[Insight-users] How to smooth the segmented surface

Thu Mar 22 10:33:31 EDT 2012

Your code looks logical. Can you test it with lower dimensionality as in
this example<http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter>?
Use
white triangle instead of square, and different x and y spacings. Maybe
that way you will spot a problem.

2012/3/22 Xiaopeng Yang <yxp233 at postech.ac.kr>

> I used linear interpolation in my code. Please have a look at my code:****
>
> ** **
>
>        typedef itk::IdentityTransform< double, 3 > ****
>
>               TransformType; ****
>
> ** **
>
>        typedef itk::LinearInterpolateImageFunction< OutputImageType,
> double > ****
>
>               InterpolatorType; ****
>
> ** **
>
>        typedef itk::ResampleImageFilter< OutputImageType, OutputImageType
> > ****
>
>               ResampleFilterType; ****
>
> ** **
>
>        InterpolatorType::Pointer interpolator = InterpolatorType::New(); *
> ***
>
> ** **
>
>        TransformType::Pointer transform = TransformType::New(); ****
>
>        transform->SetIdentity(); ****
>
> ** **
>
>        OutputImageType::SizeType inputSize =
> filter2->GetOutput()->GetLargestPossibleRegion().GetSize();//filter2 is
> the segmented binary image****
>
>     ****
>
>        OutputImageType::SpacingType inputSpacing =
> filter2->GetOutput()->GetSpacing();****
>
> ** **
>
>        OutputImageType::SpacingType outputSpacing;****
>
>        outputSpacing[0] = inputSpacing[0];****
>
>        outputSpacing[1] = inputSpacing[1];****
>
>        outputSpacing[2] = 0.7;****
>
> ** **
>
>        OutputImageType::SizeType outputSize; ****
>
>        typedef OutputImageType::SizeType::SizeValueType SizeValueType; ***
> *
>
>        outputSize[0] = static_cast<SizeValueType>(inputSize[0] *
> inputSpacing[0] / outputSpacing[0] + .5); ****
>
>        outputSize[1] = static_cast<SizeValueType>(inputSize[1] *
> inputSpacing[1] / outputSpacing[1] + .5); ****
>
>        outputSize[2] = static_cast<SizeValueType>(inputSize[2] *
> inputSpacing[2] / outputSpacing[2] + .5); ****
>
> ** **
>
>        ResampleFilterType::Pointer resampler = ResampleFilterType::New();
> ****
>
>        resampler->SetInput( filter2->GetOutput() ); ****
>
>        resampler->SetTransform( transform ); ****
>
>        resampler->SetInterpolator( interpolator ); ****
>
>        resampler->SetOutputOrigin ( filter2->GetOutput()->GetOrigin()); **
> **
>
>        resampler->SetOutputSpacing ( outputSpacing ); ****
>
>        resampler->SetOutputDirection (
> filter2->GetOutput()->GetDirection()); ****
>
>        resampler->SetSize ( outputSize ); ****
>
>        resampler->UpdateLargestPossibleRegion();****
>
>        //resampler->Update ();****
>
>    ****
>
>        ExportFilterType2::Pointer itkExporter4 =
> ExportFilterType2::New();  ****
>
>        itkExporter4->SetInput( resampler->GetOutput() );****
>
>        itkExporter4->Update();****
>
> ** **
>
>        vtkImageImport* vtkImporter4 = vtkImageImport::New();  ****
>
>        ConnectPipelines(itkExporter4, vtkImporter4);****
>
> ** **
>
>        vtkContourFilter *iso = vtkContourFilter::New();****
>
>        iso->SetInput(vtkImporter4->GetOutput());****
>
>        iso->ComputeScalarsOn();****
>
>        iso->SetValue(0,128.1);****
>
> ** **
>
>        vtkPolyDataMapper *isoMapper = vtkPolyDataMapper::New();****
>
>        isoMapper->SetInput(iso->GetOutput());****
>
>        isoMapper->ScalarVisibilityOff();****
>
> ** **
>
>        iso->Delete();****
>
> ** **
>
>        vtkActor *isoActor1 = vtkActor::New();****
>
>        isoActor1->SetMapper(isoMapper);****
>
>        isoActor1->GetProperty()->SetColor(1.0, 0.49, 0.25);****
>
>        ****
>
>        isoMapper->Delete();****
>
>        ****
>
>        ren_L->AddActor(isoActor1);****
>
>        ****
>
> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
> *Sent:* Thursday, March 22, 2012 6:48 PM
>
> *To:* Xiaopeng Yang
> *Cc:* Kent Ogden; insight-users at itk.org
> *Subject:* Re: [Insight-users] How to smooth the segmented surface****
>
> ** **
>
> For the resampling you have to make sure to use either linear, cubic, or
> some more advanced interpolation scheme, not the nearest neighbor which is
> the default I think.****
>
> 2012/3/22 Xiaopeng Yang <yxp233 at postech.ac.kr>****
>
> I resampled the segmented mask images. But when I apply vtkcontourfilter
> to generate a 3D surface, only iso-surfaces of the original slices of the
> mask images are generated, not including the resampled slices. Thus the
> results look the same as before. Still stairs appear.****
>
>  ****
>
> Thanks,****
>
> Xiaopeng ****
>
> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
> *Sent:* Wednesday, March 21, 2012 7:07 PM
> *To:* Xiaopeng Yang
> *Cc:* Kent Ogden; insight-users at itk.org****
>
>
> *Subject:* Re: [Insight-users] How to smooth the segmented surface****
>
>  ****
>
> You can resample<http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/ResampleImageFilter>the image, or use linear
> interpolator<http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/LinearInterpolateImageFunction>
> .****
>
> On Tue, Mar 20, 2012 at 14:07, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> ****
>
> Hi Kent,****
>
>  ****
>
> Do you know any interpolate class in ITK which can generate more slices?
> For volumetry, I guess I can use the original data.****
>
>  ****
>
> Thanks,****
>
> Xiaopeng****
>
>  ****
>
> *From:* Kent Ogden [mailto:ogdenk at upstate.edu]
> *Sent:* Tuesday, March 20, 2012 9:50 PM
> *To:* insight-users at itk.org; Xiaopeng Yang****
>
>
> *Subject:* Re: [Insight-users] How to smooth the segmented surface****
>
>  ****
>
> Xiaopeng, ****
>
>  ****
>
> This is a fundamental limitation of your data that can only truly be
> solved by reconstructing thinner slices at the time of the scan.  You could
> interpolate between images to generate more slices, which would result in a
> smoother looking rendering.  If you are trying to make quantitative
> measurements (e.g. volume) you must be careful about these kinds of
> manipulations though. ****
>
>  ****
>
> Kent ****
>
>  ****
>
>
>
> >>> "Xiaopeng Yang" <yxp233 at postech.ac.kr> 3/19/2012 10:17 PM >>>****
>
> Dear Users, ****
>
>   ****
>
> I have tried to segment the liver from 5 mm CT slices. When I tried to
> visualize the segmented liver in 3D, I found that the surface of the 3D
> liver was discrete, just like stairs. I guess that is because of the 5 mm
> interval between CT slices. Do you guys have any good idea how to make the
> 3D surface of the liver look continuous and smooth? ****
>
>   ****
>
> Thanks, ****
>
> Xiaopeng ****
>
> ** **
>
> _____________________________________
> 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.php
>
> 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****
>
>  ****
>
> ** **
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20120322/42c69904/attachment.htm>