[Insight-users] 3D segmentation of LUNGS ( Region growing algorithm ) Need help
wassim_belhadj at topnet.tn
wassim_belhadj at topnet.tn
Wed Mar 4 06:27:58 EST 2009
Hi,
Thank you very much for your help.
I was able to do the segmentation on an "unsigned char" raw file ( 512 *
512 * 494 ).
The filter gave me a binary mask of the two lungs.
I tried to apply the same algorithm to separate 2D dicom (512 *512) that
form the Raw file.
These Dicom file are encoded in 16 bit (signed short).
I changed only the lowerThreshold (-950) and the upperThreshold (-550) and
SetReplaceValue to 1100.
I have not had the same result. Some images contain only the left side of
the lungs.
That was not the case on the images coded on 8 bit.
I doubt that itk::Image does not support "signed short" type.
Can you help me please.
Thank you in advance
/***********************/
typedef signed short InternalPixelType;
typedef signed short OutputPixelType;
const unsigned int Dimension = 2 ;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
....
/***********************/
On Mon, 23 Feb 2009 07:29:43 -0500, Luis Ibanez <luis.ibanez at kitware.com>
wrote:
> Hi Wassim,
>
>
> The error below simply means that the type of ImageFileWriter
> that you are instantiating doesn't match the output image type
> of the the connectedThreshold filter.
>
>
> Please change the declaration:
>
> >> > typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> >> > InternalImageType > ConnectedFilterType;
>
>
> to
>
>
> >> > typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> >> > OutputImageType > ConnectedFilterType;
>
>
> So that the output type of the region growing filter match
> the expected input type of the writer.
>
>
>
> Regards,
>
>
> Luis
>
>
>
> --------------------------------
> wassim_belhadj at topnet.tn wrote:
>> Hi Luis,
>>
>> You said me that I don't need a Cast filter.
>>
>> If I don't use a CastingFilterType::Pointer I have this Error message
>> at
>> line :
>>
>> writer->SetInput( connectedThreshold->GetOutput() )
>>
>> cannot convert parameter 1 from 'itk::Image<TPixel,VImageDimension> *'
to
>> 'const itk::Image<TPixel,VImageDimension> *'
>>
>> I am using ImageJ and trial Volview version for looking at the output
>> image.I have got the same result.
>>
>>
>> I located my seed points on a 2D Slice ( lungs parts).
>>
>> Thank you in advance
>>
>>
>>
>> On Fri, 20 Feb 2009 12:30:19 -0500, Luis Ibanez
<luis.ibanez at kitware.com>
>> wrote:
>>
>>>Hi Wassim,
>>>
>>>
>>> Important Rule: Start Simple
>>>
>>>
>>>You don't need the Smoothing filter (until proven otherwise),
>>>You don't need the Cast filter
>>>You don't need the ITK-VTK import export code.
>>>
>>>
>>>
>>>You code could be reduced to:
>>>
>>>
>>> > #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( "c:/VTKEdge_Base_Test/images/Input.mhd" );
>>> > writer->SetFileName( "c:/VTKEdge_Base_Test/images/Output.mhd" );
>>> >
>>> >
>>> > typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>>> > InternalImageType > ConnectedFilterType;
>>> >
>>> > ConnectedFilterType::Pointer connectedThreshold =
>>> > ConnectedFilterType::New();
>>> >
>>> > connectedThreshold->SetInput( reader->GetOutput() );
>>> > writer->SetInput( connectedThreshold->GetOutput() );
>>> >
>>> >
>>> > const InternalPixelType lowerThreshold = -700 ;
>>> > const InternalPixelType upperThreshold = 200 ;
>>> >
>>> > connectedThreshold->SetLower( lowerThreshold );
>>> > connectedThreshold->SetUpper( upperThreshold );
>>> >
>>> > connectedThreshold->SetReplaceValue( 255 );
>>> >
>>> > InternalImageType::IndexType index;
>>> > index[0] = 180;
>>> > index[1] = 296 ;
>>> >
>>> > connectedThreshold->SetSeed( index );
>>> >
>>> > InternalImageType::IndexType index2;
>>> > index2[0] = 153;
>>> > index2[1] = 274;
>>> >
>>> >
>>> > connectedThreshold->SetSeed( index2 );
>>> >
>>> > try
>>> > {
>>> > writer->Update();
>>> > }
>>> > catch( itk::ExceptionObject & excep )
>>> > {
>>> > std::cerr << "Exception caught !" << std::endl;
>>> > std::cerr << excep << std::endl;
>>> > }
>>> >
>>> > return 0;
>>> > }
>>>
>>>
>>>
>>>
>>>BTW: in your code below you were calling SetInput()
>>> in the threshold filter twice, with two different
>>> inputs. Only the second would take place. This is
>>> fixed in the code above.
