I&#39;m sorry I can&#39;t help further. It works fine on my system. Maybe someone else can comment.<br><br>Bill<br><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 4:05 PM, Sarah Waldron <span dir="ltr">&lt;<a href="mailto:sarah.waldron11@yahoo.com">sarah.waldron11@yahoo.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
Yes I pressed &quot;c&quot; then changed the directory for ITK when it gave me an error. Then I pressed &quot;g&quot;. Then I typed make in the terminal and got this error although a make file did become created in the folder. <br>
<div class="im"><br>--- On <b>Mon, 11/16/09, Bill Lorensen <i>&lt;<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;</i></b> wrote:<br></div><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<div class="im"><br>From: Bill Lorensen &lt;<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;<br>Subject: Re: [Insight-users] image preprocessing<br>To: &quot;Sarah Waldron&quot; &lt;<a href="mailto:sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>&gt;<br>
Cc: &quot;Luis Ibanez&quot; &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>&gt;, <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br></div>Date: Monday, November 16, 2009, 8:45 PM<div>
<div></div><div class="h5"><br><br><div>When you run ccmake, I assume you configure and generate? Are there errors reported?<br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 3:26 PM,
 Sarah Waldron <span dir="ltr">&lt;<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">

<div>Ok I did what you said, and I set the ITK-directory. But it is still not building. Here&#39;s the terminal output:<br><br>sarah@sarah-laptop:~$ ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true InsightApplications-3.10.0/MRIBiasCorrection/<br>

<br><br>sarah@sarah-laptop:~$ make<br>make: *** No targets specified and no makefile found.  Stop.<br><br></div>--- On <b>Mon, 11/16/09, Bill Lorensen <i>&lt;<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;</i></b> wrote:<br>

<blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Bill Lorensen &lt;<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;<div>

<br>Subject: Re: [Insight-users] image preprocessing<br>To: &quot;Sarah Waldron&quot; &lt;<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>&gt;<br></div>
<div>Cc: &quot;Luis Ibanez&quot; &lt;<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>&gt;, <a rel="nofollow" href="http://mc/compose?to=insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>

Date: Monday, November 16, 2009, 6:26 PM<br><br></div><div><div></div><div><div>Sarah,<br><br>Try this:<br><br>ccmake -DBUILD_OUTSIDE_INSIGHT_APPLICATIONS:bool=true ../InsightApplications//MRIBiasCorrection/<br>
<br>where ../InsightApplications//MRIBiasCorrection/ points to your source.<br><br>Then, you will need to define ITK_DIR during the configure process.<br>
<br>Bill<br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 1:09 PM, Bill Lorensen <span dir="ltr">&lt;<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Sarah,<br><br>Sorry, I just tried my suggestion and I get the same errors. I do not see an ITK_DIR in my cache.<br><font color="#888888"><br>Bill</font><div><div></div><div><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 1:00 PM, Bill Lorensen <span dir="ltr">&lt;<a rel="nofollow" href="http://mc/compose?to=bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>&gt;</span> wrote:<br>



<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">When you ran ccmake did you specify ITK_DIR to tell the app where to find itk&#39;s build?<div>



<div></div><div><br><br><div class="gmail_quote">On Mon, Nov 16, 2009 at 12:22 PM, Sarah Waldron <span dir="ltr">&lt;<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo..com</a>&gt;</span> wrote:<br>




