image preprocessing

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image preprocessing

by Sarah Waldron :: Rate this Message:

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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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Re: image preprocessing

by Luis Ibanez :: Rate this Message:

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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@...> 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

Re: image preprocessing

by Sarah Waldron :: Rate this Message:

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I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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

Re: image preprocessing

by Bill Lorensen-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Bill Lorensen-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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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Re: image preprocessing

by Bill Lorensen-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Sarah Waldron :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

Ok I did what you said, and I set the ITK-directory. But it is still not building. Here's the terminal output:

sarah@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.
sarah@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Sarah Waldron :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

Ok I did what you said, and I set the ITK-directory. But it is still not building. Here's the terminal output:

sarah@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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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Re: image preprocessing

by Bill Lorensen-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> 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@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>

Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Sarah Waldron :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>

Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Bill Lorensen-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> 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@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>

Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>

Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www.itk.org/mailman/listinfo/insight-users

Re: image preprocessing

by Sarah Waldron :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

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@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> wrote:

From: Bill Lorensen <bill.lorensen@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>
Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/

sarah@sarah-laptop:~$ make
make: *** No targets specified and no makefile found. Stop.

--- On Mon, 11/16/09, Bill Lorensen <bill.lorensen@...> wrote:

From: Bill Lorensen <bill.lorensen@...>

Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah.waldron11@...>

Cc: "Luis Ibanez" <luis.ibanez@...>, insight-users@...
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@...> 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@...> 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@...> wrote:

I tried to build the files in
InsightApplications/MRIBiasCorrection
by typing:

ccmake .
make

but I get all these errors:

sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .

sarah@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@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$

Can someone tell me what's wrong.
Sarah.

--- On Thu, 11/5/09, Luis Ibanez <luis.ibanez@...> wrote:

From: Luis Ibanez <luis.ibanez@...>
Subject: Re: [Insight-users] image preprocessing
To: "Sarah Waldron" <sarah..waldron11@...>
Cc: insight-users@...
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@...> 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:
http://www..itk.org/mailman/listinfo/insight-users