>>>
>>>
>>>Also, please let us know what visualization tool
>>> you are using for looking at the output image.
>>> That is: How are you arriving to the conclusion
>>> that the output image is all set to
>>> zero values.
>>>
>>>
>>>If the image is actually all set to zero values, then
>>>the most common reason is that your seed points are
>>>located in incorrect places (e.g. in places whose
>>>intensity is not in the range -700HU to 200HU.
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>>
>>> Luis
>>>
>>>
>>>
>>>------------------------------------
>>>wassim_belhadj at topnet.tn wrote:
>>>
>>>>Hi Luis,
>>>>
>>>>Thank you very much for your help.
>>>>
>>>>I just followed the steps you gave me. It's a bit difficult for a
>>>>beginner
>>>>ITK user.
>>>>
>>>>
>>>>The segmentation was not conclusive (A black Volume result).
>>>>
>>>>
>>>>can you help me ?
>>>>
>>>>
>>>>Below my Input.mhd :
>>>>
>>>>
>>
>>
/***************************************************************************************************/
>>
>>
/***************************************************************************************************/
>>
>>>>NDims = 3
>>>>DimSize = 512 512 494
>>>>ElementSpacing =0.777344 0.777344 0.7
>>>>Position = 0 0 0
>>>>ElementByteOrderMSB = False
>>>>ElementType = MET_SHORT
>>>>HeaderSize = -1
>>>>ElementDataFile = prodhom.raw
>>>>
>>>>
>>
>>
/***************************************************************************************************/
>>
>>
/***************************************************************************************************/
>>
>>>>This is the code that I used :
>>>>
>>>>
>>
>>
/***************************************************************************************************/
>>
>>
/***************************************************************************************************/
>>
>>>>#include "itkConnectedThresholdImageFilter.h"
>>>>#include "itkImage.h"
>>>>#include "itkCastImageFilter.h"
>>>>#include "itkCurvatureFlowImageFilter.h"
>>>>#include "itkImageFileReader.h"
>>>>#include "itkImageFileWriter.h"
>>>>#include "itkVTKImageExport.h"
>>>>#include "itkVTKImageImport.h"
>>>>
>>>>int main( int argc, char *argv[])
>>>>{
>>>>
>>>> typedef signed short InternalPixelType;
>>>> typedef signed short OutputPixelType;
>>>> const unsigned int Dimension = 3;
>>>> typedef itk::Image< InternalPixelType, Dimension >
InternalImageType;
>>>> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>>>> typedef itk::CastImageFilter< InternalImageType, OutputImageType
>>>>
>>>>
>>>>>CastingFilterType;
>>>>
>>>> CastingFilterType::Pointer caster = CastingFilterType::New();
>>
>>
>>>>
>>>> typedef itk::ImageFileReader< InternalImageType > ReaderType;
>>>> typedef itk::ImageFileWriter< OutputImageType > WriterType;
>>>>
>>>> ReaderType::Pointer reader = ReaderType::New();
>>>> WriterType::Pointer writer = WriterType::New();
>>>>
>>>> reader->SetFileName( "c:/VTKEdge_Base_Test/images/Input.mhd" );
>>>> writer->SetFileName( "c:/VTKEdge_Base_Test/images/Output.mhd" );
>>>>
>>>> typedef itk::CurvatureFlowImageFilter< InternalImageType,
>>>>InternalImageType > CurvatureFlowImageFilterType;
>>>>
>>>> CurvatureFlowImageFilterType::Pointer smoothing =
>>>>CurvatureFlowImageFilterType::New();
>>>>
>>>> typedef itk::ConnectedThresholdImageFilter< InternalImageType,
>>>>InternalImageType > ConnectedFilterType;
>>>>
>>>> ConnectedFilterType::Pointer connectedThreshold =
>>>>ConnectedFilterType::New();
>>>>
>>>> smoothing->SetInput( reader->GetOutput() );
>>>> connectedThreshold->SetInput( smoothing->GetOutput() );
>>>> connectedThreshold->SetInput( reader->GetOutput() );
>>>> caster->SetInput( connectedThreshold->GetOutput() );
>>>> writer->SetInput( caster->GetOutput() );
>>>>
>>>> smoothing->SetNumberOfIterations( 5 );
>>>> smoothing->SetTimeStep( 0.125 );
>>>>
>>>> const InternalPixelType lowerThreshold = -700 ;
>>>> const InternalPixelType upperThreshold = 200 ;
>>>>
