COMP: Items identified by cppcheck

cppcheck is a static analizer that identified
several places where improvements to the code
could be made.

itkMABMISImageOperationFilter.hxx:265: performance: Variable 'dist' is reassigned a value before the old one has been used.
itkMABMISSimulateData.hxx:179: performance: Variable 'num' is reassigned a value before the old one has been used.
IGR3D_MABMIS_Testing.cxx:411: performance: Variable 'iTreeValid' is reassigned a value before the old one has been used.
IGR3D_MABMIS_Testing.cxx:692: performance: Variable 'val' is reassigned a value before the old one has been used.
IGR3D_MABMIS_Testing.cxx:694: performance: Variable 'val' is reassigned a value before the old one has been used.
itkMABMISDeformationFieldFilter.hxx:242: style: Found duplicate branches for 'if' and 'else'.
itkMABMISImageOperationFilter.hxx:233: style: The scope of the variable 'value1' can be reduced.
itkMABMISImageOperationFilter.hxx:233: style: The scope of the variable 'value2' can be reduced.
itkMABMISDeformationFieldFilter.hxx:353: style: The scope of the variable 'idx_x' can be reduced.
itkMABMISDeformationFieldFilter.hxx:353: style: The scope of the variable 'idx_y' can be reduced.
itkMABMISDeformationFieldFilter.hxx:353: style: The scope of the variable 'idx_z' can be reduced.
itkMABMISDeformationFieldFilter.hxx:522: style: The scope of the variable 'idx_x' can be reduced.
itkMABMISDeformationFieldFilter.hxx:522: style: The scope of the variable 'idx_y' can be reduced.
itkMABMISDeformationFieldFilter.hxx:522: style: The scope of the variable 'idx_z' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'b' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'c' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'd' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'b1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'c1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:761: style: The scope of the variable 'd1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'b' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'c' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'd' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'b1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'c1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'd1' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'combined' can be reduced.
itkMABMISDeformationFieldFilter.hxx:822: style: The scope of the variable 'weight' can be reduced.
itkMABMISDeformationFieldFilter.hxx:358: style: Variable 'idx_x' is assigned a value that is never used.
itkMABMISDeformationFieldFilter.hxx:359: style: Variable 'idx_y' is assigned a value that is never used.
itkMABMISDeformationFieldFilter.hxx:360: style: Variable 'idx_z' is assigned a value that is never used.
itkMABMISDeformationFieldFilter.hxx:527: style: Variable 'idx_x' is assigned a value that is never used.
itkMABMISDeformationFieldFilter.hxx:528: style: Variable 'idx_y' is assigned a value that is never used.
itkMABMISDeformationFieldFilter.hxx:529: style: Variable 'idx_z' is assigned a value that is never used.
itkMABMISSimulateData.hxx:86: style: Variable 'size_df' is assigned a value that is never used.
itkMABMISSimulateData.hxx:478: style: Variable 'dim' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:326: style: Variable 'numSimulatedAtlase' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:748: style: Variable 'neighborSize' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1054: style: Variable 'atlas_simulated_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1058: style: Variable 'dir_sep' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1064: style: Variable 'i' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1274: style: Variable 'atlas_simulated_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1275: style: Variable 'atlas_total_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1281: style: Unused variable: originalIntensityImageFileNames
IGR3D_MABMIS_Testing.cxx:1282: style: Unused variable: deformedImgFileNames
IGR3D_MABMIS_Testing.cxx:1283: style: Unused variable: deformedImgFileNamesImg
IGR3D_MABMIS_Testing.cxx:1284: style: Unused variable: deformedSegFileNames
IGR3D_MABMIS_Testing.cxx:1285: style: Unused variable: deformedSegFileNamesImg
IGR3D_MABMIS_Testing.cxx:1286: style: Unused variable: deformationFieldFileNames
IGR3D_MABMIS_Testing.cxx:1330: style: Variable 'dir_sep' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1386: style: Variable 'deformedSegmentFileNameImg' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1458: style: Variable 'atlas_simulated_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1459: style: Variable 'atlas_total_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1463: style: Variable 'dir_sep' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1483: style: Unused variable: fixedImageFileName
IGR3D_MABMIS_Testing.cxx:1484: style: Unused variable: fixedSegmentFileName
IGR3D_MABMIS_Testing.cxx:1618: style: Variable 'atlas_simulated_size' is assigned a value that is never used.
IGR3D_MABMIS_Testing.cxx:1619: style: Variable 'atlas_total_size' is assigned a value that is never used.
itkMABMISAtlasXMLFile.h:27: performance: Variable 'm_DataDirectory' is assigned in constructor body. Consider performing initialization in initialization list.
itkMABMISAtlasXMLFile.h:28: performance: Variable 'm_OutputDirectory' is assigned in constructor body. Consider performing initialization in initialization list.
IGR3D_MABMIS_Training.cxx:772: style: Unused variable: allDeformationFieldFileName
itkMABMISAtlasXMLFile.cxx:112: performance: Function parameter 'input' should be passed by reference.
IGR3D_MABMIS_Testing.cxx:1753: style: The function 'ReadImgInfo' is never used.
IGR3D_MABMIS_Testing.cxx:248: style: The function 'strtrim' is never used.