[ITK-users] problem with 3d region growing

[Christopher Mullins]

The ConnectedThresholdImageFilter example [1] might be of use.

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/Segmentation/ConnectedThresholdImageFilter.cxx

On Wed, Feb 4, 2015 at 3:14 PM, samah bouzidi <samah.bouzidi at gmail.com>
wrote:

> hi Matt,
>
> thank you for replying.
>
> I can't find the error in my code (a black volume result)
>
> can you please look at my code.
>
>
>
> Regards
> Samah
>
>
>
> 2015-02-04 20:36 GMT+01:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Hi Samah,
>>
>> Welcome to ITK!
>>
>> For a 3D image, the third index of the seed does need to be defined.
>>
>> To apply a filter on each slice independently, use the
>> SliceBySliceImageFilter [1].
>>
>> HTH,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html
>>
>> On Wed, Feb 4, 2015 at 1:59 PM, samah bouzidi <samah.bouzidi at gmail.com>
>> wrote:
>> > hello itk users,
>> >
>> > I am a beginner ITK users. I am trying to segment a volume using region
>> > growing algorithm. I am able to do it in a 2D image (dicom) but not for
>> a
>> > volume.
>> > 1) I saw that for 3D region growing the seed point have 3 coordinates
>> (x, y,
>> > z). In my case, z is the slice number (i am using .img format). Can I
>> use an
>> > (x,y) seed point?
>> > 2) I have another idea,  reading an image series  and applied the
>> filter for
>> > each image and then writing them in volume. Are there any examples (
>> applied
>> > a filter in image series) that one could help me?
>> >
>> > regards
>> > Samah.
>> >
>> > My source code is as follows
>> > ================================
>> > #include "itkConnectedThresholdImageFilter.h"
>> > #include "itkImage.h"
>> > #include "itkImageFileReader.h"
>> > #include "itkImageFileWriter.h"
>> >
>> > int main( int argc, char *argv[])
>> > {
>> >   typedef   signed short         InternalPixelType;
>> >   typedef   unsigned char        OutputPixelType;
>> >   const     unsigned int           Dimension = 3;
>> >   typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>> >
>> >   typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>> >
>> >   typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>> >   typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>> >
>> >   ReaderType::Pointer reader = ReaderType::New();
>> >   WriterType::Pointer writer = WriterType::New();
>> >
>> >     reader->SetFileName(
>> "/home/doctorant/Téléchargements/Images/in.img" );
>> >     writer->SetFileName(
>> "/home/doctorant/Téléchargements/Images/out.img");
>> >
>> >
>> >   typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>> > OutputImageType > ConnectedFilterType;
>> >
>> >   ConnectedFilterType::Pointer connectedThreshold =
>> > ConnectedFilterType::New();
>> >
>> >   connectedThreshold->SetInput( reader->GetOutput() );
>> >   writer->SetInput( connectedThreshold->GetOutput() );
>> >
>> >
>> >   const InternalPixelType lowerThreshold =  -1050  ;
>> >   const InternalPixelType upperThreshold = -600;
>> >
>> >   connectedThreshold->SetLower(  lowerThreshold  );
>> >   connectedThreshold->SetUpper(  upperThreshold  );
>> >
>> >   connectedThreshold->SetReplaceValue( 255 );
>> >
>> >
>> >
>> >
>> >   InternalImageType::IndexType  index;
>> >   index[0] = 250;
>> >   index[1] = 239;
>> >
>> >   connectedThreshold->SetSeed( index );
>> >
>> >
>> >   try
>> >     {
>> >     writer->Update();
>> >     }
>> >   catch( itk::ExceptionObject & excep )
>> >     {
>> >     std::cerr << "Exception caught !" << std::endl;
>> >     std::cerr << excep << std::endl;
>> >     }
>> >
>> >   return 0;
>> > }
>> >
>> > _____________________________________
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>> >
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>> >
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>> >
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>> >
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>> >
>>
>
>
> _____________________________________
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>
> 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
>
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>


-- 
Christopher Mullins
R&D Engineer
Kitware Inc.,
919.869.8871
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