Dicom monochrom image conversion problem

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jb
Posts: 3
Joined: Wed, 2005-04-06, 11:34
Location: Zurich, Switzerland

Dicom monochrom image conversion problem

#1 Post by jb »

Hi,

When I convert the monochrom dicom image as attached below I get the following warnings and the output image is full of noise. Regardless whether I convert to bmp, tiff, png, etc.

The monochrom dicom image
http://www.uptime.ch/pub/bone.dicom
The output of the conversion with noise
http://www.uptime.ch/pub/bone.pgm
The output how it should be when correctly converted
http://www.uptime.ch/pub/bone.jpg

Code: Select all

dcm2pnm --write-24-bit-bmp bone.dicom bone.bmp
WARNING: invalid value for 'PixelHeight' (0) ... assuming 1 !
WARNING: invalid value for 'PixelWidth' (0) ... assuming 1 !
WARNING: invalid value for 'OverlayBitsAllocated' (1) ... assuming 16 !
Thanks in advance for your help
Last edited by jb on Thu, 2005-04-07, 07:37, edited 1 time in total.

Jörg Riesmeier
ICSMED DICOM Services
ICSMED DICOM Services
Posts: 2217
Joined: Fri, 2004-10-29, 21:38
Location: Oldenburg, Germany

#2 Post by Jörg Riesmeier »

The image violates the DICOM standard in a number of ways. The reason for the "noise" is a wrong value of (60xx,0100) Overlay Bits Allocated -- as the warning indicates -- and incorrectly encoded overlay plane data. The standard specifies in part 3:
If the overlay data are embedded in the Image Pixel Data (7FE0,0010), the value of this Attribute shall be the same as Bits Allocated (0028,0100).
Last edited by Jörg Riesmeier on Wed, 2005-04-06, 15:12, edited 1 time in total.

jb
Posts: 3
Joined: Wed, 2005-04-06, 11:34
Location: Zurich, Switzerland

#3 Post by jb »

Thank you for the quick response!
Is it possible to ignore the overlays and only to render the plain image when using the dcmtk library?
And what is the meaning of the other warning:
WARNING: invalid value for 'PixelHeight' (0) ... assuming 1 !

Jörg Riesmeier wrote:The image violates the DICOM standard in a number of ways. The reason for the "noise" is a wrong value of (60xx,0100) Overlay Bits Allocated -- as the warning indicates -- and incorrectly encoded overlay plane bits. The standard states in part 3:
If the overlay data are embedded in the Image Pixel Data (7FE0,0010), the value of this Attribute shall be the same as Bits Allocated (0028,0100).

Jörg Riesmeier
ICSMED DICOM Services
ICSMED DICOM Services
Posts: 2217
Joined: Fri, 2004-10-29, 21:38
Location: Oldenburg, Germany

#4 Post by Jörg Riesmeier »

jb wrote:Is it possible to ignore the overlays and only to render the plain image when using the dcmtk library?
Sure, just set the option "-O" (--no-overlays) when calling dcm2pnm. You should probably also enable the stored VOI windows by adding "+Wi 1" (--use-window) to the command line.
jb wrote:And what is the meaning of the other warning:
This means that the stored value for (0028,0030) Pixel Spacing is invalid ("0\0").

jb
Posts: 3
Joined: Wed, 2005-04-06, 11:34
Location: Zurich, Switzerland

#5 Post by jb »

Thank you for the great support!

It works fine with the option -O.

Juerg Bircher

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