<div dir="ltr"><div>hi,<br><br><span id="result_box" class="" lang="en"><span class="">I finished the</span> <span class="">slice</span> <span class="">by</span> <span class="">slice</span> <span class="">region growing</span> <span class="">version of</span> <span class="">code.</span> <span class="">unfortunately</span> <span class="">I have these</span> <span class="">error</span><span>s:</span><br><br> <span class="">1) no</span> <span class="">matching</span> <span class="">function</span> <span class="">for call</span> <span class="">to '</span><span>itk</span> <span class="">::</span> <span class="">ConnectedThresholdImageFilter</span> <span class=""><</span><span>itk</span> <span class="">::</span> <span class="">Image <</span><span class="">short int</span><span>,</span> <span class="">2u</span><span>></span><span>,</span> <span class="">itk</span> <span class="">::</span> <span class="">Image <</span><span>unsigned char</span><span>,</span> <span class="">2u</span><span>></span><span>> ::</span> <span class="">SetSeed</span> <span class="">(</span><span>itk</span> <span class="">::</span> <span class="">Image <</span><span>short int</span><span>,</span> <span class="">3u</span><span>> ::</span> <span class="">INDEXTYPE</span> <span class="">&</span><span class="">) '</span><br><span class="">connectedThreshold-</span><span class="">></span> <span class="">SetSeed</span> <span class="">(index)</span></span><br><br>2) /home/doctorant/src/InsightToolkit-4.7.0/Modules/Segmentation/RegionGrowing/include/itkConnectedThresholdImageFilter.hxx:53:1: note:   no known conversion for argument 1 from ‘itk::Image<short int, 3u>::IndexType {aka itk::Index<3u>}’ to ‘const IndexType& {aka const itk::Index<2u>&}’<br><br></div><div><br></div>here is my code :<br><br>#include "itkConnectedThresholdImageFilter.h"

<br>#include "itkImage.h"

<br>#include "itkImageFileReader.h"

<br>#include "itkImageFileWriter.h"

<br>#include "itkSliceBySliceImageFilter.h"

<br>#include "iostream"

<br> <br>int main( int argc, char *argv[])

<br>{

<br>  typedef   signed short         InternalPixelType;

<br>  typedef   unsigned char        OutputPixelType;

<br>  const     unsigned int         Dimension = 3;

<br>  const     int                  sliceDim =2; 

<br>  typedef itk::Image< InternalPixelType, Dimension > InternalImageType; // input

<br>  typedef itk::Image< OutputPixelType, Dimension > OutputImageType; //output

<br> <br>  typedef  itk::ImageFileReader< InternalImageType > ReaderType;

<br>  typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

<br> <br>  ReaderType::Pointer reader = ReaderType::New();

<br>  WriterType::Pointer writer = WriterType::New();

<br> <br>  reader->SetFileName( "/home/doctorant/Téléchargements/Images/in.img" );

<br>  writer->SetFileName( "/home/doctorant/Téléchargements/Images/out.img");

<br> <br> <br>  typedef itk::SliceBySliceImageFilter< InternalImageType,OutputImageType> SliceBySliceFilterType;

<br> <br>  SliceBySliceFilterType::Pointer sliceBySliceFilter = SliceBySliceFilterType::New();

<br> <br>  typedef itk::ConnectedThresholdImageFilter< SliceBySliceFilterType::InternalInputImageType,

<br>          SliceBySliceFilterType::InternalOutputImageType > ConnectedFilterType;

<br>  ConnectedFilterType::Pointer connectedThreshold =ConnectedFilterType::New();

<br> <br>  const InternalPixelType lowerThreshold =  -3700 ;

<br>  const InternalPixelType upperThreshold = -600;

<br> <br> connectedThreshold->SetLower(  lowerThreshold   ); 

// error here<br> connectedThreshold->SetUpper(  upperThreshold  ); 

//error here<br>    connectedThreshold->SetReplaceValue( 255 ); 

// error here<br> <br>    InternalImageType::IndexType  index;

<br>    index[0] = 257;

<br>    index[1] = 449;

<br>    connectedThreshold->SetSeed(index); 

// error here<br> <br>  sliceBySliceFilter -> SetInput(reader->GetOutput());

<br>  sliceBySliceFilter->SetFilter(connectedThreshold);

<br>  writer->SetInput( sliceBySliceFilter->GetOutput());

<br>  try

<br>    {

<br>    writer->Update();

<br>    }

<br>  catch( itk::ExceptionObject & excep )

<br>    {

<br>    std::cerr << "Exception caught !" << std::endl;

<br>    std::cerr << excep << std::endl;

<br>    }

<br> <br>  return 0;

} </div><div class="gmail_extra"> <div class="gmail_quote">2015-02-06 21:59 GMT+01:00 samah bouzidi <span dir="ltr"><<a href="mailto:samah.bouzidi@gmail.com" target="_blank">samah.bouzidi@gmail.com</a>>: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>hi,  </div><div><span lang="en">sincerely, I fail to understand the response of this filter, the algorithm succeeds to segment the region .however, in 3D, the first  slice is the same  used to check the segmentation in 2D, <span lang="en">I am not getting at least for the first slice the region obtained in 2D. </div><div><span lang="en">ps: the modified code takes into account the third dimension : <span class=""> <span lang="en"><span lang="en">InternalImageType::IndexType  index;   index[0] = 250;   index[1] = 239; </div><div><span lang="en"><span lang="en">  index[2]= 1; </div><div><span lang="en"><span lang="en">   connectedThreshold->SetSeed( index ); <span lang="en"><span lang="en">any help will be appreciated.

thanks in advance.

