1 #ifndef __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
2 #define __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
4 #include "bbSlicer_EXPORT.h"
5 #include "bbtkAtomicBlackBox.h"
14 #include <ModuleDescriptionUtilities.h>
15 #include <ModuleDescriptionParser.h>
16 #include <ModuleParameterGroup.h>
17 #include <ModuleDescription.h>
18 #include <ModuleParameter.h>
20 #include "CreationTool.h"
24 class bbSlicer_EXPORT MRIBiasFieldCorrection
26 public bbtk::AtomicBlackBox {
27 BBTK_BLACK_BOX_INTERFACE ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
31 BBTK_DECLARE_INPUT ( InputImage , std::string );
32 BBTK_DECLARE_INPUT ( InputMask , std::string );
33 BBTK_DECLARE_INPUT ( OutputImage , std::string );
34 BBTK_DECLARE_INPUT ( AlgorithmType , std::string );
35 BBTK_DECLARE_INPUT ( ShrinkFactor , int );
36 BBTK_DECLARE_INPUT ( MaximumNumberOfIterations , int );
37 BBTK_DECLARE_INPUT ( NumberOfFittingLevels , int );
38 BBTK_DECLARE_INPUT ( WienerFilterNoise , double );
39 BBTK_DECLARE_INPUT ( FullWidthAtHalfMaximum , double );
40 BBTK_DECLARE_INPUT ( ConvergenceThreshold , double );
44 BBTK_PROCESS ( Process ) ;
47 void execute ( std::string lib , int _argc , char * _argv[] ) ;
50 BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
51 BBTK_NAME ( "MRIBiasFieldCorrection" ) ;
52 BBTK_AUTHOR ( "Sylvain Jaume MIT" ) ;
53 BBTK_DESCRIPTION ( "Corrects 3D MRI images corrupted by MRI gain field effect. This module removes the slow-varying intensity variation from a 3D image. The output image has a higher contrast locally and the visualization and reading of the image are improved. This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation see EMSegment module. The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume MIT for NA-MIC http://na-mic.org." ) ;
54 BBTK_CATEGORY ( "Legacy.Filtering" ) ;
56 // GENERATED DESCRPTION
58 BBTK_INPUT(MRIBiasFieldCorrection , InputImage , "InputImage" , std::string, "");
59 BBTK_INPUT(MRIBiasFieldCorrection , InputMask , "InputMask" , std::string, "");
60 BBTK_INPUT(MRIBiasFieldCorrection , OutputImage , "OutputImage" , std::string, "");
61 BBTK_INPUT(MRIBiasFieldCorrection , AlgorithmType , "AlgorithmType" , std::string, "");
62 BBTK_INPUT(MRIBiasFieldCorrection , ShrinkFactor , "ShrinkFactor" , int, "");
63 BBTK_INPUT(MRIBiasFieldCorrection , MaximumNumberOfIterations , "MaximumNumberOfIterations" , int, "");
64 BBTK_INPUT(MRIBiasFieldCorrection , NumberOfFittingLevels , "NumberOfFittingLevels" , int, "");
65 BBTK_INPUT(MRIBiasFieldCorrection , WienerFilterNoise , "WienerFilterNoise" , double, "");
66 BBTK_INPUT(MRIBiasFieldCorrection , FullWidthAtHalfMaximum , "FullWidthAtHalfMaximum" , double, "");
67 BBTK_INPUT(MRIBiasFieldCorrection , ConvergenceThreshold , "ConvergenceThreshold" , double, "");
69 // EO GENERATED DESCRIPTION
71 BBTK_END_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection ) ;
74 #endif // __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__