[Insight-users] image preprocessing

Mon Nov 16 13:00:44 EST 2009

When you ran ccmake did you specify ITK_DIR to tell the app where to find
itk's build?

On Mon, Nov 16, 2009 at 12:22 PM, Sarah Waldron
<sarah.waldron11 at yahoo.com>wrote:

> 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<http://mc/compose?to=sarah.waldron11@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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>>
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>>
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>>
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>>
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>>
>
>
> _____________________________________
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>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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>
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