[Insight-users] image preprocessing

Tue Nov 17 11:29:24 EST 2009

Ok it worked now. I just hadn't deleted the old cmakecache file.
Sorry about that.
Thanks!
Sarah

--- 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, 9:08 PM

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> 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> 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> 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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Kitware offers ITK Training Courses, for more information visit:

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