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List: insight-users
Subject: Re: [ITK-users] Binary Contour with outliers
From: "Becksfort, Jared" <Jared.Becksfort () STJUDE ! ORG>
Date: 2018-01-26 16:56:37
Message-ID: MWHPR04MB11698FC2B51C7D6BE2B70AD792E00 () MWHPR04MB1169 ! namprd04 ! prod ! outlook ! com
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Yes, sorry. I sent another email with the proper format shortly thereafter. Sorry \
for the noise.
Jared
________________________________
From: Jon Haitz Legarreta <jhlegarreta@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:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.itk.org%2Fg \
uidelines&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a \
1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=xPacI3N%2B2bxM6VjGt5o%2Be7JQjrd7fAtQS12nDxDmdWk%3D&reserved=0
Also, providing a minimal, compilable code snippet (either through a
GitHub gist) or by attaching your own files reproducing the issue
(.cxx files, CMakeLists.txt, your own input data, etc.) would help.
Note that we are transitioning from this mailing list to discourse:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.itk.org&dat \
a=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa8 \
92264871b677d3b3e377af72%7C0&sdata=Ml2KzsOGytZ5ylV9khEWD0rs3QA89TRY2W8IWdCO8tw%3D&reserved=0
So we'd be grateful if you could post your question there taking into
account the above.
Cheers,
JON HAITZ
--
On 26 January 2018 at 00:56, Becksfort, Jared
<Jared.Becksfort@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%2F \
> Documentation.html&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb \
> 308d564937a1b%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@itk.org on behalf of matt.mccormick@kitware.com> wrote:
> Hi,
>
> By running OpeningByReconstructionImageFilter:
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2 \
> Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjared.bec \
> ksfort%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@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.
> >
> > The ITK community is transitioning from this mailing list to
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> >
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> >
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>
>
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>
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Email Disclaimer: www.stjude.org/emaildisclaimer
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[Attachment #3 (text/html)]
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<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} \
--></style> </head>
<body dir="ltr">
<div id="divtagdefaultwrapper" \
style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" \
dir="ltr"> <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> <p \
style="margin-top:0;margin-bottom:0"><br> </p>
<p style="margin-top:0;margin-bottom:0">Jared</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<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>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<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>
<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.it \
k.org%2Fguidelines&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95 \
bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=xPacI3N%2B2bxM6VjGt5o \
%2Be7JQjrd7fAtQS12nDxDmdWk%3D&reserved=0">https://na01.safelinks.protection.outloo \
k.com/?url=https%3A%2F%2Fdiscourse.itk.org%2Fguidelines&data=01%7C01%7CJared.Becks \
fort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af7 \
2%7C0&sdata=xPacI3N%2B2bxM6VjGt5o%2Be7JQjrd7fAtQS12nDxDmdWk%3D&reserved=0</a><br>
<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>
<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.it \
k.org&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a \
1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=Ml2KzsOGytZ5ylV9khEWD0rs3QA89TRY2W \
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3A%2F%2Fdiscourse.itk.org&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b \
7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=Ml2KzsOGytZ5ylV9khEWD0rs3QA89TRY2W8IWdCO8tw%3D&reserved=0</a><br>
<br>
So we'd be grateful if you could post your question there taking into<br>
account the above.<br>
<br>
Cheers,<br>
JON HAITZ<br>
<br>
--<br>
<br>
<br>
<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%2FOverlayLabelMapOnTopOfAnIma \
ge%2FDocumentation.html&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b79 \
44b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=j7IB4JaPUdTP%2BnMM4ez7Hb4aiuOQ%2Fk41WI2RCh%2FvQJA%3D&reserved=0">
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FITKExample \
s%2Fsrc%2FFiltering%2FImageFusion%2FOverlayLabelMapOnTopOfAnImage%2FDocumentation.html \
&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C \
22340fa892264871b677d3b3e377af72%7C0&sdata=j7IB4JaPUdTP%2BnMM4ez7Hb4aiuOQ%2Fk41WI2RCh%2FvQJA%3D&reserved=0</a><br>
><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%2FDoxyg \
en%2Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjar \
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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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