[Insight-users] image preprocessing

Bill Lorensen bill.lorensen at gmail.com
Mon Nov 16 16:08:50 EST 2009 

I'm sorry I can't help further. It works fine on my system. Maybe someone
else can comment.

Bill


On Mon, Nov 16, 2009 at 4:05 PM, Sarah Waldron <sarah.waldron11 at yahoo.com>wrote:

> Yes I pressed "c" then changed the directory for ITK when it gave me an
> error. Then I pressed "g". Then I typed make in the terminal and got this
> error although a make file did become created in the folder.
>
> --- 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, 8:45 PM
>
>
> 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<http://mc/compose?to=sarah.waldron11@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<http://mc/compose?to=bill.lorensen@gmail.com>
>> >* wrote:
>>
>>
>> From: Bill Lorensen <bill.lorensen at gmail.com<http://mc/compose?to=bill.lorensen@gmail.com>
>> >
>>
>> Subject: Re: [Insight-users] image preprocessing
>> To: "Sarah Waldron" <sarah.waldron11 at yahoo.com<http://mc/compose?to=sarah.waldron11@yahoo.com>
>> >
>> Cc: "Luis Ibanez" <luis.ibanez at kitware.com<http://mc/compose?to=luis.ibanez@kitware.com>>,
>> insight-users at itk.org <http://mc/compose?to=insight-users@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:
>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> 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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>>>>>
>>>>>
>>>>
>>>
>>
>>
>
>
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