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<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>I am trying to convert a vtk mesh to a Binary image. I
followed the examples given in the ITK software guide. I used spatial object
in order to obtain a Binary image (1 inside the mesh) 0 outside.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'> Instead of that I obtained an image with 1 for the
pixel belonging to the contour and 0 for the rest (inclusing the pixels that
are inside the region delimited by the contour)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Does any body know if there are some condition on
mesh to make the generation of binary image possible.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Here is the source code for the binary image
generation.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Thanks in advance for your help<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=blue
face="Courier New"><span lang=EN-GB style='font-size:10.0pt;font-family:"Courier New";
color:blue'>typedef</span></font><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> itk::Mesh< <font
color=blue><span style='color:blue'>double</span></font>, 3 > MeshType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font>
itk::MeshSpatialObject< MeshType > SpatialObjectType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font> itk::Image< <font
color=blue><span style='color:blue'>unsigned</span></font> <font color=blue><span
style='color:blue'>char</span></font>, 3 > ImageType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font> itk::Image< <font
color=blue><span style='color:blue'>double</span></font>, 3> RefImageType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font>
itk::SpatialObjectToImageFilter< SpatialObjectType, ImageType >
MeshFilterType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font>
itk::VTKPolyDataReader< MeshType > MeshReaderType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font>
itk::ImageFileWriter< ImageType > ImageWriterType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>typedef</span></font>
itk::ImageFileReader< RefImageType > RefImageReaderType;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>/// load vtk mesh<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cout
<< <font color="#a31515"><span style='color:#A31515'>"load vtk
mesh"</span></font> << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> MeshReaderType::Pointer
mesh_reader = MeshReaderType::New();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_reader->SetFileName(
mesh_path );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_reader->Update();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> SpatialObjectType::Pointer
mesh = SpatialObjectType::New();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh->SetMesh(
mesh_reader->GetOutput() ); <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>/// reference image<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cout
<< <font color="#a31515"><span style='color:#A31515'>"load reference
image"</span></font> << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> RefImageReaderType::Pointer
ref_image_reader = RefImageReaderType::New();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ref_image_reader->SetFileName(
ref_image );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ref_image_reader->Update();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ref_image_reader->GetOutput()->Print(std::cout);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 color=green face="Courier New"><span style='font-size:10.0pt;font-family:
"Courier New";color:green'>/// image pointer<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> ImageType::Pointer
image;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 color=green face="Courier New"><span lang=EN-GB style='font-size:10.0pt;
font-family:"Courier New";color:green'>/// generate output image<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cout
<< <font color="#a31515"><span style='color:#A31515'>"generate
output image"</span></font> << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> MeshFilterType::Pointer
mesh_filter = MeshFilterType::New();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->SetOrigin(
ref_image_reader->GetOutput()->GetOrigin() );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->SetSize(
ref_image_reader->GetOutput()->GetLargestPossibleRegion().GetSize() );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->SetSpacing(
ref_image_reader->GetOutput()->GetSpacing() );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>//mesh_filter->SetDirection(
ref_image_reader->GetOutput()->GetDirection() );<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->SetOutsideValue(1);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->SetInsideValue(23);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>mesh_filter->SetInput(mesh);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt;font-family:
"Courier New"'>ref_image_reader->Delete();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>try<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> {<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->Update();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>catch</span></font>( itk::ExceptionObject
& excep )<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> {<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cerr
<< <font color="#a31515"><span style='color:#A31515'>"Exception
Caught !"</span></font> << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cerr
<< excep << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> }<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>//
mesh_reader->GetOutput()->Print(std::cout);<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>// mesh->Print(std::cout);<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>//
mesh->GetMesh()->Print(std::cout);<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->GetInput()->Print(std::cout);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> mesh_filter->Print(std::cout);<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>/// save image<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cout
<< <font color="#a31515"><span style='color:#A31515'>"save
image"</span></font> << std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> ImageWriterType::Pointer
image_writer = ImageWriterType::New();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> std::cout
<< <font color="#a31515"><span style='color:#A31515'>"saving image:
"</span></font> << image_path + <font color="#a31515"><span
style='color:#A31515'>"/"</span></font> + image_name <<
std::endl;<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> image_writer->SetFileName(
image_path + <font color="#a31515"><span style='color:#A31515'>"/"</span></font>
+ image_name );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> image_writer->SetInput(
mesh_filter->GetOutput() );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>image_writer->Update();<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> </span></font><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-----------------------------------------------</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Noura Azzabou, PhD <br>
Labo RMN AIM-CEA<br>
Institut de Myologie - Bat Babinski<br>
G.H. Pitie-Salpetriere, 83 Bd Hopital<br>
75651 Paris CEDEX 13, France<br>
Tél. : 33 (0)1 42 16 58 92<br>
Fax : 33 (0) 1 42 16 58 97</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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