[Insight-users] Segmenting Visible Human Data

[Stefan Lindenau]

Hi Joshua,

I think that it is maybe possible to use the watershed algorithm in my 
case, so I just wanted to give the Streaming Watershed segmentation 
example a trial.
But it doesn't compile. I am using Visual Studio 6.0.

Here is my compiler output for the itkRelabelerApp:

--------------------Configuration: itkRelabelerApp - Win32 
Release--------------------
Compiling...
itkRelabelerApp.cxx
C:\Surgical Simulator\InsightToolkit-1.4.0\Code\Common\itkOffset.h(183) 
: warning C4200: nonstandard extension used : zero-sized array in 
struct/union
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkIndex.h(79) : see 
reference to class template instantiation 'itk::Offset<0>' being compiled
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkImageRegion.h(78) : see 
reference to class template instantiation 'itk::Index<0>' being compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(65) : see 
reference to class template instantiation 'itk::ImageRegion<0>' being 
compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(90) : see 
reference to class template instantiation 
'itk::sws::RawFileReader<TOutputImage>' being compiled
C:\Surgical Simulator\InsightToolkit-1.4.0\Code\Common\itkIndex.h(234) : 
warning C4200: nonstandard extension used : zero-sized array in struct/union
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkImageRegion.h(78) : see 
reference to class template instantiation 'itk::Index<0>' being compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(65) : see 
reference to class template instantiation 'itk::ImageRegion<0>' being 
compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(90) : see 
reference to class template instantiation 
'itk::sws::RawFileReader<TOutputImage>' being compiled
C:\Surgical Simulator\InsightToolkit-1.4.0\Code\Common\itkSize.h(189) : 
warning C4200: nonstandard extension used : zero-sized array in struct/union
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkImageRegion.h(82) : see 
reference to class template instantiation 'itk::Size<0>' being compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(65) : see 
reference to class template instantiation 'itk::ImageRegion<0>' being 
compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(90) : see 
reference to class template instantiation 
'itk::sws::RawFileReader<TOutputImage>' being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkImageRegion.h(264) : error 
C2229: class 'itk::ImageRegion<0>' has an illegal zero-sized array
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(65) : see 
reference to class template instantiation 'itk::ImageRegion<0>' being 
compiled
        H:\Stefan\surgical sim\VHD processing 
progs\StreamedWatershedSegmentation\itkSWSRawFileReader.h(90) : see 
reference to class template instantiation 
'itk::sws::RawFileReader<TOutputImage>' being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(330) : 
error C2653: 'Detail' : is not a class or namespace name
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(330) : 
error C2143: syntax error : missing ';' before '<'
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(330) : 
error C2059: syntax error : '<'
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(330) : 
error C2238: unexpected token(s) preceding ';'
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(331) : 
error C2653: 'Detail' : is not a class or namespace name
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(331) : 
error C2059: syntax error : '<'
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(331) : 
error C2238: unexpected token(s) preceding ';'
        C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(339) : 
see reference to class template instantiation 'SameDimension<D1,D2>' 
being compiled
C:\Surgical 
Simulator\InsightToolkit-1.4.0\Code\Common\itkConceptChecking.h(341) : 
fatal error C1903: unable to recover from previous error(s); stopping 
compilation
Error executing cl.exe.

itkRelabelerApp.exe - 9 error(s), 3 warning(s)

I am sure that this problem is caused by the itkSWSRawFileReader.
Is it possible to replace this reader by an ImageFileReader with 
RawImageIO?

I have just changed one application to use the ImageFileReader, what is 
not a real problem. But I am not sure which Options of rawImageIO I have 
to set to get an effect that is similar to the use of the Regions in the 
itkSWSRawFileReader.
Or is it just possible to set one compiler flag to make the programs 
compile (my favourite choice ;->)?

Has anyone a idea how I can solve this issue?

Thank you
Stefan

Joshua Cates wrote:

>Hi Stefan,
>
>We have had good success segmenting localized regions of the visible human
>data using the watersheds algorithm (see
>http://www . sci . utah . edu/~cates/papers/Cates_MedIA2003 . pdf).  
>Unfortunately the ITK watersheds algorithm does not scale very gracefully
>to huge datasets.  We did some work on this a while back and our results
>can be found in the InsightApplications/StreamingWatershedSegmentation
>directory, which streams data through the ITK watershed filters. 
>
>First it is important to understand how the ITK watershed algorithm works.  
>We produce an initial (typically oversegmented) transform of regions.  
>The initial transform is then used to compute a hierarchy of region merges
>that allows us to output segmentations at increasingly coarse levels of
>detail.
>
>There are two main factors that limit performance on large datasets. The
>first is that the watershed transform is applied globally so huge datasets
>produce huge numbers of regions.  This is mainly a memory issue and is
>solved by the streaming approach.  The real problem is then in generating
>the merge hierarchy.  Computation time increases nonlinearly with size and
>we have not found a way to parallellize the merge algorithm.  
>
>Note that computation time and memory consumption of the algorithm is
>determined more by the amount of information in a dataset than by the size
>of the dataset. (Nonlinear diffusion is an excellent way to reduce detail
>and preserve object boundary features.) So whether or not this algorithm
>will be appropriate for you depends on the scale of the anatomy you are
>trying to segment.
>
>Hope this helps,
>
>Josh.
>
>
>
>
>______________________________
> Josh Cates			
> Scientific Computing and Imaging Institute
> University of Utah
> Email: cates at sci . utah . edu
> Phone: (801) 587-7697
> URL:   http://www . sci . utah . edu/~cates
>
>
>On Thu, 6 Nov 2003, Stefan Lindenau wrote:
>
>  
>
>>Hi,
>>
>>I have to do a segmentation on a part of the female Dataset of the 
>>Visible Human. I think this part will be as big as 4GB.
>>After reading documentation and former Mailinglist postings I came to 
>>the conclusion that the Watershed Algorithm in conjunction with the 
>>SegmentationEditorFltkGUI would be an appropriate approach.
>>
>>The goal is to use the segmented data in the VTK to render for example 
>>the ribs of the Visible Woman. The SegmentationEditor provides a nice UI 
>>to choose the appropriate elements in the segmented image and to 
>>manipulate them.
>>
>>My concern lies on the memory consumption of the processing. Is it 
>>realistic to use this approach with a consumer computer? Maybe another 
>>algorithm would fit better to my needs.
>>
>>Thank you
>>Stefan
>>
>>
>>
>>_______________________________________________
>>Insight-users mailing list
>>Insight-users at itk . org
>>http://www . itk . org/mailman/listinfo/insight-users
>>
>>    
>>
>
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>