>>>> connectedThreshold->SetLower( lowerThreshold );
>>>> connectedThreshold->SetUpper( upperThreshold );
>>>>
>>>> connectedThreshold->SetReplaceValue( 255 );
>>>>
>>>> InternalImageType::IndexType index;
>>>> index[0] = 180;
>>>> index[1] = 296 ;
>>>>
>>>> connectedThreshold->SetSeed( index );
>>>>
>>>> InternalImageType::IndexType index2;
>>>> index2[0] = 153;
>>>> index2[1] = 274;
>>>>
>>>>
>>>> connectedThreshold->SetSeed( index2 );
>>>>
>>>> try
>>>> {
>>>> writer->Update();
>>>> }
>>>> catch( itk::ExceptionObject & excep )
>>>> {
>>>> std::cerr << "Exception caught !" << std::endl;
>>>> std::cerr << excep << std::endl;
>>>> }
>>>>
>>>> return 0;
>>>>}
>>>>
>>
>>
/***************************************************************************************************/
>>
>>
/***************************************************************************************************/
>>
>>
/***************************************************************************************************/
>>
>>>>Best regards, Wassim
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>On Wed, 18 Feb 2009 10:20:55 -0500, Luis Ibanez
>>
>> <luis.ibanez at kitware.com>
>>
>>>>wrote:
>>>>
>>>>
>>>>>Hi Wassim,
>>>>>
>>>>>Please do the following:
>>>>>
>>>>>0) Extract a region of interest that includes the Trackea,
>>>>> and the full Lungs, but not the head of the patient
>>>>> (e.g. cut below the head, somewhere in the neck).
>>>>> You can use the RegionOfInterestImageFilter for this.
>>>>>
>>>>
>>>>
>>
http://www.itk.org/Insight/Doxygen/html/classitk_1_1RegionOfInterestImageFilter.html
>>
>>>>>1) Use the ConnectedThresholdImageFilter
>>>>>
>>>>
>>>>
>>
http://www.itk.org/Insight/Doxygen/html/classitk_1_1ConnectedThresholdImageFilter.html
>>
>>>>>2) Set seed points inside the Trackea
>>>>> (one seed point should be enough
>>>>>
>>>>>3) Set the lower threshold to -700 Hounsfield Units
>>>>>
>>>>>4) Set the upper threshodl to -200 Hounsfield Units
>>>>>
>>>>>5) Run the filter
>>>>>
>>>>>
>>>>>This shoudld give you a binary mask of the two lungs.
>>>>>
>>>>>If you find many holes inside the mask, you could
>>>>>clean it up with the Morphological filters or the
>>>>>Voting Hole filling filters.
>>>>>
>>>>>
>>>>> Start typing.... :-)
>>>>>
>>>>>
>>>>>Once you are done, please keep in mind that we are
>>>>>happy to get "case studies" as papers to the Insight
>>>>>Journal. http://www.insight-journal.org/
>>>>>
>>>>>These, more than "papers", are actually "technical
>>>>>reports". Yours could be entitled "Using ITK for
>>>>>Lung segmentation".
>>>>>
>>>>>Please let us know if you need any help on writing
>>>>>this report.
>>>>>
>>>>>
>>>>>
>>>>> Regards,
>>>>>
>>>>>
>>>>> Luis
>>>>>
>>>>>
>>>>>
>>>>>------------
>>>>>wassim_belhadj at topnet.tn wrote:
>>>>>
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>I'am using VTK and Qt4 for volume rendering.
>>>>>>
>>>>>>I'm trying to define values of pixel that define LUNGS.
>>>>>>
>>>>>>I assigned opacity to each pixel by checking its intensity value
with
>>>>>>Hounsfield Units values.
>>>>>>
>>>>>>I obtained a volume that contains the lungs and skin/air.
>>>>>>
>>>>>>
>>>>>>I varied the opacity values to eliminate the skin that surrounds the
>>>>>>lungs
>>>>>>but I have not succeeded.
>>>>>>
>>>>>>VTK users asked me to do a segmentation (region growing algorithm )
to
>>>>>>display ONLY the lungs.
>>>>>>
>>>>>>http://www.vtk.org/pipermail/vtkusers/2009-February/099524.html
>>>>>>
>>>>>>Can you help me?
>>>>>>
>>>>>>How do I proceed (ITK-VTK)?
>>>>>>
>>>>>>Have you an example of 3D segmentation (region growing algorithm)?
>>>>>>
>>>>>>Regards, Wassim
>>>>>>_____________________________________
>>>>>>Powered by www.kitware.com
>>>>>>
>>>>>>Visit other Kitware open-source projects at
>>>>>>http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>>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
>>>>>>
>>>>
>>>>
>>
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