[Insight-users] image preprocessing

Bill Lorensen bill.lorensen at gmail.com
Mon Nov 16 13:26:03 EST 2009 

Sarah,

Try this:

ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true
../InsightApplications//MRIBiasCorrection/

where ../InsightApplications//MRIBiasCorrection/ points to your source.

Then, you will need to define ITK_DIR during the configure process.

Bill

On Mon, Nov 16, 2009 at 1:09 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> 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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>>>> http://www.kitware.com/products/protraining.html
>>>>
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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:
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>>>
>>
>
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