[Insight-users] Question about measurements in a volume

[Luis Ibanez]

Hi Sotiris,


1) In order to perform measurements you must
    make sure that you have correct values for
    the pixel spacing of your volume in physical
    units (e.g. millimeters, microns, centimeters).


2) Unfortunately JPEG files do not contain such
    information.  If you want to make serious
    measurements you *MUST* use DICOM images. This
    image fileformat will contain correct information
    regarding the size of pixels in physical units.


3) JPEG was designed for storing images of natural
    scenes using a reasonable lossy compression scheme.
    JPEG is good for birthday pictures, your family
    photographs, the picture of a house in front of a
    lake, and the picture of a dog sitting in the yard.

    DICOM was designed for storing medical images, such
    as CT, MRI, PET.

    For full information about DICOM, you must look at

               http://medical.nema.org/

    If you are managing medical images you *should not*
    use JPEG as a fileformat for your data.


4) VTK uses the convention of Computer Graphics for
    the coodinate system: origin on the top-left corner,
    and +Y axis pointing down the screen. ITK uses the
    convention of math and physics: origin on the bottom
    left corner, and +Y axis pointing up the screen.

    You must be very careful with this in medical applications
    because reverting the +Y axis will lead to confuse
    left-right on the patient.


Regards,


    Luis



--------------------------
Sotiris Dimopoulos wrote:

> Hi!
> 
> I have a pack of CT slices ( JPEG & DICOM format ) and
> i want use itk for the image processing and vtk for
> the visualization...I have this questions :
> 
> 1)Will i be able to obtain *measurements* in the
> volume that i'll produce (which wiil be displayed in
> vtk) for the images in the formats that i have?
>  
> 2)Does JPEAG format give that information?
> 
> 3)Which is the difference between dicom & jpeag
> format?  
> 
> And something else...
> 
> I've done the reading of an image in both formats and
> when a dispay the image in vtk,a get it upside down...
> (the code is at the end).Why is that???
> 
> 
> Thanks in advance!
> 
> //itk include files
> 
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageToVTKImageFilter.h"
> #include "itkDICOMImageIO2.h"
> 
> //vtk include files
> 
> #include "vtkRenderer.h"
> #include "vtkRenderWindow.h"
> #include "vtkActor2D.h"
> #include "vtkImageMapper.h"
> #include "vtkRenderWindowInteractor.h"
> 
> 
> 
> int main( int , char ** argv)
> {
>   
> 
>   
>   typedef itk::Image<signed short,2>             
> ImageType;
>   typedef itk::ImageFileReader< ImageType >      
> ReaderType;
> 
> // Create the dicom reader
> 
>   itk::DICOMImageIO2::Pointer dicomIO =
> itk::DICOMImageIO2::New();
> 
>   ReaderType::Pointer reader = ReaderType::New();
> 
>  const char * filename = "C:/Documents and
> Settings/sotiris/Desktop/OSTA/osta
> 3,5/DICOM/1.2.840.113619.2.22.287.1.3371.20041110.303616/1.2.840.113619.2.22.287.1.3371.2.20041110.303732/1.2.840.113619.2.22.287.1.3371.2.46.20041110.304236.dcm";
>   
> 
>   reader->SetFileName( filename );
> 
>   reader->SetImageIO( dicomIO );
> 
>  
>   reader->Update();
> 
> 
> 
>     ImageType::Pointer image = reader->GetOutput();
>   
>     
> 	//Get the origin of the image
> 	
> 	
> 	const ImageType::PointType& orgn =
> image->GetOrigin();
> 
>      std::cout << "Origin = ";
>      std::cout << orgn[0] << ", " << orgn[1] <<
> std::endl;
> 
>  
> 	 //Get the Spacing
> 
>     const ImageType::SpacingType& sp =
> image->GetSpacing();  
> 
>     std::cout << "Spacing = ";
>     std::cout << sp[0] << ", " << sp[1] << std::endl;
> 
>   //Check the dimensions...How???
> 
>   //Exit the itk pipeline and enter the vtk pipeline
>    
>    typedef itk::ImageToVTKImageFilter<ImageType>
> ConnectorType;   
>    
>    ConnectorType::Pointer connector=
> ConnectorType::New();
>    connector->SetInput(reader ->GetOutput() );
> 
> 
>     // Create the Image Mapper
> 
>     vtkImageMapper *mapper = vtkImageMapper::New();
>          mapper -> SetInput(connector -> GetOutput());
>          mapper -> SetColorWindow(255);
>          mapper -> SetColorLevel(128);
>         
>      // Create the Actor
> 
>     vtkActor2D *actor = vtkActor2D::New();
>          actor -> SetMapper(mapper);
> 
> 
>      // Create the Rendering Window for viewing what
> you've done
> 
>     vtkRenderer *imager = vtkRenderer::New();
>            imager -> AddActor2D(actor);
>        
>   
>     vtkRenderWindow *imgWin = vtkRenderWindow::New();
>            imgWin -> AddRenderer(imager);
>            
>               
>     vtkRenderWindowInteractor *iren =
> vtkRenderWindowInteractor::New();
>            iren -> SetRenderWindow(imgWin);
>            
>            imager->SetBackground(1,1,1);
>            imgWin->SetSize(500,500);
> 
> 
>     imgWin -> Render();
>     iren->Start();
> 
>     
>   // Clean up
>           
>          mapper -> Delete();
> 	     actor -> Delete();
> 		 imager -> Delete();
> 		 imgWin -> Delete();
>          iren -> Delete();
>  
> 
>  return 0;
> }
> 
> 
> 
> 
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