[Insight-users] MRIBiasCorrection Example: problem reading meta files

[digvijay singh]

hello luis and others
i tried compiling the the MRIBiasCorrector Example(solaris8 gcc 
2.95--) and was able to do that successfully. However upon trying 
to run one of the executables IntensityHistogram3D with the 
following usage:
MRIBiasCorrection 1.0 (21.June.2001)
usage: IntensityHistogram3D --file file
        [--mask] file --bin-size double

--file file
         image file [meta image format]
--mask file
         mask image. If mask is specified, this program
         uses the pixels greater than zero only in the mask file
--bin-size double
         intensity interval

example: IntensityHistogram3D --file sampl.mhd
          --mask sample.mask.mhd --bin-size 100

upon the command line:IntensityHistogram3D --file 
/home/vertebra/digvijay/itk/proj_1/MRIBiasCorrection --bin-size 
100
i got the following error.

NDims required and not defined.
MetaObject: Read: MET_Read Failed
MetaImage: M_Read: Error parsing file
MetaImage: Read: Cannot parse file

itk::ExceptionObject (0xffbeee88)
Location: "Unknown"

The details of the file are
NDims = 3
DimSize = 181 217 180
ElementType = MET_UCHAR
ElementSpacing = 1.0 1.0 1.0
ElementByteOrderMSB = False
ElementDataFile = brainweb1e1a10f20.raw

i tried converting to mhd and reading from other examples as well 
 from the brainweb project but was not able to rectify the 
problem.
Kindly advise.
thanks
digvijay

the cmakelists.txt file is:
SET(ITK_SOURCE_DIR 
/home/encephalon/mstyner/itk/Insight_Nightly/Insight)
SET(ITK_LIB_DIR 
/home/encephalon/mstyner/itk/Insight_Nightly/lib)
SET(ITK_BINARY_DIR 
/home/encephalon/mstyner/itk/Insight_Nightly/build)

SET(HOME  /home/vertebra/digvijay)

SET(ITK_PROJECT_DIR ${HOME}/itk/proj_1/MRIBiasCorrection)


INCLUDE (${CMAKE_ROOT}/Modules/FindOpenGL.cmake)
INCLUDE (${CMAKE_ROOT}/Modules/FindGLU.cmake)





LINK_DIRECTORIES( ${ITK_LIB_DIR} )

INCLUDE_DIRECTORIES(
${ITK_SOURCE_DIR}/Utilities
${ITK_SOURCE_DIR}/Utilities/MetaIO
${ITK_SOURCE_DIR}/Code/IO
${ITK_SOURCE_DIR}/Code/Common
${ITK_SOURCE_DIR}/Code/BasicFilters
${ITK_SOURCE_DIR}/Code/Algorithms
${ITK_SOURCE_DIR}/Code/Numerics
${ITK_SOURCE_DIR}/Code/Numerics/Statistics
${ITK_SOURCE_DIR}/Examples/MRIBiasCorrection
${ITK_SOURCE_DIR}/Code/Common
${ITK_SOURCE_DIR}/Code/BasicFilters
${ITK_SOURCE_DIR}/Code/Algorithms
${ITK_SOURCE_DIR}/Code/IO
${ITK_SOURCE_DIR}/Auxiliary/FltkImageViewer
${ITK_BINARY_DIR}/Auxiliary/FltkImageViewer
${ITK_SOURCE_DIR}/Code/Numerics/vxl
${ITK_SOURCE_DIR}/Code/Numerics/vxl/vcl
${ITK_BINARY_DIR}
${ITK_BINARY_DIR}/Code/Numerics/vxl/vcl
${ITK_PROJECT_DIR}

${OPENGL_INCLUDE_PATH}
)

SOURCE_FILES(ImageCorrector_SRCS
OptionList.cxx
ImageCorrector.cxx
)


SOURCE_FILES(BiasImageGenerator_SRCS
OptionList.cxx
BiasImageGenerator.cxx
)


SOURCE_FILES(BiasFieldEstimator_SRCS
OptionList.cxx
BiasFieldEstimator.cxx
)

SOURCE_FILES(InterSliceIntensityCorrector_SRCS
OptionList.cxx
InterSliceIntensityCorrector.cxx
)

SOURCE_FILES(IntensityHistogram3D_SRCS
OptionList.cxx
IntensityHistogram3D.cxx
)

SOURCE_FILES(SlabIdentifier_SRCS
OptionList.cxx
SlabIdentifier.cxx
)

SOURCE_FILES(EnergyTablePlotter_SRCS
OptionList.cxx
EnergyTablePlotter.cxx
)


SOURCE_FILES(BiasCorrector_SRCS
OptionList.cxx
BiasCorrector.cxx
)

LINK_DIRECTORIES(
${ITK_BINARY_DIR}/Code/BasicFilters
${ITK_BINARY_DIR}/Code/Numerics
${ITK_BINARY_DIR}/Code/Numerics/Statistics
${ITK_BINARY_DIR}/Code/IO
)


LINK_DIRECTORIES( ${ITK_LIB_DIR} )

LINK_LIBRARIES (
ITKCommon
ITKIO
ITKBasicFilters
ITKStatistics
ITKNumerics
MetaIO
VXLNumerics
VXLNumerics
ITKAlgorithms
ITKBasicFilters
ITKNumerics
itkpng
ITKStatistics
MetaIO
itkzlib
param
vtkFltk
FltkImageViewer
FEM
ITKCommon
${FLTK_LIBRARY}
${OPENGL_LIBRARY}
${GLU_LIBRARY}
-lpthread -ldl -lm

)

ADD_DEFINITIONS(-ftemplate-depth-50 -D_PTHREADS)


ADD_EXECUTABLE(BiasFieldEstimator BiasFieldEstimator_SRCS)
ADD_EXECUTABLE(BiasImageGenerator BiasImageGenerator_SRCS)
ADD_EXECUTABLE(IntensityHistogram3D IntensityHistogram3D_SRCS)
ADD_EXECUTABLE(InterSliceIntensityCorrector 
InterSliceIntensityCorrector_SRCS)
ADD_EXECUTABLE(SlabIdentifier SlabIdentifier_SRCS)
ADD_EXECUTABLE(EnergyTablePlotter EnergyTablePlotter_SRCS)
ADD_EXECUTABLE(ImageCorrector ImageCorrector_SRCS)
ADD_EXECUTABLE(BiasCorrector BiasCorrector_SRCS)