[Insight-users] image preprocessing

Bill Lorensen bill.lorensen at gmail.com
Mon Nov 16 15:45:26 EST 2009 

When you run ccmake, I assume you configure and generate? Are there errors
reported?

On Mon, Nov 16, 2009 at 3:26 PM, Sarah Waldron <sarah.waldron11 at yahoo.com>wrote:

> Ok I did what you said, and I set the ITK-directory. But it is still not
> building. Here's the terminal output:
>
> sarah at sarah-laptop:~$ ccmake
> -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true
> InsightApplications-3.10.0/MRIBiasCorrection/
>
>
> sarah at sarah-laptop:~$ make
> make: *** No targets specified and no makefile found.  Stop.
>
> --- On *Mon, 11/16/09, Bill Lorensen <bill.lorensen at gmail.com>* wrote:
>
>
> From: Bill Lorensen <bill.lorensen at gmail.com>
>
> Subject: Re: [Insight-users] image preprocessing
> To: "Sarah Waldron" <sarah.waldron11 at yahoo.com>
> Cc: "Luis Ibanez" <luis.ibanez at kitware.com>, insight-users at itk.org
> Date: Monday, November 16, 2009, 6:26 PM
>
> 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<http://mc/compose?to=bill.lorensen@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<http://mc/compose?to=bill.lorensen@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<http://mc/compose?to=sarah.waldron11@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<http://mc/compose?to=luis.ibanez@kitware.com>
>>>> >* wrote:
>>>>
>>>>
>>>> From: Luis Ibanez <luis.ibanez at kitware.com<http://mc/compose?to=luis.ibanez@kitware.com>
>>>> >
>>>> Subject: Re: [Insight-users] image preprocessing
>>>> To: "Sarah Waldron" <sarah..waldron11 at yahoo.com<http://mc/compose?to=sarah..waldron11@yahoo.com>
>>>> >
>>>> Cc: insight-users at itk.org <http://mc/compose?to=insight-users@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
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> 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
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
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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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