"tpwr1","tpwr1f"); calc_rf(&p2_rf,"tpwr2","tpwr2f"); /* Initialize gradient structures *********************/ init_slice(&ss_grad,"ss",thk); init_slice(&ss2_grad,"ss2",thk*thk2fact); init_dephase(&crush_grad,"crush"); init_slice_refocus(&ssr_grad,"ssr"); if (FP_LT(tcrushro,alfa)) tcrushro=alfa; init_readout_butterfly(&ro_grad,"ro",lro,np,sw,gcrushro,tcrushro); init_readout_refocus(&ror_grad,"ror"); init_phase(&pe_grad,"pe",lpe,nv); init_generic(&spoil_grad,"spoil",gspoil,tspoil); /* Gradient calculations ******************************/ calc_readout(&ro_grad, WRITE,"gro","sw","at"); ro_grad.m0ref *= grof; calc_readout_refocus(&ror_grad,&ro_grad,NOWRITE,"gror"); calc_phase(&pe_grad,NOWRITE,"gpe","tpe"); calc_slice(&ss_grad,&p1_rf,WRITE,"gss"); calc_slice(&ss2_grad,&p2_rf,WRITE,"gss2"); calc_slice_refocus(&ssr_grad,&ss_grad,WRITE,"gssr"); calc_generic(&spoil_grad,WRITE,"",""); /* Make sure crushing in PE dimension does not refocus signal from 180 */ crushm0=fabs(gcrush*tcrush); pem0=0.0; gcrushp=0.0; if (pecrush) pem0=pe_grad.m0; calc_dephase(&crush_grad,WRITE,crushm0+pem0,"",""); gcrushr = crush_grad.amp*crushm0/crush_grad.m0; if (pecrush) gcrushp = crush_grad.amp; gcrushs = crush_grad.amp*crushm0/crush_grad.m0; /* Allow phase encode and read dephase to be separated from slice refocus */ if (sepRefocus) { /* Equalize read dephase and PE gradient durations */ calc_sim_gradient(&ror_grad,&pe_grad,&null_grad,0,WRITE); crushsign=-1; } else { if (slprofile[0] == 'y') { /* Combined slice refocusing and read dephasing, reverse gradient sign if ror > ssr integral */ refsign = (ss_grad.m0ref > ro_grad.m0ref) ? 1.0 : -1.0; ss_grad.m0ref -= ro_grad.m0ref; calc_slice_refocus(&ssr_grad,&ss_grad,NOWRITE,"gssr"); } /* Equalize both refocus and PE gradient durations */ calc_sim_gradient(&ror_grad,&pe_grad,&ssr_grad,0,WRITE); } /* Create optional prepulse events ********************/ if (fsat[0] == 'y') create_fatsat(); if (sat[0] == 'y') create_satbands(); if (mt[0] == 'y') create_mtc(); if (ir[0] == 'y') create_inversion_recovery(); if (diff[0] == 'y') init_diffusion(&diffusion,&diff_grad,"diff",gdiff,tdelta); sgl_error_check(sglerror); /* Min TE *********************************************/ te = granularity(te,2*GRADIENT_RES); /* tau1, tau2 are the sum of events in each half echo period */ /* tau1, tau2 include a GRADIENT_RES as this is minimum delay time */ tau1 = ss_grad.rfCenterBack + ssr_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront + 2*GRADIENT_RES; tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho + GRADIENT_RES; if (sepRefocus) tau2 += ror_grad.duration; temin = 2*MAX(tau1,tau2); /* Diffusion ******************************************/ if (diff[0] == 'y') { /* granulate tDELTA */ tDELTA = granularity(tDELTA,GRADIENT_RES); /* taudiff is the duration of events between diffusion gradients */ taudiff = ss2_grad.duration + 2*crush_grad.duration + GRADIENT_RES; /* set minimum diffusion structure requirements for gradient echo: taudiff, tDELTA, te and minte[0] */ set_diffusion(&diffusion,taudiff,tDELTA,te,minte[0]); /* set additional diffusion structure requirements for spin echo: tau1 and tau2 */ set_diffusion_se(&diffusion,tau1,tau2); /* calculate the diffusion structure delays. address &temin is required in order to update temin accordingly */ calc_diffTime(&diffusion,&temin); } /* TE delays ******************************************/ if (minte[0] == 'y') { te = temin; putvalue("te",te); } if (FP_LT(te,temin)) { abort_message("TE too short, minimum TE = %.3f ms\n",temin*1000); } te_delay1 = te/2 - tau1 + GRADIENT_RES; te_delay2 = te/2 - tau2 + GRADIENT_RES; if (navigator[0] == 'y') { /* tau1, tau2 are the sum of events in each half echo period */ tau1 = ro_grad.timeFromEcho + pe_grad.duration + crush_grad.duration + ss2_grad.rfCenterFront; tau2 = ss2_grad.rfCenterBack + crush_grad.duration + ro_grad.timeToEcho; if (FP_GT(tau1,tau2)) { te_delay3 = GRADIENT_RES; te_delay4 = tau1-tau2+GRADIENT_RES; } else { te_delay3 = tau2-tau1+GRADIENT_RES; te_delay4 = GRADIENT_RES; } navTime = te_delay3 + ss2_grad.duration + 2*crush_grad.duration + ro_grad.duration + te_delay4 + 2*GRADIENT_RES; } /* Check nsblock, the number of slices blocked together (used for triggering and/or inversion recovery) */ check_nsblock(); /* Min TR *********************************************/ trmin = ss_grad.rfCenterFront + te + ro_grad.timeFromEcho + pe_grad.duration + 2*GRADIENT_RES; /* Increase TR if any options are selected ************/ if (spoilflag[0] == 'y') trmin += spoil_grad.duration; if (navigator[0] == 'y') trmin += navTime; if (sat[0] == 'y') trmin += satTime; if (fsat[0] == 'y') trmin += fsatTime; if (mt[0] == 'y') trmin += mtTime; if (ticks > 0) trmin += GRADIENT_RES; /* Adjust for all slices ******************************/ trmin *= ns; /* Inversion recovery *********************************/ if (ir[0] == 'y') { /* tauti is the additional time beyond IR component to be included in ti */ /* satTime, fsatTime and mtTime all included as those modules will be after IR */ tauti = satTime + fsatTime + mtTime + GRADIENT_RES + ss_grad.rfCenterFront; /* calc_irTime checks ti and returns the time of all IR components */ trmin += calc_irTime(tauti,trmin,mintr[0],tr,&trtype); } if (mintr[0] == 'y') { tr = trmin; putvalue("tr",tr); } if (FP_LT(tr,trmin)) { abort_message("TR too short, minimum TR = %.3f ms\n",trmin*1000); } /* TR delay *******************************************/ tr_delay = granularity((tr-trmin)/ns,GRADIENT_RES); /* Calculate B values *********************************/ if (ix == 1) { /* Calculate bvalues according to main diffusion gradients */ calc_bvalues(&diffusion,"dro","dpe","dsl"); /* Add components from additional diffusion encoding imaging gradients peculiar to this sequence */ /* Initialize variables */ dgro = 0.5*(ror_grad.duration+ro_grad.timeToEcho); Gro = ro_grad.m0ref/dgro; Dgro = dgro; if (!sepRefocus) Dgro = te-ss_grad.rfCenterBack-ro_grad.timeToEcho; dgss = 0.5*(ss_grad.rfCenterBack+ssr_grad.duration); Gss = ss_grad.m0ref/dgss; Dgss = dgss; dgss2 = ss2_grad.duration/2; Dgss2 = dgss2; dcrush = crush_grad.duration-crush_grad.tramp; Dcrush = crush_grad.duration+ss2_grad.duration; for (i = 0; i < diffusion.nbval; i++) { /* set droval, dpeval and dslval */ set_dvalues(&diffusion,&droval,&dpeval,&dslval,i); /* Readout */ diffusion.bro[i] += bval(Gro,dgro,Dgro); diffusion.bro[i] += bval(crushsign*gcrushr,dcrush,Dcrush); diffusion.bro[i] += bval_nested(gdiff*droval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush); if (!sepRefocus) { diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,gdiff*droval,tdelta,tDELTA); diffusion.bro[i] += bval_nested(Gro,dgro,Dgro,crushsign*gcrushr,dcrush,Dcrush); } /* Phase */ if (pecrush) { diffusion.bpe[i] += bval(gcrushp,dcrush,Dcrush); diffusion.bpe[i] += bval_nested(gdiff*dpeval,tdelta,tDELTA,gcrushp,dcrush,Dcrush); } /* Slice */ diffusion.bsl[i] += bval(Gss,dgss,Dgss); diffusion.bsl[i] += bval(gcrushs,dcrush,Dcrush); diffusion.bsl[i] += bval(ss2_grad.ssamp,dgss2,Dgss2); diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,gcrushs,dcrush,Dcrush); diffusion.bsl[i] += bval_nested(gdiff*dslval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2); diffusion.bsl[i] += bval_nested(gcrushs,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2); /* Readout/Phase Cross-terms */ diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush); diffusion.brp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush); if (pecrush) diffusion.brp[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushp,dcrush,Dcrush); if (!sepRefocus) { diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gdiff*dpeval,tdelta,tDELTA); if (pecrush) diffusion.brp[i] += bval_cross(Gro,dgro,Dgro,gcrushp,dcrush,Dcrush); } /* Readout/Slice Cross-terms */ diffusion.brs[i] += bval2(crushsign*gcrushr,gcrushs,dcrush,Dcrush); diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,gcrushs,dcrush,Dcrush); diffusion.brs[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,crushsign*gcrushr,dcrush,Dcrush); diffusion.brs[i] += bval_cross(gdiff*droval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2); if (!sepRefocus) { diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gdiff*dslval,tdelta,tDELTA); diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,gcrushs,dcrush,Dcrush); diffusion.brs[i] += bval_cross(Gro,dgro,Dgro,ss2_grad.ssamp,dgss2,Dgss2); } /* Slice/Phase Cross-terms */ diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,gcrushs,dcrush,Dcrush); diffusion.bsp[i] += bval_cross(gdiff*dpeval,tdelta,tDELTA,ss2_grad.ssamp,dgss2,Dgss2); if (pecrush) { diffusion.bsp[i] += bval2(gcrushs,gcrushp,dcrush,Dcrush); diffusion.bsp[i] += bval_cross(gdiff*dslval,tdelta,tDELTA,gcrushp,dcrush,Dcrush); diffusion.bsp[i] += bval_cross(gcrushp,dcrush,Dcrush,ss2_grad.ssamp,dgss2,Dgss2); } } /* End for-all-directions */ /* Write the values */ write_bvalues(&diffusion,"bval","bvalue","max_bval"); } /* Generate phase-ramped pulses ***********************/ offsetlist(pss,ss_grad.ssamp,0,freq90,ns,seqcon[1]); offsetlist(pss,ss2_grad.ssamp,0,freq180,ns,seqcon[1]); shape90 = shapelist(p1_rf.pulseName,ss_grad.rfDuration,freq90,ns,ss_grad.rfFraction,seqcon[1]); shape180 = shapelist(p2_rf.pulseName,ss2_grad.rfDuration,freq180,ns,ss2_grad.rfFraction,seqcon[1]); /* Set pe_steps for profile or full image *************/ pe_steps = prep_profile(profile[0],nv,&pe_grad,&null_grad); F_initval(pe_steps/2.0,vpe_offset); /* Shift DDR for pro **********************************/ roff = -poffset(pro,ro_grad.roamp); /* Adjust experiment time for VnmrJ *******************/ if (ssc<0) { if (seqcon[2] == 'c') g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*arraydim)); else