[Insight-users] DICOM RT Images
Hoole, Andrew
andrew.hoole at addenbrookes.nhs.uk
Fri Jun 2 07:29:05 EDT 2006
Hi All
I am having a bit of difficulty displaying an image from a DICOM RT Image
file. I can probably work around it but I'm not sure if I should have too.
My issue is as follows:
DICOM RT Image pixel data is stored starting at the top left hand corner of
the image then rastered right and down with the last pixel in the sequence
being the bottom right hand pixel. The origin of the image is the top left
corner of the image. So far this is pretty much the same as axial DICOM CT
images. For DICOM RT Images however the co-ordinate system: Positive X left
to right, positive Y bottom to top - i.e. the image data is sent with
decreasing Y values. So if I use the ITK stuff and set the origin of the
image according to the origin which is specified in the original file then
the image comes out mirrored vertically about the horizontal line through
the specified origin.
Does all that make any sense. For example an image of width, height of
512,512 and origin -256,256 and pixel size 1mm is actually centred on the
origin.
Any ideas how I can easily handle this mirroring.
thanks
Andrew Hoole
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UK Email: andrew.hoole at addenbrookes.nhs.uk
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-----Original Message-----
From: Bill Lorensen [mailto:bill.lorensen at gmail.com]
Sent: 01 June 2006 18:03
To: Hoole, Andrew
Cc: insight insight
Subject: Re: [Insight-users] Reading Dicom files
Andrew,
You can still get at this information. We store all dicom tags in the meta
data dictionary for the image. Look at the dicom processing examples in
Examples/IO to see how to get the meta data dictionary. Once you have it,
you can use the ExposeMetaData method to get the values for a given tag.
Bill
On 6/1/06, Hoole, Andrew <andrew.hoole at addenbrookes.nhs.uk
<mailto:andrew.hoole at addenbrookes.nhs.uk> > wrote:
Hi Bill
The image which I have been using is a DRR from our planning system -
RTImage modality. I have looked in the DICOM and the spacing is in
(0x3002,0x0011) and the position is in (0x3002,0x0012). This is probably
the issue - it handles normal images not DICOM RT images.
Andrew Hoole
-------------------------------------------------------------------------
Medical Physics, Box 152
Cambridge University Hospitals NHS Trust
Addenbrooke's Hospital
Hills Rd
Cambridge Tel: (+44) (0)1223-216544
CB2 2QQ Fax: (+44) (0)1223-257137
UK Email: andrew.hoole at addenbrookes.nhs.uk
<mailto:andrew.hoole at addenbrookes.nhs.uk>
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-----Original Message-----
From: Bill Lorensen [mailto: bill.lorensen at gmail.com
<mailto:bill.lorensen at gmail.com> ]
Sent: 01 June 2006 17:35
To: Hoole, Andrew
Cc: insight-users at itk.org <mailto:insight-users at itk.org>
Subject: Re: [Insight-users] Reading Dicom files
Andrew,
The reader does read the pixel spacing and origin. What is the source of
your dicom images?
Bill
On 6/1/06, Hoole, Andrew < <mailto:andrew.hoole at addenbrookes.nhs.uk>
andrew.hoole at addenbrookes.nhs.uk> wrote:
Hi All
I'm new to the ITK stuff and having been working through the User guide. I
have used the code in the guide to read a DICOM file and display it in a
window. When I read the file it doesn't appear to read the information
related to the pixel size or the origin of the image. This information is
embedded in the DICOM is there a way to make the reader get this data or is
the problem with the image which I hook onto the output of the reader. The
code I am using is as follows:
typedef signed short InputPixelType;
const unsigned int InputDimension = 2;
typedef itk::Image< InputPixelType, InputDimension >
InputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName("c:\\temp\\test.dcm");
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
try {
reader->Update();
}
catch (itk::ExceptionObject & e){
AfxMessageBox("Exception in file reader
",MB_OK,NULL);
return;
}
typedef itk::Point< double, InputImageType::ImageDimension >
PointType;
PointType point;
InputImageType::IndexType pixelIndex;
InputImageType::PixelType pixelValue;
InputImageType::Pointer image = reader->GetOutput();
InputImageType::SpacingType spacing;
spacing[0] = 0.5; // spacing along X
spacing[1] = 0.5; // spacing along Y
image->SetSpacing( spacing );
InputImageType::PointType origin;
origin[0] = -128.0; // coordinates of the
origin[1] = -128.0; // first pixel in N-D
image->SetOrigin( origin );
As you can see I am manually setting the pixel size and origin which is not
ideal.
Regards
Andrew Hoole
-------------------------------------------------------------------------
Medical Physics, Box 152
Cambridge University Hospitals NHS Trust
Addenbrooke's Hospital
Hills Rd
Cambridge Tel: (+44) (0)1223-216544
CB2 2QQ Fax: (+44) (0)1223-257137
UK Email: andrew.hoole at addenbrookes.nhs.uk
<mailto:andrew.hoole at addenbrookes.nhs.uk>
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<http://www.addenbrookes.org.uk/email_disclaimer.html>
http://www.addenbrookes.org.uk/email_disclaimer.html>
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