/usr/share/odin/sequences/mk_prop.cpp is in odin 1.8.4-1ubuntu2.
This file is owned by root:root, with mode 0o644.
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class METHOD_CLASS : public SeqMethod {
private:
JDXint Blades;
JDXbool ShortAxis;
JDXfloat BladeOversampling;
JDXbool TakeMinEchoTime;
JDXbool RampSampling;
JDXenum RampMode;
JDXfloat RampSteepness;
JDXbool FatSaturation;
JDXfloat T1Ernst;
JDXint DummyCycles;
JDXint NumOfGradEchoes;
JDXint NumOfSamples;
JDXdouble PulseDur;
JDXbool fMRITrigger;
JDXbool UpDownBlade;
JDXbool FieldMap;
JDXbool EPIRef;
SeqPulsar exc;
SeqSat fatsat;
SeqAcqEPI epiacq;
SeqDelay epiacq_dummy;
SeqAcqEPI epiacq_template;
SeqAcqDeph deph;
SeqAcqDeph deph_template;
SeqObjLoop sliceloop;
SeqObjLoop reploop;
SeqObjLoop bladeloop;
SeqObjLoop dummyloop;
SeqDelay trdelay;
SeqObjList scan;
SeqObjList dummypart;
SeqObjList templatepart;
SeqObjList imagingpart;
SeqObjList slicepart;
SeqObjList slicepart_dummy;
SeqObjList slicepart_template;
SeqObjList preppart;
SeqDelay exc2acq;
SeqTrigger trigger;
SeqGradTrapezParallel crusher;
SeqDelay crusherdelay;
SeqFieldMap fmapscan;
SeqVecIter phaseiter;
SeqRotMatrixVector bladerot;
SeqMagnReset reset;
// stuff for EPIRef
SeqAcqEPI epiacq_ref;
SeqDelay epiacq_ref_dummy;
SeqAcqEPI epiacq_ref_template;
SeqAcqEPI epiacq_ref_grappa;
SeqAcqDeph deph_ref;
SeqAcqDeph deph_ref_template;
SeqAcqDeph deph_ref_grappa;
SeqObjLoop grappaloop_ref;
SeqDelay trdelay_ref;
SeqObjList templatepart_ref;
SeqObjList grappapart_ref;
SeqObjList imagingpart_ref;
SeqObjList slicepart_grappa_ref;
SeqObjList slicepart_template_ref;
SeqDelay exc2acq_ref;
dvector bladeangels;
public:
// This constructor creates an empty EPI sequence
METHOD_CLASS(const STD_string& label) : SeqMethod(label) {
set_description("2D-PROPELLER-EPI with EPI reference scan.");
}
void method_pars_init() {
// In this function, parameters are initialized and default values are set
commonPars->set_MatrixSize(readDirection,128);
commonPars->set_MatrixSize(phaseDirection,128,noedit);
commonPars->set_NumOfRepetitions(1);
commonPars->set_RepetitionTime(1000.0);
commonPars->set_AcqSweepWidth(100.0);
Blades=8;
Blades.set_description("Number of PROPELLER blades");
ShortAxis=false;
ShortAxis.set_description("Readout direction along short axis of blades");
BladeOversampling=1.0;
BladeOversampling.set_minmaxval(0.0,100.0);
BladeOversampling.set_unit("%").set_description("Oversampling (overlap) in short direction of blade");
RampSampling=false;
RampSampling.set_description("Perform sampling during gradient ramps");
RampMode.add_item("linear",linear);
RampMode.add_item("sinusoidal",sinusoidal);
RampMode.add_item("half_sinusoidal",half_sinusoidal);
RampMode.set_actual(linear);
RampMode.set_description("The shape of the ramps of the read gradient");
RampSteepness=1.0;
RampSteepness.set_description("Relative steepness (slew rate) of the EPI readout ramps");
FatSaturation=true;
FatSaturation.set_description("Saturation of fat resonance prior to excitation");
T1Ernst=1300.0;
T1Ernst.set_minmaxval(0.0,5000.0).set_description("If non-zero, the flip angle will be set to the Ernst angle using this T1 for optimum SNR");
TakeMinEchoTime=true;
TakeMinEchoTime.set_description("Use minimum possible TE");
DummyCycles=3;
DummyCycles.set_description("Number of dummy shots before actual acquisition");
fMRITrigger=true;
fMRITrigger.set_description("External triggering");
UpDownBlade=false;
UpDownBlade.set_description("Sample each blade twice with opposite phase-encoding direction");
FieldMap=false;
FieldMap.set_description("Fieldmap pre-scan for distortion correction");
PulseDur=2.0; // avoid initial high RF amplitude
PulseDur.set_description("Pulse duration of excitation/refocusing pulse");
EPIRef=false;
EPIRef.set_description("Interleaved EPI reference scan");
// register method parameters for user interface, parameter files, etc.