<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">




I tried to build the files in<br>
 InsightApplications/MRIBiasCorrection<br>
by typing:<br>
<br>
ccmake  . <br>
make<br>
<br>
but I get all these errors:<br>
<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ ccmake .<br>
<br>
<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ make<br>
Scanning dependencies of target BiasCorrector<br>
[  6%] Building CXX object CMakeFiles/BiasCorrector.dir/BiasCorrector.o<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector..cxx:19:26:
error: vnl/vnl_math.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:20:28: error: itkWin32Header.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:25:22: error: itkArray.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:24:45:
error: itkMRIBiasFieldCorrectionFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:25:46:
error: itkMinimumMaximumImageCalculator.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector..cxx:26:43:
error: itkBinaryThresholdImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:27:36:
error: itkImageRegionIterator.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:28:58:
error: itkZeroCrossingBasedEdgeDetectionImageFilter.h: No such file or
directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:29:45:
error: itkBinaryBallStructuringElement.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:30:46:
error: itkBinaryCrossStructuringElement..h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:31:40:
error: itkBinaryDilateImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10..0/MRIBiasCorrection/BiasCorrector.cxx:32:32:
error: itkMaskImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:33:32:
error: itkCastImageFilter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:34:23: error: itkIndent.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:35:26:
error: itkHistogram.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:20:32:
error: itkExceptionObject.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:21:35:
error: itkMetaImageIOFactory.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:22:32:
error: itkImageFileReader.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils..h:23:32:
error: itkImageFileWriter.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:25:45:
error: itkImageRegionIteratorWithIndex.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:26:30:
error: itkNumericTraits.h: No such file or directory<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:27:34:
error: itkOrientImageFilter.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,<br>
                 from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:20:28: error: vnl/vnl_vector.h: No such file or directory<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:23:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: ‘itk’ has not been declared<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/OptionList.h:56: error: expected ‘,’ or ‘...’ before ‘&lt;’ token<br>
In file included from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/imageutils.h:29,<br>
                 from /home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/BiasCorrector.cxx:36:<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: variable or field ‘dump’ declared void<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: ‘vnl_vector’ was not declared in this scope<br>
/home/sarah/InsightApplications-3.10.0/MRIBiasCorrection/myutils.h:28: error: expected primary-expression before ‘double’<br>
make[2]: *** [CMakeFiles/BiasCorrector.dir/BiasCorrector.o] Error 1<br>
make[1]: *** [CMakeFiles/BiasCorrector.dir/all] Error 2<br>
make: *** [all] Error 2<br>
sarah@sarah-laptop:~/InsightApplications-3.10.0/MRIBiasCorrection$ <br>
<br>
Can someone tell me what&#39;s wrong.<br>
Sarah.<br><br>--- On <b>Thu, 11/5/09, Luis Ibanez <i>&lt;<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>&gt;</i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">




<br>From: Luis Ibanez &lt;<a rel="nofollow" href="http://mc/compose?to=luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>&gt;<br>Subject: Re: [Insight-users] image preprocessing<br>To: &quot;Sarah Waldron&quot; &lt;<a rel="nofollow" href="http://mc/compose?to=sarah..waldron11@yahoo.com" target="_blank">sarah..waldron11@yahoo.com</a>&gt;<br>




Cc: <a rel="nofollow" href="http://mc/compose?to=insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>Date: Thursday, November 5, 2009, 2:29 AM<div><div></div><div><br><br><div><br>Hi Sarah,<br><br>You may want to try the same filters that are used for correcting <br>




for MRI intensity inhomogeneity.<br><br>See the directory:<br>InsightApplications/MRIBiasCorrection<br><br>These classes approximate the illumination distribution with a <br>
polynomial, and then use the polynomial in order to normalize<br>the intensity across space.<br><br>You may also find useful the following paper of the Insight Journal:<br><br>&quot;N4ITK:  Nick&#39;s N3 ITK Implementation For MRI Bias Field Correction&quot;<div>





Tustison N., Gee J.</div>
<div>PICSL, University of Pennsylvania<br><br></div><a rel="nofollow" href="http://www.insight-journal.org/browse/publication/640" target="_blank">http://www.insight-journal.org/browse/publication/640</a><br><br><a rel="nofollow" href="http://hdl.handle.net/10380/3053" target="_blank">http://hdl.handle.net/10380/3053</a><br>





<br><br><br>     Regards,<br><br><br>             Luis<br><br><br>----------------------------------------------------------------------------<br><div class="gmail_quote">On Wed, Nov 4, 2009 at 5:28 PM, Sarah Waldron <span dir="ltr">&lt;<a rel="nofollow" href="http://mc/compose?to=sarah.waldron11@yahoo.com" target="_blank">sarah.waldron11@yahoo.com</a>&gt;</span> wrote:<br>





<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">





<div>Hi,</div>
<div>I&#39;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&#39;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?</div>






<div>Thanks,</div>
<div>Sarah</div></td></tr></tbody></table><font color="#888888"><br>



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