/usr/share/odin/sequences/odinonep.cpp is in odin 1.8.4-1ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 | #include <odinseq/seqall.h>
class METHOD_CLASS : public SeqMethod {
public:
METHOD_CLASS(const STD_string& label);
void method_pars_init();
void method_seq_init();
void method_rels();
void method_pars_set();
private:
JDXenum OnepulseMode;
JDXint NumOfSamples;
JDXdouble PulseDuration;
JDXdouble FreqOffset;
SeqPulsarBP exc;
SeqPulsarBP refoc;
SeqAcq acq;
SeqDelay relaxdelay;
SeqDelay exc2refoc;
SeqDelay refoc2acq;
SeqObjLoop acculoop;
SeqObjList scanpart;
SeqGradConstPulse spoiler;
SeqVector averagevec; // index vector for averages
SeqVecIter phaseiter;
};
////////////////////////////////////////////////////////////////////////////
METHOD_CLASS::METHOD_CLASS (const STD_string& label)
: SeqMethod(label) {
set_description("A simple onepulse experiment (non-selective RF pulse + acquisition).");
}
////////////////////////////////////////////////////////////////////////////
void METHOD_CLASS::method_pars_init() {
OnepulseMode.add_item("FID");
OnepulseMode.add_item("SpinEcho");
OnepulseMode.set_actual("FID");
commonPars->set_EchoTime(0.0);
NumOfSamples=1024;
PulseDuration=1.0;
FreqOffset=0.0;
append_parameter(OnepulseMode,"OnepulseMode");
append_parameter(NumOfSamples,"NumOfSamples");
append_parameter(PulseDuration,"PulseDuration");
append_parameter(FreqOffset,"FreqOffset");
}
////////////////////////////////////////////////////////////////////////////
void METHOD_CLASS::method_seq_init() {
exc=SeqPulsarBP("exc",PulseDuration,commonPars->get_FlipAngle(),systemInfo->get_main_nucleus());
exc.set_pulse_type(excitation);
refoc=SeqPulsarBP("refoc",PulseDuration,180.0,systemInfo->get_main_nucleus());
refoc.set_pulse_type(refocusing);
acq=SeqAcq("acq",(unsigned int)NumOfSamples,commonPars->get_AcqSweepWidth(),1.0,systemInfo->get_main_nucleus());
exc.set_freqoffset(FreqOffset);
refoc.set_freqoffset(FreqOffset);
acq.set_freqoffset(FreqOffset);
if(commonPars->get_RFSpoiling()) {
exc.set_phasespoiling(4, 90.0);
acq.set_phasespoiling(4, 90.0);
refoc.set_phasespoiling(4, 90.0, 90.0);
phaseiter=SeqVecIter("phaseiter");
phaseiter.add_vector(exc.get_phaselist_vector());
phaseiter.add_vector(acq.get_phaselist_vector());
phaseiter.add_vector(refoc.get_phaselist_vector());
} else {
refoc.set_phase(90.0);
}
spoiler=SeqGradConstPulse("spoiler",sliceDirection,0.5*systemInfo->get_max_grad(),2.0);
relaxdelay=SeqDelay("relaxdelay");
exc2refoc=SeqDelay("exc2refoc");
refoc2acq=SeqDelay("refoc2acq");
acculoop=SeqObjLoop("acculoop");
if(OnepulseMode=="SpinEcho") scanpart= exc + exc2refoc + spoiler + refoc + spoiler + refoc2acq + acq + relaxdelay;
else scanpart= exc + acq + spoiler + relaxdelay;
if(commonPars->get_RFSpoiling()) scanpart += phaseiter;
averagevec=SeqVector("averagevec",commonPars->get_NumOfRepetitions());
set_sequence( acculoop(scanpart)[averagevec] );
}
////////////////////////////////////////////////////////////////////////////
void METHOD_CLASS::method_rels() {
float min_echo_time1=0.0;
float min_echo_time2=0.0;
if(OnepulseMode=="SpinEcho") {
min_echo_time1=(exc.get_duration()-exc.get_magnetic_center())+spoiler.get_duration()+refoc.get_magnetic_center();
min_echo_time2=(refoc.get_duration()-refoc.get_magnetic_center())+spoiler.get_duration()+acq.get_acquisition_center();
} else {
min_echo_time1=(exc.get_duration()-exc.get_magnetic_center())+acq.get_acquisition_center();
}
if(commonPars->get_EchoTime()<min_echo_time1) commonPars->set_EchoTime(min_echo_time1);
if(commonPars->get_EchoTime()<min_echo_time2) commonPars->set_EchoTime(min_echo_time2);
exc2refoc=commonPars->get_EchoTime()-min_echo_time1;
refoc2acq=commonPars->get_EchoTime()-min_echo_time2;
if(scanpart.get_duration()>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scanpart.get_duration());
relaxdelay.set_duration(commonPars->get_RepetitionTime()-scanpart.get_duration());
}
////////////////////////////////////////////////////////////////////////////
void METHOD_CLASS::method_pars_set() {
acq.set_reco_vector(average,averagevec);
recoInfo->set_Recipe("averagecoll | averagesum | kspace | fft | slicecoll | image | store"); // Quick hack to display a single spectrum from multiple averages
}
////////////////////////////////////////////////////////////////////////////
// entry point for the sequence module
ODINMETHOD_ENTRY_POINT
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