Debug opening dicom with rotation matrix

[clitk.git] / tools / clitkDicom2Image.cxx

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 399168c958cfa0f916b8769879f62a50481d86e7..5c9889b2e202bd437ebbfdff346a4c1cf64098f3 100644 (file)
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -91,7 +91,7 @@ int main(int argc, char * argv[])
     series_numbers.insert(series_number);
     theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
     theorientation[series_number] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
-    if (args_info.extract_series_flag) {
+    if (args_info.patientSystem_flag) {
       double n1 = theorientation[series_number][1]*theorientation[series_number][5]-
                   theorientation[series_number][2]*theorientation[series_number][4];
       double n2 = theorientation[series_number][3]*theorientation[series_number][2]-
@@ -201,6 +201,7 @@ int main(int argc, char * argv[])
     // Read write serie
     vvImageReader::Pointer reader = vvImageReader::New();
     reader->SetInputFilenames(sorted_files);
+    reader->SetPatientCoordinateSystem(args_info.patientSystem_flag);
     reader->Update(vvImageReader::DICOM);
     if (reader->GetLastError().size() != 0) {
       std::cerr << reader->GetLastError() << std::endl;
@@ -241,7 +242,7 @@ int main(int argc, char * argv[])
     }
     vvImageWriter::Pointer writer = vvImageWriter::New();
     writer->SetInput(image);
-    if (args_info.extract_series_flag && !image->GetTransform().empty())
+    if (args_info.patientSystem_flag && !image->GetTransform().empty())
       writer->SetSaveTransform(true);
     writer->SetOutputFileName(outfile);
     writer->Update();