[Insight-users] image preprocessing

[Sarah Waldron]

I tried to build the files in

 InsightApplications/MRIBiasCorrection

by typing:



ccmake  . 

make



but I get all these errors:



sarah at sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .





sarah at sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ make

Scanning dependencies of target BiasCorrector

[  6%] Building CXX object CMakeFiles/BiasCorrector.dir/BiasCorrector.o

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:19:26:
error: vnl/vnl_math.h: No such file or directory

In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:20:28: error: itkWin32Header.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:25:22: error: itkArray.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:24:45:
error: itkMRIBiasFieldCorrectionFilter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:25:46:
error: itkMinimumMaximumImageCalculator.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:26:43:
error: itkBinaryThresholdImageFilter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:27:36:
error: itkImageRegionIterator.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:28:58:
error: itkZeroCrossingBasedEdgeDetectionImageFilter.h: No such file or
directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:29:45:
error: itkBinaryBallStructuringElement.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:30:46:
error: itkBinaryCrossStructuringElement.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:31:40:
error: itkBinaryDilateImageFilter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:32:32:
error: itkMaskImageFilter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:33:32:
error: itkCastImageFilter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:34:23: error: itkIndent.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:35:26:
error: itkHistogram.h: No such file or directory

In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:20:32:
error: itkExceptionObject.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:21:35:
error: itkMetaImageIOFactory.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:22:32:
error: itkImageFileReader.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:23:32:
error: itkImageFileWriter.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:25:45:
error: itkImageRegionIteratorWithIndex.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:26:30:
error: itkNumericTraits.h: No such file or directory

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:27:34:
error: itkOrientImageFilter.h: No such file or directory

In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,

                 from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:20:28: error: vnl/vnl_vector.h: No such file or directory

In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: ‘itk’ has not been declared

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: expected ‘,’ or ‘...’ before ‘<’ token

In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,

                 from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: variable or field ‘dump’ declared void

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: ‘vnl_vector’ was not declared in this scope

/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: expected primary-expression before ‘double’

make[2]: *** [CMakeFiles/BiasCorrector.dir/BiasCorrector.o] Error 1

make[1]: *** [CMakeFiles/BiasCorrector.dir/all] Error 2

make: *** [all] Error 2

sarah at sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ 



Can someone tell me what's wrong.

Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez at kitware.com> wrote:

From: Luis Ibanez <luis.ibanez at kitware.com>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11 at yahoo.com>
Cc: insight-users at itk.org
Date: Thursday, November 5, 2009, 2:29 AM


Hi Sarah,

You may want to try the same filters that are used for correcting 
for MRI intensity inhomogeneity.

See the directory:
InsightApplications/MRIBiasCorrection

These classes approximate the illumination distribution with a 

polynomial, and then use the polynomial in order to normalize
the intensity across space.

You may also find useful the following paper of the Insight Journal:

"N4ITK:  Nick's N3 ITK Implementation For MRI Bias Field Correction"
Tustison N., Gee J.
PICSL, University of Pennsylvania

http://www.insight-journal.org/browse/publication/640

http://hdl.handle.net/10380/3053




     Regards,


             Luis


----------------------------------------------------------------------------
On Wed, Nov 4, 2009 at 5:28 PM, Sarah Waldron <sarah.waldron11 at yahoo.com> wrote:


Hi,
I'm new to ITK. I have a series of brain images taken with a camera that when combined are supposed to form a 3 dimensional volume. The camera had a flash and the slices don't all have the same lighting and shadowing effects. Does anyone have any suggestions how to correct this so that all the images have the same light distribution?

Thanks,
Sarah




      
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