ArrayXcd MP2RAGE::signal(const double M0, const double T1, const double B1, const double eta) const {
return One_MP2RAGE(m_flip, m_TR, m_N, m_TD, M0, T1, B1, eta);
}
int main(int argc, char **argv) {
args::ArgumentParser parser(
"Calculates T1/B1 maps from MP2/3-RAGE data\nhttp://github.com/spinicist/QUIT");
args::Positional<std::string> input_path(parser, "INPUT FILE", "Path to complex MP-RAGE data");
args::HelpFlag help(parser, "HELP", "Show this help message", {'h', "help"});
args::Flag verbose(parser, "VERBOSE", "Print more information", {'v', "verbose"});
args::ValueFlag<int> threads(parser,
"THREADS",
"Use N threads (default=4, 0=hardware limit)",
{'T', "threads"},
QI::GetDefaultThreads());
args::ValueFlag<std::string> outarg(
parser, "OUTPREFIX", "Add a prefix to output filenames", {'o', "out"});
args::ValueFlag<std::string> json_file(
parser, "FILE", "Read JSON input from file instead of stdin", {"file"});
args::ValueFlag<float> beta_arg(
parser,
"BETA",
"Regularisation factor for robust contrast calculation "
"(https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099676)",
{'b', "beta"},
0.0);
args::Flag t1(parser, "T1", "Calculate T1 map via spline look-up", {'t', "t1"});
QI::ParseArgs(parser, argc, argv, verbose, threads);
auto inFile = QI::ReadImage<QI::SeriesXF>(QI::CheckPos(input_path), verbose);
auto ti_1 = itk::ExtractImageFilter<QI::SeriesXF, QI::VolumeXF>::New();
auto ti_2 = itk::ExtractImageFilter<QI::SeriesXF, QI::VolumeXF>::New();
auto region = inFile->GetLargestPossibleRegion();
region.GetModifiableSize()[3] = 0;
ti_1->SetExtractionRegion(region);
ti_1->SetDirectionCollapseToSubmatrix();
ti_1->SetInput(inFile);
region.GetModifiableIndex()[3] = 1;
ti_2->SetExtractionRegion(region);
ti_2->SetDirectionCollapseToSubmatrix();
ti_2->SetInput(inFile);
QI::Log(verbose, "Generating MP2 contrasts");
using BinaryFilter = itk::BinaryGeneratorImageFilter<QI::VolumeXF, QI::VolumeXF, QI::VolumeF>;
auto MP2Filter = BinaryFilter::New();
MP2Filter->SetInput1(ti_1->GetOutput());
MP2Filter->SetInput2(ti_2->GetOutput());
const float &beta = beta_arg.Get();
MP2Filter->SetFunctor([&](const std::complex<float> &p1, const std::complex<float> &p2) {
return MP2Contrast(p1, p2, beta);
});
MP2Filter->Update();
const std::string out_prefix = outarg ? outarg.Get() : QI::StripExt(input_path.Get());
QI::WriteImage(MP2Filter->GetOutput(), out_prefix + "_MP2" + QI::OutExt(), verbose);
if (t1) {
QI::Log(verbose, "Reading sequence information");
rapidjson::Document input =
json_file ? QI::ReadJSON(json_file.Get()) : QI::ReadJSON(std::cin);
QI::MP2RAGESequence mp2rage_sequence(input["MP2RAGE"]);
QI::Log(verbose, "Building look-up spline");
int num_entries = 100;
Eigen::ArrayXd T1_values = Eigen::ArrayXd::LinSpaced(num_entries, 0.25, 4.0);
Eigen::ArrayXd MP2_values(num_entries);
for (int i = 0; i < num_entries; i++) {
const auto sig = One_MP2RAGE(1., T1_values[i], 1., mp2rage_sequence);
const float mp2 = MP2Contrast(sig[0], sig[1]);
if ((i > 0) && (mp2 > MP2_values[i - 1])) {
num_entries = i;
break;
} else {
MP2_values[i] = mp2;
}
}
QI::Log(verbose, "Lookup table length = {}", num_entries);
QI::SplineInterpolator mp2_to_t1(MP2_values.head(num_entries), T1_values.head(num_entries));
if (beta) {
QI::Log(verbose, "Recalculating unregularised MP2 image");
MP2Filter->SetFunctor(
[&](const std::complex<float> &p1, const std::complex<float> &p2) {
return MP2Contrast(p1, p2, 0.0);
});
MP2Filter->Update();
}
using UnaryFilter = itk::UnaryGeneratorImageFilter<QI::VolumeF, QI::VolumeF>;
auto T1LookupFilter = UnaryFilter::New();
T1LookupFilter->SetInput(MP2Filter->GetOutput());
auto lookup = [&](const float &p) { return mp2_to_t1(p); };
T1LookupFilter->SetFunctor(lookup);
QI::Log(verbose, "Calculating T1");
T1LookupFilter->Update();
QI::WriteImage(T1LookupFilter->GetOutput(), out_prefix + "_MP2_T1" + QI::OutExt(), verbose);
}
QI::Log(verbose, "Finished.");
return EXIT_SUCCESS;
}