[Insight-users] image preprocessing

Bill Lorensen bill.lorensen at gmail.com
Mon Nov 16 13:09:50 EST 2009 

Sarah,

Sorry, I just tried my suggestion and I get the same errors. I do not see an
ITK_DIR in my cache.

Bill

On Mon, Nov 16, 2009 at 1:00 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> 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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>>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> 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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