diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h index f1f0041c1e..d9c3296fcf 100644 --- a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h +++ b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h @@ -1,148 +1,152 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkTractAnalyzer_h_ #define __mitkTractAnalyzer_h_ #include "QuantificationExports.h" #include #include "mitkImage.h" #include "mitkImageCast.h" #include #include namespace mitk{ -/** \class TractAnalyzer - */ +/** + * \brief Creates a region of interest for tract-specific analysis of existing TBSS data + * + * This class needs a 3D image (typically a mean FA skeleton as produced by the standard TBSS pipeline of FSL) + * and a user-defined point set defining the points through which the region of interest should pass. + */ class Quantification_EXPORT TractAnalyzer { public: TractAnalyzer(); ~TractAnalyzer() {} /** Image type definitions */ typedef itk::Image CharImageType; typedef itk::Image FloatImageType; /** \brief Main method for region of interest calculation * * A region of interest is calculated adding the segments between the points on the ROI * that was specified by the user. */ void MakeRoi(); /** \brief Sets the input image * * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS). */ mitk::TbssRoiImage::Pointer GetRoiImage() { return m_TbssRoi; } /** \brief Sets the input image * * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS). */ void SetInputImage(mitk::Image::Pointer inputImage) { m_InputImage = inputImage; } /** \brief Sets the user-defined point set * * Set the user-defined point sets. The region of interest must pass through these points. */ void SetPointSet(mitk::PointSet::Pointer pointSet) { m_PointSetNode = pointSet; } /** \brief Sets a lower bound for the threshold. * * Low fractional anisotropy values can indicate partial volume of non white matter tissue. * This thresholds limits the search for a region of interest to voxels with a minimum value. */ void SetThreshold(double threshold) { m_Threshold = threshold; } /** \brief Returns a string with the indices of points on the region of interest * * The region of interest calculated by the TractAnalyzer contains a list of ITK indices. * This method returns a string containing these indices for display in the GUI */ std::string GetPathDescription() { return m_PathDescription; } protected: /** \brief Calculates a segment of the region of interest * * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS). */ std::vector< itk::Index<3> > CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint); /** \brief Output TbssRoiImage */ mitk::TbssRoiImage::Pointer m_TbssRoi; /** \brief Inputimage */ mitk::Image::Pointer m_InputImage; /** \brief Threshold for ROI search */ double m_Threshold; /** \brief User defined point set */ mitk::PointSet::Pointer m_PointSetNode; /** \brief Path description in as string for display in GUI */ std::string m_PathDescription; private: }; } #endif //__itkTractAnalyzer_h_