g_setExpTime(trmean*(ntmean*pe_steps*arraydim - ssc*pe_steps*arraydim)); } else g_setExpTime(trmean*ntmean*pe_steps*arraydim + tr*ssc); /* Slice profile **************************************/ if (slprofile[0] == 'y' && !sepRefocus) ror_grad.amp = 0; /* Set phase cycle table ******************************/ if (sepRefocus) settable(t2,1,ph180); // Phase encode is just before readout else settable(t2,2,ph180); /* PULSE SEQUENCE *************************************/ status(A); // Set status A rotate(); // Set gradient rotation according to psi, phi and theta triggerSelect(trigger); // Select trigger input 1/2/3 obsoffset(resto); // Set spectrometer frequency delay(GRADIENT_RES); // Delay for frequency setting initval(fabs(ssc),vssc); // Compressed steady-state counter if (seqcon[2]=='s') assign(zero,vssc); // Zero for standard peloop assign(one,vacquire); // real-time acquire flag setacqvar(vacquire); // Turn on acquire when vacquire is zero /* trigger */ if (ticks > 0) F_initval((double)nsblock,vtrigblock); /* Begin phase-encode loop ****************************/ peloop(seqcon[2],pe_steps,vpe_steps,vpe_ctr); if (trtype) delay(ns*tr_delay); // relaxation delay /* Compressed steady-states: 1st array & transient, all arrays if ssc is negative */ if ((ix > 1) && (ssc > 0)) assign(zero,vssc); sub(vpe_ctr,vssc,vpe_ctr); // vpe_ctr counts up from -ssc assign(zero,vssc); if (seqcon[2] == 's') assign(zero,vacquire); // Always acquire for non-compressed loop else { ifzero(vpe_ctr); assign(zero,vacquire); // Start acquiring when vpe_ctr reaches zero endif(vpe_ctr); } /* Read external kspace table if set ******************/ if (table) getelem(t1,vpe_ctr,vpe_mult); else { ifzero(vacquire); sub(vpe_ctr,vpe_offset,vpe_mult); elsenz(vacquire); sub(zero,vpe_offset,vpe_mult); // Hold PE mult at initial value for steady states endif(vacquire); } /* Phase cycle ****************************************/ getelem(t2,vpe_ctr,vph180); // For phase encoding with slice rephase add(oph,vph180,vph180); // 180 deg pulse phase alternates +/- 90 from receiver mod2(ct,vph2); dbl(vph2,vph2); add(vph180,vph2,vph180); // Alternate phase for 180 on odd transients /* Begin multislice loop ******************************/ msloop(seqcon[1],ns,vms_slices,vms_ctr); if (!trtype) delay(tr_delay); // Relaxation delay if (ticks > 0) { modn(vms_ctr,vtrigblock,vtest); ifzero(vtest); // if the beginning of an trigger block xgate(ticks); grad_advance(gpropdelay); delay(GRADIENT_RES); elsenz(vtest); delay(GRADIENT_RES); endif(vtest); } sp1on(); delay(GRADIENT_RES); sp1off(); // Scope trigger /* Prepulse options ***********************************/ if (ir[0] == 'y') inversion_recovery(); if (sat[0] == 'y') satbands(); if (fsat[0] == 'y') fatsat(); if (mt[0] == 'y') mtc(); /* Slice select RF pulse ******************************/ obspower(p1_rf.powerCoarse); obspwrf(p1_rf.powerFine); delay(GRADIENT_RES); obl_shapedgradient(ss_grad.name,ss_grad.duration,0,0,ss_grad.amp,NOWAIT); delay(ss_grad.rfDelayFront); shapedpulselist(shape90,ss_grad.rfDuration,oph,rof1,rof2,seqcon[1],vms_ctr); delay(ss_grad.rfDelayBack); /* Slice refocus gradient *****************************/ if (sepRefocus) obl_shapedgradient(ssr_grad.name,ssr_grad.duration,0,0,-ssr_grad.amp,WAIT); else /* Include phase encode and readout dephase gradient if refocus gradients not separated */ pe_shapedgradient(pe_grad.name,pe_grad.duration,ror_grad.amp,0,-ssr_grad.amp*refsign,pe_grad.increment,vpe_mult,WAIT); if (diff[0] == 'y') { delay(diffusion.d1); diffusion_dephase(&diffusion,dro,dpe,dsl); delay(diffusion.d2); } else delay(te_delay1); /* Refocusing RF pulse ********************************/ obspower(p2_rf.powerCoarse); obspwrf(p2_rf.powerFine); delay(GRADIENT_RES); obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT); obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT); delay(ss2_grad.rfDelayFront); shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr); delay(ss2_grad.rfDelayBack); obl_shapedgradient(crush_grad.name,crush_grad.duration,crushsign*gcrushr,gcrushp,gcrushs,WAIT); if (diff[0] == 'y') { delay(diffusion.d3); diffusion_rephase(&diffusion,dro,dpe,dsl); delay(diffusion.d4); } else delay(te_delay2); /* Readout dephase, phase encode & readout gradients **/ roff = -poffset(pro,ro_grad.roamp); // incase inverted navigator is acquired if (slprofile[0] == 'y') { /* Readout gradient only if refocus gradients not separated */ if (sepRefocus) obl_shapedgradient(ror_grad.name,ror_grad.duration,0,0,-ror_grad.amp,WAIT); obl_shapedgradient(ro_grad.name,ro_grad.duration,0,0,ro_grad.amp,NOWAIT); } else { /* Readout gradient only if refocus gradients not separated */ if (sepRefocus) pe_shapedgradient(pe_grad.name,pe_grad.duration,-ror_grad.amp,0,0,-pe_grad.increment,vpe_mult,WAIT); obl_shapedgradient(ro_grad.name,ro_grad.duration,ro_grad.amp,0,0,NOWAIT); } /* Acquisition ****************************************/ delay(ro_grad.atDelayFront-alfa); startacq(alfa); acquire(np,1.0/sw); delay(ro_grad.atDelayBack); endacq(); /* Rewind Phase encoding ******************************/ pe_shapedgradient(pe_grad.name,pe_grad.duration,0,0,0,pe_grad.increment,vpe_mult,WAIT); /* Navigator acquisition ******************************/ if (navigator[0] == 'y') { delay(te_delay3); obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT); obl_shapedgradient(ss2_grad.name,ss2_grad.duration,0,0,ss2_grad.amp,NOWAIT); delay(ss2_grad.rfDelayFront); shapedpulselist(shape180,ss2_grad.rfDuration,vph180,rof2,rof2,seqcon[1],vms_ctr); delay(ss2_grad.rfDelayBack); obl_shapedgradient(crush_grad.name,crush_grad.duration,-crushsign*gcrushr,0,-gcrushs,WAIT); delay(te_delay4); obl_shapedgradient(ro_grad.name,ro_grad.duration,navsign*ro_grad.amp,0,0,NOWAIT); delay(ro_grad.atDelayFront-alfa); startacq(alfa); acquire(np,1.0/sw); delay(ro_grad.atDelayBack); endacq(); } if (spoilflag[0] == 'y') { obl_shapedgradient(spoil_grad.name,spoil_grad.duration,navsign*spoil_grad.amp,0,spoil_grad.amp,WAIT); } endmsloop(seqcon[1],vms_ctr); endpeloop(seqcon[2],vpe_ctr); /* Inter-image delay **********************************/ sub(ntrt,ct,vtrimage); decr(vtrimage); ifzero(vtrimage); delay(trimage); endif(vtrimage); /* Duty cycle *****************************************/ calc_grad_duty(tr); }
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); }
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); }
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); }
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); }