├── .gitignore ├── 00_Versioning ├── 00_Versioning.pptx ├── 00_Versioning_Git.pptx ├── Introduction_to_Version_Control_using_Git_and_Github.pdf └── code │ └── testDocument.txt ├── 01_Setup ├── 01_Setup.pptx └── code │ └── hello_world.cxx ├── 02_CMake ├── CMake.pptx └── code │ ├── CMakeLists.txt │ └── src │ └── main.cxx ├── 03_OOP ├── 03_OOP.pptx └── code │ ├── CMakeLists.txt │ └── src │ ├── classes │ ├── add.h │ ├── base.h │ └── difference.h │ └── main.cxx ├── 04_STL ├── STL.pptx └── code │ ├── CMakeLists.txt │ └── src │ ├── stl.cxx │ └── template.cxx ├── 05_CPP11 ├── CPP11_contd.pptx └── code │ ├── CMakeLists.txt │ └── src │ ├── lambda.cxx │ ├── sharedptr.cxx │ └── uniqueptr.cxx ├── 06_ITK-1_Segmentation ├── ITK-Segmentation.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ ├── T2.nii │ └── output.nii │ └── src │ └── main.cxx ├── 07_ITK-2_Multiplication ├── ITK-Multiplication.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ ├── FA.nii.gz │ └── mask.nii.gz │ └── src │ └── main.cxx ├── 08_ITK-3_Registration ├── ITK-Registration.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ ├── 1.nii.gz │ ├── 2.nii.gz │ ├── 2mask.nii.gz │ ├── output.nii │ ├── output1000.nii │ ├── output20.nii │ ├── rev_output_image.nii │ └── rev_output_mask.nii │ └── src │ └── main.cxx ├── 09_ITK-4_LinearAlgebra ├── ITK-LinearAlgebra.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ └── src │ └── main.cxx ├── 10_ITK-5_PipelineConstruction ├── ITK-Pipeline.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ ├── T2.nii.gz │ ├── T2_ref.nii.gz │ └── output.nii.gz │ └── src │ └── main.cxx ├── 11_ErrorHandling ├── ErrorHandling.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ └── src │ ├── assert.cxx │ └── exception.cxx ├── 12_UnitTesting ├── UnitTesting.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ └── testImage.nii.gz │ ├── src │ ├── BasicApp.h │ ├── cbicaCmdParser.cpp │ ├── cbicaCmdParser.h │ ├── cbicaITKSafeImageIO.h │ ├── cbicaUtilities.cpp │ ├── cbicaUtilities.h │ └── main.cxx │ └── testing │ ├── CMakeLists.txt │ └── testExe.cxx ├── 13_ITK-6_ML ├── ITK-ML.pptx └── code │ ├── CMakeLists.txt │ ├── README.md │ ├── data │ ├── README.txt │ ├── machine_learning │ │ ├── 301D00252-20040121.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00252-20040121.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00252-20040121.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00252-20040121.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00252-20040121.manual.mask.nii.gz │ │ ├── 301D00252-20040121_foreground.nii.gz │ │ ├── 301D00262-20040114.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00262-20040114.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00262-20040114.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00262-20040114.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00262-20040114.manual.mask.nii.gz │ │ ├── 301D00262-20040114_foreground.nii.gz │ │ ├── 301D00293-20040211.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00293-20040211.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00293-20040211.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00293-20040211.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00293-20040211.manual.mask.nii.gz │ │ ├── 301D00293-20040211_foreground.nii.gz │ │ ├── 301D00368-20040329.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.manual.mask.nii.gz │ │ ├── 301D00368-20040329_foreground.nii.gz │ │ ├── 301D00373-20040319.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00373-20040319.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00373-20040319.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00373-20040319.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00373-20040319.manual.mask.nii.gz │ │ ├── 301D00373-20040319_foreground.nii.gz │ │ ├── 301D00377-20040311.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00377-20040311.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00377-20040311.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00377-20040311.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00377-20040311.manual.mask.nii.gz │ │ ├── 301D00377-20040311_foreground.nii.gz │ │ ├── 302D10226-20040128.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10226-20040128.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10226-20040128.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10226-20040128.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10226-20040128.manual.mask.nii.gz │ │ ├── 302D10226-20040128_foreground.nii.gz │ │ ├── 302D10245-20040126.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10245-20040126.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10245-20040126.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10245-20040126.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10245-20040126.manual.mask.nii.gz │ │ ├── 302D10245-20040126_foreground.nii.gz │ │ ├── 302D10347-20040406.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10347-20040406.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10347-20040406.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10347-20040406.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 302D10347-20040406.manual.mask.nii.gz │ │ ├── 302D10347-20040406_foreground.nii.gz │ │ ├── 303D20103-20040204.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 303D20103-20040204.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 303D20103-20040204.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 303D20103-20040204.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 303D20103-20040204.manual.mask.nii.gz │ │ ├── 303D20103-20040204_foreground.nii.gz │ │ └── list.csv │ └── test │ │ ├── 301D00293-20040211.T2.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00293-20040211_foreground.nii.gz │ │ ├── 301D00368-20040329.FL.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.PD.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ ├── 301D00368-20040329.T1.byte_nii.coreg.smooth.brain.correct.match.nii.gz │ │ └── 301D00368-20040329.manual.mask.nii.gz │ └── src │ ├── TestITK.h │ ├── TestITK.hxx │ ├── cbicaCmdParser.cpp │ ├── cbicaCmdParser.h │ ├── cbicaITKImageInfo.cpp │ ├── cbicaITKImageInfo.h │ ├── cbicaITKSafeImageIO.h │ ├── cbicaUtilities.cpp │ ├── cbicaUtilities.h │ └── main.cxx ├── 14_LinearAlgebra_Armadillo ├── LinearAlgebra_Armadillo.pptx └── code │ ├── CMakeLists.txt │ ├── data │ └── testImage.nii.gz │ └── src │ ├── cbicaCmdParser.cpp │ ├── cbicaCmdParser.h │ ├── cbicaITKSafeImageIO.h │ ├── cbicaUtilities.cpp │ ├── cbicaUtilities.h │ └── main.cxx ├── 15_MachineLearning_Shark └── code │ └── README.md ├── 16_ITK-6_DICOMHandling ├── DICOMHandling.pptx └── code │ ├── CMakeLists.txt │ └── src │ ├── cbicaUtilities.cpp │ ├── cbicaUtilities.h │ ├── dwiConversion.cxx │ └── simpleConversion.cxx ├── 17_CMake-CTest-CDash ├── CMake-CTest-CDash.pptx └── code │ ├── CMakeLists.txt │ ├── CTestConfig.cmake │ ├── data │ └── testImage.nii.gz │ ├── src │ ├── BasicApp.h │ ├── cbicaCmdParser.cpp │ ├── cbicaCmdParser.h │ ├── cbicaITKSafeImageIO.h │ ├── cbicaUtilities.cpp │ ├── cbicaUtilities.h │ └── main.cxx │ └── testing │ ├── CMakeLists.txt │ └── testExe.cxx ├── 18_MatlabToArma └── code │ ├── 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