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<p class=MsoNormal>Hi Luis & Users,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span lang=EN-GB>Few days back you suggested me to read 3
papers.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>A) "Flux driven medial curve
extraction"<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> </span><a
href="http://www.insight-journal.org/browse/publication/165"><span lang=EN-GB>http://www.insight-journal.org/browse/publication/165</span></a><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> Mellado X.,
Larrabide I., Hernandez M., Frangi A.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> Pompeu Fabra
University, University of Zaragoza<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> ****useful
pre processing step for my application<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>B) "Fast Marching Minimal
Path Extraction in ITK"<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> </span><a
href="http://www.insight-journal.org/browse/publication/213"><span lang=EN-GB>http://www.insight-journal.org/browse/publication/213</span></a><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> Mueller
D.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>
Queensland University of Technology<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> ****Not
very useful for my application as i cannot provide seed point, start point or
end point,<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> as i have
to extract few 100,000 tubular shaped fibres. I am looking for an automatic solution.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>C) "Generalizing
vesselness with respect to dimensionality and shape"<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> </span><a
href="http://www.insight-journal.org/browse/publication/175"><span lang=EN-GB>http://www.insight-journal.org/browse/publication/175</span></a><span
lang=EN-GB><o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>
Antiga L.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>
Mario Negri Institute, Italy<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> <o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB> ****useful
and i am trying to use the example and try to use for my application.<o:p></o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoPlainText><span lang=EN-GB>Apart from the above 2 paper which suits
my application, i am interested to use Gradient vector flow snakes.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>As the gradient vector flow of tubular
structure point towards the center of the tube. I plan to use GVF along with hessian
matrix and Frangi’s vesselness<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>measure to extract the tubular shape.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>I am trying to run the itkgradientvectorflow.cxx
example. I made some changes in the code. The changes are based on a itk user
email i found in itk user achieves. <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>The pipeline is:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>Input image -> gradient magnitude image filter
(edge map) -> gradient image filter -> gradient vector flow.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>The input image is 3D Ct image and pixel
type is unsigned short. No. Of iteration = 200, noise = 300.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>I do not get compilation error. The output
of the pipeline is empty image. I used paraview to visualise the output image,
but the image was empty.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>I am interested in realising the gradient
vector flow. Some help to solve the issue will be highly appreciated.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:blue'>int</span><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> main( <span
style='color:blue'>int</span> argc, <span style='color:blue'>char</span> *
argv[] )<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>{<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>if</span>( argc < 5 ) <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> { <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> std::cerr
<< <span style='color:#A31515'>"Usage: "</span> <<
std::endl;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> std::cerr
<< argv[0] << <span style='color:#A31515'>" inputImageFile
outputImageFile"</span>;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> std::cerr
<< <span style='color:#A31515'>" numberOfIterations
noiseLevel"</span> << std::endl;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>return</span> EXIT_FAILURE;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>const</span> <span style='color:blue'>unsigned</span> <span
style='color:blue'>int</span> Dimension = 3;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> <span style='color:blue'>unsigned</span>
<span style='color:blue'>short</span> InputPixelType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> <span style='color:blue'>float</span>
MagPixelType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::CovariantVector< <span
style='color:blue'>float</span>, Dimension > OutputPixelType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::Image< InputPixelType,
Dimension > InputImageType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::Image< MagPixelType, Dimension >
MagImageType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::Image< OutputPixelType, Dimension
> OutputImageType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'> //set image
reader filter<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::ImageFileReader< InputImageType
> ReaderType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> ReaderType::Pointer
reader = ReaderType::New();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
reader->SetFileName( argv[1] );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> reader->Update();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:green'>//set gradient magnitude filter</span><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span>
itk::GradientMagnitudeImageFilter<InputImageType, MagImageType>
MagnitudeType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
MagnitudeType::Pointer magnitude = MagnitudeType::New();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
magnitude->SetInput( reader->GetOutput() ) ;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
magnitude->Update();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'> //set
gradient image filter</span><span lang=EN-GB style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::GradientImageFilter<MagImageType, <span
style='color:blue'>float</span>, <span style='color:blue'>float</span>>
GradientType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> GradientType::Pointer
gradient = GradientType::New();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
gradient->SetInput( magnitude->GetOutput() );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
gradient->Update();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'> //set
gradient vector flow filter</span><span lang=EN-GB style='font-size:10.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::GradientVectorFlowImageFilter<
OutputImageType, OutputImageType > FilterType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> FilterType::Pointer
filter = FilterType::New();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> filter->SetInput(
gradient->GetOutput() );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>const</span> <span style='color:blue'>unsigned</span> <span
style='color:blue'>int</span> numberOfIterations = atoi( argv[3] );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>const</span> <span style='color:blue'>double</span>
noiseLevel = atof( argv[4] );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
filter->SetIterationNum( numberOfIterations );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
filter->SetNoiseLevel( noiseLevel );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> filter->Update();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'> //set writer
image filter</span><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>typedef</span> itk::ImageFileWriter< OutputImageType
> WriterType;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> WriterType::Pointer
writer = WriterType::New();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>
writer->SetFileName( argv[2] );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> writer->SetInput(
filter->GetOutput() );<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> writer->Update();<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New";color:green'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'> <span
style='color:blue'>return</span> EXIT_SUCCESS;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'>}<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-GB
style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB>Regards,<o:p></o:p></span></p>
<p class=MsoNormal>Kana<o:p></o:p></p>
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