[Insight-users] output of segmentation to DICOM
InfoSeekerr
ali.mahmoud.habib at gmail.com
Tue Mar 2 16:52:54 EST 2010
while trying to read the output of WatershedType file , how can I fix that.
because I need the output file for vtk output
itk::ERROR: MetaImageIO(18160008): File cannot be written: c\label.mhd
Reason: No such file or directory
Location: void __thiscall itk::MetaImageIO::Write(const void *)
File: ..\..\..\Code\IO\itkMetaImageIO.cxx
Line: 1396
at itk.itkImage_SS3.Write(String filename)
at itk.itkImage.Write(String filename)
at ConsoleApplication1.Program.Main(String[] args) in C:\Users\Eng. Ali
Mahmo
ud\Documents\Visual Studio
2005\Projects\ConsoleApplication1\ConsoleApplication1
\Program.cs:line 52
I used the following code :
try
{
Console.WriteLine(DateTime.Now.ToShortTimeString());
// read the DICOm series
itkImageBase input = itkImage_SS3.New();
// Read the DICOM image from the given directory
input.ReadDicomDirectory(@"G:\Master
Degree\DataSet\case2\DICOM\PA1\ST1\SE2");
// Display some image information
Console.WriteLine(String.Format("Name={0}", input.Name));
Console.WriteLine(String.Format("PixelType={0}",
input.PixelType));
Console.WriteLine(String.Format("Dimension={0}",
input.Dimension));
Console.WriteLine(String.Format("Size={0}", input.Size));
Console.WriteLine(String.Format("Spacing={0}",
input.Spacing));
Console.WriteLine(String.Format("Origin={0}",
input.Origin));
Console.WriteLine(String.Format("Buffer={0}",
input.Buffer));
ImageType label = itkImage.New(input.PixelType,
input.Dimension);
// Watershed
WatershedType filterWatershed = WatershedType.New(input);
filterWatershed.SetInput(input);
filterWatershed.Threshold = 0.05;
filterWatershed.Level = 0.8;
filterWatershed.Update();
// Relabel
RelabelType filterRelabel = RelabelType.New(label, label);
filterRelabel.SetInput(filterWatershed.GetOutput());
filterRelabel.Update();
filterRelabel.GetOutput(label);
input.DisconnectPipeline();
label.DisconnectPipeline();
// Write the label image to disk
label.Write(@"c\label.mhd");
}
catch (Exception ex)
{
Console.WriteLine(ex.ToString());
}
Console.WriteLine(DateTime.Now.ToShortTimeString());
Console.ReadLine();
}
Luis Ibanez wrote:
>
> Hi Ali,
>
>
> 1) Regarding the output of the Watershed filter,
> Please look at the examples:
>
> Insight/Examples/
> WatershedSegmentation1.cxx
> WatershedSegmentation2.cxx
>
> These examples are described in the
> ITK Software Guide:
>
> http://www.itk.org/ItkSoftwareGuide.pdf
>
>
> You can save the output images using the
> MetaImage file format, or the VTK file format.
>
> Simply use .mhd or .vtk as filename extensions
> respectively.
>
>
>
> 2) You could view these images with:
>
> a) ParaView (www.paraview.org)
> b) Slicer (www.slicer.org)
>
> (Among others...)
>
>
> 3) The classes used for connecting ITK and VTK
> are described in the following Tutorial:
>
> "Getting Started II: Using ITK with VTK"
> http://www.itk.org/CourseWare/Training/GettingStarted-II.pdf
>
> You will find the source code under
>
> InsightApplications/Auxiliary/vtk
> http://public.kitware.com/cgi-bin/viewcvs.cgi/Auxiliary/vtk/?root=InsightApplications
>
>
>
> 4) Regarding connecting ITK and VTK, you will also
> find useful to look at the following Insight Journal
> paper:
>
> "Seamless VTK-ITK pipeline connection for image data handling"
> http://www.insight-journal.org/browse/publication/146
> http://hdl.handle.net/1926/495
>
> The corresponding source code
> can also be found in the directory:
>
> InsightApplications/Auxiliary/vtk
> http://public.kitware.com/cgi-bin/viewcvs.cgi/Auxiliary/vtk/?root=InsightApplications
>
>
>
> 5) For basic examples on how to use VTK
> to visualize segmentation generated by ITK,
> you may want to look at:
>
> InsightApplications/Auxiliary/vtk
> itkReadITKImage3DExtractContourVTK.cxx
> itkReadITKImage3DSegmentShowVTK.cxx
> itkReadITKImageSegmentShowVTK.cxx
> itkReadITKImageShowSplineVTK.cxx
> itkReadITKImageShowVTK.cxx
>
>
> 6) You may also find useful to look at the following
> segmentation applications that use the watershed
> filter:
>
> InsightApplications/SegmentationEditor
> http://public.kitware.com/cgi-bin/viewcvs.cgi/SegmentationEditor/?root=InsightApplications
>
> InsightApplications/SegmentationEditorFltkGui
> http://public.kitware.com/cgi-bin/viewcvs.cgi/SegmentationEditorFltkGui/?root=InsightApplications
>
>
> Both of them use the Watershed filter,
> and both of them use VTK visualization.
>
>
>
> 7) Finally,
> Please note that CMake works fine in Windows Vista.
>
> You may have run into the common problem with
> the Windows Vista UAC, that forces you to run
> CMake (and the Visual Studio IDE) as Administrator.
>
> For solutions,
> Please look at this email from the archives:
> http://www.itk.org/pipermail/insight-users/2008-May/025682.html
>
>
>
> Regards,
>
>
> Luis
>
>
>
> --------------------------------------------------------------------------
> On Fri, Feb 26, 2010 at 9:28 PM, Ali Habib <ali.mahmoud.habib at gmail.com>
> wrote:
>> Dear all,
>>
>> I want to save the output of wateshed segmentation (using ITK ) and save
>> it
>> to suitable formate such that I can by using VTK read and apply
>> vtkcontour
>> or vtkmarchingcube filter to display the 3D
>> this because I can't find the classess responsible for connecting ITK and
>> VTK piplens, and cann't use cmake in my viista PC
>>
>> best regards
>> _____________________________________
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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.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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