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<p style="margin-top:0;margin-bottom:0">Yes, sorry. I sent another email with the proper format shortly thereafter. Sorry for the noise.</p>
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<p style="margin-top:0;margin-bottom:0">Jared</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Jon Haitz Legarreta <jhlegarreta@vicomtech.org><br>
<b>Sent:</b> Friday, January 26, 2018 2:04:09 AM<br>
<b>To:</b> Becksfort, Jared<br>
<b>Cc:</b> ITK Users<br>
<b>Subject:</b> Re: [ITK-users] Binary Contour with outliers</font>
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<div class="PlainText">Dear Jared,<br>
thanks for your question !<br>
<br>
Your question seems to drift apart from the one that started this<br>
thread or the subject of this thread.<br>
<br>
In order to increase the chances of it getting answered, could please<br>
post your question on a different thread?<br>
<br>
Please, read our community discussion guidelines, especially the "Keep<br>
tidy" section:<br>
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<br>
Also, providing a minimal, compilable code snippet (either through a<br>
GitHub gist) or by attaching your own files reproducing the issue<br>
(.cxx files, CMakeLists.txt, your own input data, etc.) would help.<br>
<br>
Note that we are transitioning from this mailing list to discourse:<br>
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So we'd be grateful if you could post your question there taking into<br>
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Cheers,<br>
JON HAITZ<br>
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--<br>
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<br>
On 26 January 2018 at 00:56, Becksfort, Jared<br>
<Jared.Becksfort@stjude.org> wrote:<br>
> Hello,<br>
><br>
> I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):.
<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FITKExamples%2Fsrc%2FFiltering%2FImageFusion%2FOverlayLabelMapOnTopOfAnImage%2FDocumentation.html&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=j7IB4JaPUdTP%2BnMM4ez7Hb4aiuOQ%2Fk41WI2RCh%2FvQJA%3D&reserved=0">
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><br>
> The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.<br>
><br>
> Can someone please tell me what I have done wrong? The output image is garbled beyond recognition.<br>
><br>
> Thanks,<br>
> Jared<br>
><br>
> const unsigned int Dimension = 3;<br>
><br>
> typedef float PixelType;<br>
> typedef unsigned char LabelType;<br>
><br>
> typedef itk::Image< PixelType, Dimension > ImageVolumeType;<br>
> typedef itk::Image< LabelType, Dimension > ContourVolumeType;<br>
><br>
> typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;<br>
> typedef itk::ImageFileReader< ImageVolumeType > ReaderType;<br>
><br>
> ReaderType::Pointer reader = ReaderType::New();<br>
> reader->SetFileName( infile1 );<br>
><br>
> ContourReaderType::Pointer labelReader = ContourReaderType::New();<br>
> labelReader->SetFileName(infile2);<br>
><br>
> typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;<br>
> typedef itk::LabelMap< LabelObjectType > LabelMapType;<br>
><br>
> typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;<br>
> ConverterType::Pointer converter = ConverterType::New();<br>
> converter->SetInput( labelReader->GetOutput() );<br>
><br>
> typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;<br>
> FilterType::Pointer filter = FilterType::New();<br>
> filter->SetInput( converter->GetOutput() );<br>
> filter->SetFeatureImage( reader->GetOutput() );<br>
> filter->SetOpacity(0.5);<br>
><br>
><br>
> typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;<br>
> WriterType::Pointer writer = WriterType::New();<br>
> writer->SetFileName(outfile);<br>
> writer->SetInput( filter->GetOutput() );<br>
> writer->Update();<br>
><br>
> On 1/23/18, 4:19 PM, "Insight-users on behalf of Matt McCormick" <insight-users-bounces@itk.org on behalf of matt.mccormick@kitware.com> wrote:<br>
><br>
> Hi,<br>
><br>
> By running OpeningByReconstructionImageFilter:<br>
><br>
> <a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=qbR%2BtUIsnrSfh01yNV9w94GGa%2FdEA7uXrisa%2BpVyJ0k%3D&reserved=0">
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><br>
> before the binary contour, the smaller objects can be removed.<br>
><br>
> HTH,<br>
> Matt<br>
><br>
> On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari<br>
> <bakkari.abdelkhalek@hotmail.fr> wrote:<br>
> > Hi !<br>
> ><br>
> > I applied the binary contour filter slice by slice to my binary mask. But<br>
> > the result for the Axial plane is not satisfied at all since it contains<br>
> > some outliers.<br>
> > Please, find attached my binary contour result.<br>
> > Is there any method to remove the outliers from the contour ?<br>
> ><br>
> > Thank you in advance.<br>
> ><br>
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