<br></span></span><br><br></span></span></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2015-02-04 21:24 GMT+01:00 Christopher Mullins <span dir="ltr"><<a href="mailto:christopher.mullins@kitware.com" target="_blank">christopher.mullins@kitware.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">The ConnectedThresholdImageFilter example [1] might be of use.<br><div><br></div><div>[1] <a href="https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx" target="_blank">https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx</a></div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <span dir="ltr"><<a href="mailto:samah.bouzidi@gmail.com" target="_blank">samah.bouzidi@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>hi Matt, <br><br></div>thank you for replying.<br><br></div><span>I can't find the error in my code</span> (a black volume result)<pre><span style="font-family:arial,helvetica,sans-serif">can you please look at my code.</span><br></pre></div><div><br><br></div>Regards<span><font color="#888888"><br></font></span></div><span><font color="#888888">Samah<br><div><div><div><br><br></div></div></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-02-04 20:36 GMT+01:00 Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Samah,<br>

<br>

Welcome to ITK!<br>

<br>

For a 3D image, the third index of the seed does need to be defined.<br>

<br>

To apply a filter on each slice independently, use the<br>

SliceBySliceImageFilter [1].<br>

<br>

HTH,<br>

Matt<br>

<br>

[1] <a href="http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html" target="_blank">http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html</a><br>

<div><div><br>

On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <<a href="mailto:samah.bouzidi@gmail.com" target="_blank">samah.bouzidi@gmail.com</a>> wrote:<br>

> hello itk users,<br>

><br>

> I am a beginner ITK users. I am trying to segment a volume using region<br>

> growing algorithm. I am able to do it in a 2D image (dicom) but not for a<br>

> volume.<br>

> 1) I saw that for 3D region growing the seed point have 3 coordinates (x, y,<br>

> z). In my case, z is the slice number (i am using .img format). Can I use an<br>

> (x,y) seed point?<br>

> 2) I have another idea,  reading an image series  and applied the filter for<br>

> each image and then writing them in volume. Are there any examples ( applied<br>

> a filter in image series) that one could help me?<br>

><br>

> regards<br>

> Samah.<br>

><br>

> My source code is as follows<br>

> ================================<br>

> #include "itkConnectedThresholdImageFilter.h"<br>

> #include "itkImage.h"<br>

> #include "itkImageFileReader.h"<br>

> #include "itkImageFileWriter.h"<br>

><br>

> int main( int argc, char *argv[])<br>

> {<br>

>   typedef   signed short         InternalPixelType;<br>

>   typedef   unsigned char        OutputPixelType;<br>

>   const     unsigned int           Dimension = 3;<br>

>   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;<br>

><br>

>   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;<br>

><br>

>   typedef  itk::ImageFileReader< InternalImageType > ReaderType;<br>

>   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;<br>

><br>

>   ReaderType::Pointer reader = ReaderType::New();<br>

>   WriterType::Pointer writer = WriterType::New();<br>

><br>

>     reader->SetFileName( "/home/doctorant/Téléchargements/Images/in.img" );<br>

>     writer->SetFileName( "/home/doctorant/Téléchargements/Images/out.img");<br>

><br>

><br>

>   typedef itk::ConnectedThresholdImageFilter< InternalImageType,<br>

> OutputImageType > ConnectedFilterType;<br>

><br>

>   ConnectedFilterType::Pointer connectedThreshold =<br>

> ConnectedFilterType::New();<br>

><br>

>   connectedThreshold->SetInput( reader->GetOutput() );<br>

>   writer->SetInput( connectedThreshold->GetOutput() );<br>

><br>

><br>

>   const InternalPixelType lowerThreshold =  -1050  ;<br>

>   const InternalPixelType upperThreshold = -600;<br>

><br>

>   connectedThreshold->SetLower(  lowerThreshold  );<br>

>   connectedThreshold->SetUpper(  upperThreshold  );<br>

><br>

>   connectedThreshold->SetReplaceValue( 255 );<br>

><br>

><br>

><br>

><br>

>   InternalImageType::IndexType  index;<br>

>   index[0] = 250;<br>

>   index[1] = 239;<br>

><br>

>   connectedThreshold->SetSeed( index );<br>

><br>

><br>

>   try<br>

>     {<br>

>     writer->Update();<br>

>     }<br>

>   catch( itk::ExceptionObject & excep )<br>

>     {<br>

>     std::cerr << "Exception caught !" << std::endl;<br>

>     std::cerr << excep << std::endl;<br>

>     }<br>

><br>

>   return 0;<br>

> }<br>

><br>

</div></div>> _____________________________________<br>

> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>

><br>

> Visit other Kitware open-source projects at<br>

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><br>

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><br>

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><br>

</blockquote></div><br></div>

</div></div><br>_____________________________________<br>

Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>

<br>

Visit other Kitware open-source projects at<br>

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<br>

Kitware offers ITK Training Courses, for more information visit:<br>

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<br>

Please keep messages on-topic and check the ITK FAQ at:<br>

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<br></blockquote></div><br><br clear="all"><div><br></div></div></div><span><font color="#888888">-- <br><div>Christopher Mullins<div>R&D Engineer</div><div>Kitware Inc.,</div><div><a href="tel:919.869.8871" value="+19198698871" target="_blank">919.869.8871</a></div></div>

</font></span></div>

</blockquote></div><br></div>

</div></div></blockquote></div><br></div>