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#include <odinseq/seqall.h>
class METHOD_CLASS : public SeqMethod {
private:
SeqPulsar exc;
SeqPulsarReph exc_reph;
SeqPulsarReph exc_reph_neg;
SeqAcqRead acqread;
SeqAcqRead negacqread; // need separate object since calling SeqAcqDeph on the same object with different polarity does not work
SeqAcqDeph readdeph;
SeqAcqDeph negreaddeph;
SeqGradPhaseEncFlowComp pe;
SeqGradPhaseEncFlowComp pe3d;
SeqGradConstPulse crusher;
SeqDelay exc2acq;
SeqDelay relaxdelay;
SeqObjList gradpart;
SeqObjList scan;
SeqObjList readout;
SeqObjLoop peloop;
SeqObjLoop peloop3d;
SeqObjLoop reploop;
SeqVecIter phaseiter;
LDRfloat T1Ernst;
public:
METHOD_CLASS(const STD_string& label) : SeqMethod(label) {
set_description("Fully flow-compensated FLASH sequence for Susceptibility Weighted Imaging. ");
}
void method_pars_init() {
geometryInfo->set_Mode(voxel_3d);
commonPars->set_MatrixSize(readDirection,256);
commonPars->set_MatrixSize(phaseDirection,256,noedit);
commonPars->set_RepetitionTime(50.0);
commonPars->set_EchoTime(28.0);
T1Ernst=1300.0;
T1Ernst.set_minmaxval(0.0,5000.0).set_description("For optimum SNR, the flip angle will be set to the Ernst angle using this T1");
append_parameter(T1Ernst,"T1Ernst");
// fmapscan.init("fmapscan");
// append_parameter(fmapscan.get_parblock(),"FieldMapPars");
}
void method_seq_init(){
Log<Seq> odinlog(this,"method_seq_init");
///////////////// Pulses: /////////////////////
// Excitation Pulse
float spatres=3.0;
float slicethick=geometryInfo->get_FOV(sliceDirection)-2.0*spatres;
if(slicethick<spatres) slicethick=spatres;
exc=SeqPulsarSinc("exc", slicethick, false, 4.0, commonPars->get_FlipAngle(), spatres, 512);
exc.set_filter("Gauss");
exc.set_freqoffset(systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_offset(sliceDirection) );
exc.set_pulse_type(excitation);
// ODINLOG(odinlog,significantDebug) << "exc.rel_magnetic_center/get_pulsduration" << exc.get_rel_magnetic_center() << "/" << exc.get_pulsduration() << STD_endl;
// ODINLOG(odinlog,significantDebug) << "exc.get_Gz()" << exc.get_Gz() << STD_endl;
// rephasing lobe for excitation pulse
exc_reph=SeqPulsarReph("exc_reph",exc);
exc_reph_neg=SeqPulsarReph("exc_reph",exc);
exc_reph_neg.invert_strength();
////////////////// Geometry: /////////////////////////////////
// calculate the resolution in the read Channel and set the number of phase encoding
// steps so that we will obtain a uniform resolution in read and phase Channel:
float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection));
commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit);
commonPars->set_MatrixSize(sliceDirection,int(secureDivision(geometryInfo->get_FOV(sliceDirection),resolution)+0.5),noedit);
//////////////// Phase Encoding: //////////////////////////
float t0=exc.get_duration()-exc.get_magnetic_center()+
exc_reph.get_duration()+
exc_reph.get_duration()+
exc_reph_neg.get_duration();
pe=SeqGradPhaseEncFlowComp("pe", t0, commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection),
phaseDirection, 0.25*systemInfo->get_max_grad(),
linearEncoding, noReorder, 1,
commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier());
//////////////// Phase Encoding (3D): //////////////////////////
pe3d=SeqGradPhaseEncFlowComp("pe3d", t0, commonPars->get_MatrixSize(sliceDirection),geometryInfo->get_FOV(sliceDirection),
sliceDirection, pe.get_strength(),
linearEncoding, noReorder, 1,
commonPars->get_ReductionFactor());
//////////////// Readout: //////////////////////////////
acqread=SeqAcqRead("acqread",commonPars->get_AcqSweepWidth(),commonPars->get_MatrixSize(readDirection),
geometryInfo->get_FOV(readDirection),readDirection);
negacqread=acqread;
readdeph=SeqAcqDeph("readdeph", acqread);
negreaddeph=SeqAcqDeph("negreaddeph", negacqread, spinEcho);
//////////////// RF Spoiling: //////////////////////////////
if(commonPars->get_RFSpoiling()) {
exc.set_phasespoiling();
acqread.set_phasespoiling();
phaseiter=SeqVecIter("phaseiter");
phaseiter.add_vector(exc.get_phaselist_vector());
phaseiter.add_vector(acqread.get_phaselist_vector());
}
//////////////// Crusher: //////////////////////////////
double crusher_strength=0.5*systemInfo->get_max_grad();
double crusher_integral=4.0*fabs(readdeph.get_gradintegral().sum());
double crusher_dur=secureDivision(crusher_integral, crusher_strength);
crusher=SeqGradConstPulse("crusher",readDirection,crusher_strength,crusher_dur);
//////////////// Field-map template: //////////////////////////////
// fmapscan.build_seq(100.0, SeqObjList(), commonPars->get_RepetitionTime());
//////////////// several padding delays ////////////////////
exc2acq=SeqDelay("exc2acq");
relaxdelay=SeqDelay("relaxdelay");
//////////////// total sequence: //////////////////////////////
gradpart=SeqObjList("gradpart");
scan=SeqObjList("scan");
readout=SeqObjList("readout");
peloop=SeqObjLoop("peloop");
peloop3d=SeqObjLoop("peloop3d");
reploop=SeqObjLoop("reploop");
gradpart = (negreaddeph+readdeph)/pe/pe3d;
readout = exc + exc_reph + exc_reph + exc_reph_neg + gradpart + exc2acq + readdeph + acqread + crusher;
if(commonPars->get_RFSpoiling()) readout += phaseiter;
// scan += fmapscan + relaxdelay;
scan+= reploop(
peloop3d(
peloop(
readout + relaxdelay
)[pe]
)[pe3d]
)[commonPars->get_NumOfRepetitions()];
set_sequence( scan );
}
void method_rels(){
// TE
double minTE=exc.get_duration()-exc.get_magnetic_center()+
exc_reph.get_duration()+
exc_reph.get_duration()+
exc_reph_neg.get_duration()+
gradpart.get_duration()+
readdeph.get_duration()+
acqread.get_acquisition_center();
if(commonPars->get_EchoTime()<minTE) commonPars->set_EchoTime(minTE);
exc2acq=commonPars->get_EchoTime()-minTE;
// TR
// calculate relaxdelay to get the desired repetition time
float readoutdur=readout.get_duration();
if(readoutdur > commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(readoutdur);
relaxdelay.set_duration( commonPars->get_RepetitionTime()-readoutdur );
// calculate Ernst angle accordng to TR
float flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) );
commonPars->set_FlipAngle( flipangle, noedit );
exc.set_flipangle( flipangle );
}
void method_pars_set(){
// inform the readout about the used phase encoding and slice vector (for automatic reconstruction)
acqread.set_reco_vector(line,pe);
acqread.set_reco_vector(line3d,pe3d);
recoInfo->set_PreProc3D("swi");
recoInfo->set_PostProc3D("mip");
// recoInfo->set_CmdLineOpts("-ff CosSq -fp 0.5");
}
};
// entry point for the sequence module
ODINMETHOD_ENTRY_POINT
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