append_parameter(Blades,"Blades");
append_parameter(ShortAxis,"ShortAxis");
append_parameter(TakeMinEchoTime,"TakeMinEchoTime");
append_parameter(DummyCycles,"DummyCycles");
append_parameter(RampSampling,"RampSampling");
append_parameter(FatSaturation,"FatSaturation");
append_parameter(T1Ernst,"T1Ernst");
append_parameter(FieldMap,"FieldMap");
fmapscan.init("fmapscan");
append_parameter(fmapscan.get_parblock(),"FieldMapPars");
append_parameter(PulseDur,"PulseDur");
append_parameter(fMRITrigger,"fMRITrigger");
append_parameter(UpDownBlade,"UpDownBlade");
append_parameter(EPIRef,"EPIRef");
if(systemInfo->get_platform()!=numaris_4) {
append_parameter(BladeOversampling,"BladeOversampling");
append_parameter(RampMode,"RampMode");
append_parameter(RampSteepness,"RampSteepness");
append_parameter(NumOfGradEchoes,"NumOfGradEchoes",noedit);
append_parameter(NumOfSamples,"NumOfSamples",noedit);
}
}
void method_seq_init() {
Log<Seq> odinlog(this,"method_seq_init");
float gamma=systemInfo->get_gamma();
///////////////// Pulses: /////////////////////
float slicethick=geometryInfo->get_sliceThickness();
float spatres=slicethick/4.0;
// calculate Ernst angle accordng to TR
float flipangle=commonPars->get_FlipAngle();
if(T1Ernst>0.0) {
flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) );
commonPars->set_FlipAngle( flipangle );
}
// excitation pulse
exc=SeqPulsarSinc("exc", slicethick, true,PulseDur,flipangle,spatres);
exc.set_rephased(true, 0.8*systemInfo->get_max_grad()); // short rephaser
exc.set_freqlist( gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() );
exc.set_pulse_type(excitation);
// fat saturation module
fatsat=SeqSat("fatsat",fat);
//////////////// EPI-Readout: //////////////////////////////
// square FOV
int sizeRadial=commonPars->get_MatrixSize(readDirection);
commonPars->set_MatrixSize(phaseDirection,sizeRadial,noedit);
commonPars->set_MatrixSize(sliceDirection,1,noedit);
int readpts_blade=sizeRadial;
int pelines_blade=sizeRadial;
int bladewidth=sizeRadial;
if(Blades>1) {
float min_bladewidth=sizeRadial*tan(0.5*PII/Blades); // exact solution
bladewidth=int( ( (1.0-0.01*BladeOversampling) * min_bladewidth + 0.01*BladeOversampling*sizeRadial ) +0.5 );
}
if(ShortAxis) readpts_blade=bladewidth;
else pelines_blade=bladewidth;
float os_read=2.0; // For reduced undersampling artifacts
float fov=geometryInfo->get_FOV(readDirection); // uniform FOV
epiacq=SeqAcqEPI("epiacq",commonPars->get_AcqSweepWidth(),
readpts_blade, fov,
pelines_blade, fov,
1, 1, os_read, "", 0, 0, rampType(int(RampMode)),
RampSampling, RampSteepness, 0.0);
// display sampling extents in read/phase direction
NumOfGradEchoes=epiacq.get_numof_gradechoes();
NumOfSamples=epiacq.get_npts_read();
// Template scan fo EPI, begin with copy of actual EPI
epiacq_template=epiacq;
epiacq_template.set_label("epiacq_template");
// 1D phase correction
epiacq_template.set_template_type(phasecorr_template);
// Delay instead of actual EPI readout for dummy scans
epiacq_dummy=SeqDelay("epiacq_dummy",epiacq.get_duration());
// EPI pre-dephase gradient
deph=SeqAcqDeph("deph",epiacq);
deph_template=SeqAcqDeph("deph_template",epiacq_template);
/////////////////// Rotation of Blades ////////////////////////////////////////////////
bladerot=SeqRotMatrixVector("bladerot");
bool full_cycle=UpDownBlade;
int nangles=Blades;
if(full_cycle) nangles=2*Blades;
bladeangels.resize(nangles);
for(int iangle=0; iangle<nangles; iangle++) {
RotMatrix rm("rotmatrix"+itos(iangle));
int iblade=iangle;
if(full_cycle) iblade=iangle/2;
float ang=float(iblade)/float(Blades)*PII; // 0...180 deg
if(full_cycle && iangle%2) ang+=PII; // adjacent blades have opposite direction
rm.set_inplane_rotation(ang);
bladeangels[iangle]=ang;
