[ITK] [ITK-users] Binary Contour with outliers

Becksfort, Jared Jared.Becksfort at STJUDE.ORG
Fri Jan 26 11:56:37 EST 2018 

Yes, sorry.  I sent another email with the proper format shortly thereafter.  Sorry for the noise.


Jared

________________________________
From: Jon Haitz Legarreta <jhlegarreta at vicomtech.org>
Sent: Friday, January 26, 2018 2:04:09 AM
To: Becksfort, Jared
Cc: ITK Users
Subject: Re: [ITK-users] Binary Contour with outliers

Dear Jared,
thanks for your question !

Your question seems to drift apart from the one that started this
thread or the subject of this thread.

In order to increase the chances of it getting answered, could please
post your question on a different thread?

Please, read our community discussion guidelines, especially the "Keep
tidy" section:
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Also, providing a minimal, compilable code snippet (either through a
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On 26 January 2018 at 00:56, Becksfort, Jared
<Jared.Becksfort at stjude.org> wrote:
> Hello,
>
> 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):. 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
>
> 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.
>
> Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.
>
> Thanks,
> Jared
>
> const unsigned int Dimension = 3;
>
> typedef float PixelType;
> typedef unsigned char LabelType;
>
> typedef itk::Image< PixelType, Dimension > ImageVolumeType;
> typedef itk::Image< LabelType, Dimension > ContourVolumeType;
>
> typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
> typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;
>
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( infile1 );
>
> ContourReaderType::Pointer labelReader = ContourReaderType::New();
> labelReader->SetFileName(infile2);
>
> typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
> typedef itk::LabelMap< LabelObjectType > LabelMapType;
>
> typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
> ConverterType::Pointer converter = ConverterType::New();
> converter->SetInput( labelReader->GetOutput() );
>
> typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput( converter->GetOutput() );
> filter->SetFeatureImage( reader->GetOutput() );
> filter->SetOpacity(0.5);
>
>
> typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName(outfile);
> writer->SetInput( filter->GetOutput() );
> writer->Update();
>
> On 1/23/18, 4:19 PM, "Insight-users on behalf of Matt McCormick" <insight-users-bounces at itk.org on behalf of matt.mccormick at kitware.com> wrote:
>
>     Hi,
>
>     By running OpeningByReconstructionImageFilter:
>
>       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
>
>     before the binary contour, the smaller objects can be removed.
>
>     HTH,
>     Matt
>
>     On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari
>     <bakkari.abdelkhalek at hotmail.fr> wrote:
>     > Hi !
>     >
>     > I applied the binary contour filter slice by slice to my binary mask. But
>     > the result for the Axial plane is not satisfied at all since it contains
>     > some outliers.
>     > Please, find attached my binary contour result.
>     > Is there any method to remove the outliers from the contour ?
>     >
>     > Thank you in advance.
>     >
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