基于Elastix配准C++实现+大量参数文件获取方法

elastix 5.2.0，参考官方文档可知我们需要一个.txt参数文件启动配准操作，例如将本地MRI影像配准到MNI标准空间中。

（1）基于Elastix配准

using namespace elastix;
typedef ELASTIX::ParameterMapType RegistrationParametersType;
typedef itk::ParameterFileParser ParserType;
// Create parser for transform parameters text file.
ParserType::Pointer file_parser = ParserType::New();
// Try parsing transform parameters text file.
file_parser->SetParameterFileName("...");  // parametersaffine  parametersBspline

try
{
    file_parser->ReadParameterFile();
}
catch (itk::ExceptionObject& e)
{
    std::cout << e.what() << std::endl;
    // Do some error handling!
}
// Retrieve parameter settings as map.
RegistrationParametersType parameters = file_parser->GetParameterMap();

printf("Successful!");
// 参数定义
const char* fixedImagePath = "...";   // MNI模板路径
const char* movingImagePath = "...";        // 用户MRI路径
const char* outputImagePath = "...";// 配准后图像输出路径

// 图像类型定义
constexpr unsigned int Dimension = 3;
using PixelType = float;
using FixedImageType = itk::Image<PixelType, Dimension>;
using MovingImageType = itk::Image<PixelType, Dimension>;
using FixedReaderType = itk::ImageFileReader<FixedImageType>;
using MovingReaderType = itk::ImageFileReader<MovingImageType>;
using ImageIOType = itk::NiftiImageIO;

// 读图
FixedReaderType::Pointer FixedReader = FixedReaderType::New();
ImageIOType::Pointer niftiIO = ImageIOType::New();
FixedReader->SetImageIO(niftiIO);
FixedReader->SetFileName(fixedImagePath);
FixedReader->Update();
FixedImageType::Pointer fixedImage = FixedReader->GetOutput();

MovingReaderType::Pointer MovingReader = MovingReaderType::New();
MovingReader->SetImageIO(niftiIO);
MovingReader->SetFileName(movingImagePath);
MovingReader->Update();
MovingImageType::Pointer movingImage = MovingReader->GetOutput();
// 创建参数映射
elastix::ELASTIX::ParameterMapType params;

// 配准
elastix:: ELASTIX elastix;
int error = 0;
try
{
    error = elastix.RegisterImages(
        static_cast<typename itk::DataObject::Pointer>(fixedImage.GetPointer()),
        static_cast<typename itk::DataObject::Pointer>(movingImage.GetPointer()),
        parameters, // Parameter map read in previous code
        ".",                      // 输出目录（当前目录）
        false,                    // 禁用日志文件
        true,                     // 控制台输出
        nullptr,                  // 固定图像掩膜
        nullptr                   // 移动图像掩膜
    );
}
catch (itk::ExceptionObject& e) {
    std::cerr << "Registration error: " << e.what() << std::endl;
}

if (error != 0) {
    std::cerr << "Registration failed with error code: " << error << std::endl;
}

// 应用变换到移动图像
    using ResampleFilterType = itk::ResampleImageFilter<MovingImageType, FixedImageType>;
    ResampleFilterType::Pointer resampler = ResampleFilterType::New();
// 获取结果图像
using RegistredImageType = itk::Image<PixelType, Dimension>;
if (elastix.GetResultImage().IsNotNull()) {
    RegistredImageType* resultImage = static_cast<RegistredImageType*>(
        elastix.GetResultImage().GetPointer()
        );

    // 应用变换到移动图像
    using ResampleFilterType = itk::ResampleImageFilter<MovingImageType, FixedImageType>;
    ResampleFilterType::Pointer resampler = ResampleFilterType::New();
    // 写入配准后的图像
    // 配置NIFTI头
    using WriterType = itk::ImageFileWriter<RegistredImageType>;
    WriterType::Pointer writer = WriterType::New();
    writer->SetImageIO(niftiIO);
    writer->SetFileName(outputImagePath);
    writer->SetInput(resultImage);
    writer->Update(); 
}
else {
    cout << "No image written!" << endl;
}

// 获取变换参数
elastix::ELASTIX::ParameterMapListType transformParams =
    elastix.GetTransformParameterMapList();

// 可选的变换参数处理...

（2）获取参数文件

参数文件可以通过3D Slicer中的Elastix参数文件路径获取，里面包含了刚体变换、仿射变换、非刚性BSpline变换等，可以学习。如下图所示：

注意！如果要输出图像，需要在参数文件中检查如下设置是否存在并且正确

(WriteResultImage "true")
(ResultImagePixelType "float")

后者需要和打开影像的格式一样（这里代码我为float）