bladerot.append(rm);
}
//////////////// EPI-Reference: //////////////////////////////
if(EPIRef) {
// reference gets GRAPPA and partial fourier acquisition
epiacq_ref=SeqAcqEPI("epiacq_ref",commonPars->get_AcqSweepWidth(),
sizeRadial, fov,
sizeRadial, fov,
1, commonPars->get_ReductionFactor(), os_read, "", 0, 0, rampType(int(RampMode)),
RampSampling, RampSteepness, commonPars->get_PartialFourier());
// Template scan fo EPI, begin with copy of actual EPI
epiacq_ref_template=epiacq_ref;
epiacq_ref_template.set_label("epiacq_ref_template");
// 1D phase correction
epiacq_ref_template.set_template_type(phasecorr_template);
// Full multi-shot EPI readout as GRAPPA training data
epiacq_ref_grappa=epiacq_ref;
epiacq_ref_grappa.set_label("epiacq_ref_grappa");
epiacq_ref_grappa.set_template_type(grappa_template);
// Delay instead of actual EPI readout for dummy scans
epiacq_ref_dummy=SeqDelay("epiacq_ref_dummy",epiacq_ref.get_duration());
// EPI pre-dephase gradient
deph_ref=SeqAcqDeph("deph_ref",epiacq_ref);
deph_ref_template=SeqAcqDeph("deph_ref_template",epiacq_ref_template);
deph_ref_grappa=SeqAcqDeph("deph_ref_grappa",epiacq_ref_grappa);
}
/////////////////// RF Spoiling ///////////////////////////////////////////////////////
if(commonPars->get_RFSpoiling()) {
// recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005)
int plistsize=16;
double plistincr=45.0;
exc.set_phasespoiling(plistsize, plistincr);
epiacq.set_phasespoiling(plistsize, plistincr);
epiacq_template.set_phasespoiling(plistsize, plistincr);
epiacq_ref.set_phasespoiling(plistsize, plistincr);
epiacq_ref_template.set_phasespoiling(plistsize, plistincr);
epiacq_ref_grappa.set_phasespoiling(plistsize, plistincr);
phaseiter=SeqVecIter("phaseiter");
phaseiter.add_vector(exc.get_phaselist_vector());
phaseiter.add_vector(epiacq.get_phaselist_vector());
phaseiter.add_vector(epiacq_template.get_phaselist_vector());
phaseiter.add_vector(epiacq_ref.get_phaselist_vector());
phaseiter.add_vector(epiacq_ref_template.get_phaselist_vector());
phaseiter.add_vector(epiacq_ref_grappa.get_phaselist_vector());
}
//////////////// Loops: //////////////////////////////
// loop to iterate over slices
sliceloop=SeqObjLoop("sliceloop");
// loop to iterate over repetitions
reploop=SeqObjLoop("reploop");
// loop to iterate over blades
bladeloop=SeqObjLoop("bladeloop");
// loop to iterate over dummy scans
dummyloop=SeqObjLoop("dummyloop");
grappaloop_ref=SeqObjLoop("grappaloop_ref");
//////////////// Timing Delays: //////////////////////////////
trdelay=SeqDelay("trdelay");
trdelay_ref=SeqDelay("trdelay_ref");
//////////////// Crusher Gradient: //////////////////////////////
double spoiler_strength=0.5*systemInfo->get_max_grad();
double spoiler_integral=4.0*fabs(deph.get_gradintegral().sum());
float crusher_integral=2.0*spoiler_integral;
crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, spoiler_strength);
crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation
//////////////// trigger: //////////////////////////////
trigger=SeqTrigger("fmri_trigger",1.0);
reset=SeqMagnReset("reset");
//////////////// Field-map template: //////////////////////////////
if(FieldMap) {
if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan
else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0);
}
//////////////// Build the sequence: //////////////////////////////
preppart+=reset;
// add fat saturation to template and repetitions
if(FatSaturation) preppart += fatsat;
dummypart= preppart + exc + deph + exc2acq + epiacq_dummy + crusherdelay + crusher;
templatepart= preppart + exc + deph_template + exc2acq + epiacq_template + crusherdelay + crusher;
imagingpart= preppart + exc + deph + exc2acq + epiacq + crusherdelay + crusher;
