<div dir="ltr"><div>hi,  </div><div><span id="result_box" class="" lang="en"><span class="">sincerely, <span class="">I fail <span class="">to understand <span class="">the response of this <span class="">filter, <span class="">the algorithm <span class="">succeeds to segment the region <span class="">.however, <span class="">in 3D, <span class="">the first  <span class="">slice <span class="">is the same <span class=""> used <span class="">to check <span class="">the segmentation <span class="">in 2D, <span class=""><span id="result_box" class="" lang="en"><span class="">I am not getting<span class=""> at least <span class="">for the first <span class="">slice <span class="">the region <span class="">obtained <span class="">in 2D. </div><div><span id="result_box" class="" lang="en"><span class="">ps: the modified code takes into account the third dimension : <span id="result_box" class="" lang="en"><span class=""><span lang="en">InternalImageType::IndexType  index;   index[0] = 250;   index[1] = 239; </div><div><span id="result_box" class="" lang="en"><span class=""><span lang="en">  index[2]= 1; </div><div><span id="result_box" class="" lang="en"><span class=""><span lang="en">   connectedThreshold->SetSeed( index ); <span id="result_box" class="" lang="en"><span class=""><span lang="en">any help will be appreciated.

thanks in advance.

<br></span></span><br><br></span></span></div></div><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 class="h5"><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>

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><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 class="HOEnZb"><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>