if(EPIRef) {
templatepart_ref= preppart + exc + deph_ref_template + exc2acq_ref + epiacq_ref_template + crusherdelay + crusher;
grappapart_ref= preppart + exc + deph_ref_grappa + exc2acq_ref + epiacq_ref_grappa + crusherdelay + crusher;
imagingpart_ref= preppart + exc + deph_ref + exc2acq_ref + epiacq_ref + crusherdelay + crusher;
}
templatepart.set_gradrotmatrixvector(bladerot);
imagingpart. set_gradrotmatrixvector(bladerot);
if(fMRITrigger) slicepart+= trigger; // trigger for PROPELLER interleave
slicepart_dummy = sliceloop( dummypart + trdelay )[exc];
slicepart_template = sliceloop( templatepart + trdelay )[exc];
slicepart += sliceloop( imagingpart + trdelay )[exc];
if(commonPars->get_RFSpoiling()) {
slicepart += phaseiter;
slicepart_dummy += phaseiter;
slicepart_template += phaseiter;
}
if(EPIRef) {
if(fMRITrigger) slicepart+= trigger; // trigger for EPIRef interleave
slicepart_template_ref = sliceloop( templatepart_ref + trdelay_ref )[exc];
slicepart_grappa_ref = sliceloop( grappapart_ref + trdelay_ref )[exc];
slicepart += sliceloop( imagingpart_ref + trdelay_ref )[exc];
if(commonPars->get_RFSpoiling()) {
slicepart += phaseiter;
slicepart_template_ref += phaseiter;
slicepart_grappa_ref += phaseiter;
}
}
if(FieldMap) scan += fmapscan + trdelay;
if(DummyCycles>0) {
scan+= dummyloop(
slicepart_dummy
)[DummyCycles];
}
scan += bladeloop(
slicepart_template
)[bladerot];
if(EPIRef) {
scan += slicepart_template_ref;
if(commonPars->get_ReductionFactor()>1) {
// Fully sampled k-space
scan+= grappaloop_ref(
slicepart_grappa_ref
)[deph_ref_grappa.get_epi_reduction_vector()];
}
}
scan+= reploop(
bladeloop(
slicepart
)[bladerot]
)[commonPars->get_NumOfRepetitions()];
set_sequence( scan );
}
void method_rels() {
////////////////// TE Timings: ////////////////////////////////
double exc_te=exc.get_duration()-exc.get_magnetic_center();
double min_echo_time_blade= exc_te + deph.get_duration()+epiacq.get_acquisition_center();
double min_echo_time_ref=0.0;
if(EPIRef) {
min_echo_time_ref=exc_te + deph_ref.get_duration()+epiacq_ref.get_acquisition_center();
}
double min_echo_time=STD_max(min_echo_time_blade, min_echo_time_ref);
if(commonPars->get_EchoTime()<min_echo_time) commonPars->set_EchoTime(min_echo_time);
if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time);
exc2acq= commonPars->get_EchoTime()-min_echo_time_blade;
exc2acq_ref=commonPars->get_EchoTime()-min_echo_time_ref;
////////////////// TR Timings: ////////////////////////////////
double slicedur =imagingpart.get_duration()*geometryInfo->get_nSlices();
double slicedur_ref=imagingpart_ref.get_duration()*geometryInfo->get_nSlices();
double mintr=STD_max(slicedur, slicedur_ref);
if(commonPars->get_RepetitionTime()<mintr) commonPars->set_RepetitionTime(mintr);
trdelay =secureDivision(commonPars->get_RepetitionTime()-slicedur, geometryInfo->get_nSlices());
trdelay_ref=secureDivision(commonPars->get_RepetitionTime()-slicedur_ref, geometryInfo->get_nSlices());
}
void method_pars_set() {
// extra information for the automatic reconstruction
epiacq. set_default_reco_index(userdef,0).set_reco_vector(slice,exc);
epiacq_template.set_default_reco_index(userdef,0).set_reco_vector(slice,exc);
epiacq_ref. set_default_reco_index(userdef,1).set_reco_vector(slice,exc);
epiacq_ref_template.set_default_reco_index(userdef,1).set_reco_vector(slice,exc);
epiacq_ref_grappa. set_default_reco_index(userdef,1).set_reco_vector(slice,exc);
epiacq.set_reco_vector(cycle,bladerot);
epiacq_template.set_reco_vector(cycle,bladerot);
recoInfo->set_DimValues(cycle,bladeangels);
}
};
/////////////////////////////////////////////////////
// entry point for the sequence module
ODINMETHOD_ENTRY_POINT
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