[Insight-users] InsightToolkit-3.12.0 problem reading Structure DCM

Thu Sep 17 09:48:01 EDT 2009

Hi
Hopefully my answers can help you.

2009/9/15 Maximilien Renard <iixamaxii at gmail.com>

> Hi,
>
> Sorry for my late answer.
>
> So I've checked the dicom tags of my image using
> DicomImageReadPrintTags and I've highlighted these lines :
>
> (0018|0050) Slice Thickness = 0.75
> ...
> (0020|000e) Series Instance UID =
> 1.3.12.2.1107.5.1.4.24514.4.0.2018232119198399
> ...
> (0028|0030) Pixel Spacing = 0.41015625\0.41015625
>
> So I've read a little bit on the internet and it seems that Slice
> Thickness is not what I'm searching for.
>
> The good way seems to be these tags :
>
> (0020|0032) Image Position (Patient) = -101.79492\-211.79492\-1107.5
> (0020|0037) Image Orientation (Patient) = 1\0\0\0\1\0
>
> and use them in order to :
>
> 1) compute the normal of the planes
> 2) use the Image Position to compute the position of the current slice
> on the axis (and the difference between the position of two adjacent
> slices gives the spacing between them).
>
> (
> http://newsgroups.derkeiler.com/Archive/Comp/comp.protocols.dicom/2006-01/msg00055.html
> )
>
> Since I am kind of a newbie, please forgive me if I asking
> stupidities, here are my questions :
>
> 1) How come that despite the fact that there is this Series ID, my
> images are not a serie ?
>
*The DICOM standard says that a series may be composed of several
acquisitions that are identified with the tag (0020.0012) Acquisition Number
Acquisition Number: A number identifying the single continuous gathering of
data over a period of time that resulted in this image.  *

>
> 2) Will the method to compute the Z-Spacing that I describe above work
> for all kind of CT Images ?
>
*Not, in some cases the space between slices works well, but most get the
thickness Z from the matrix of transformation definitely in the DICOM
Standard Part 3 in
C.7.6.2.1.1 Image Position And Image Orientation*

>
> 3) Doesn't ITK have a way to determine this spacing ?
>
*Yes, ITK works with the library GDCM correctly determining the Z value of
the volume.*

>
> Thank you very much for your help,
>
>
> Regards,
>
>
> Maximilien Renard
>
> 2009/9/1 Mathieu Malaterre <mathieu.malaterre at gmail.com>:
> > Your image is a CT Image Storage, this is not an RT Struct. Your pixel
> > spacing for your 2D image is perfectly fine.
> >
> > $ gdcminfo 20372451
> > MediaStorage is 1.2.840.10008.5.1.4.1.1.2 [CT Image Storage]
> > TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
> > NumberOfDimensions: 2
> > Dimensions: (512,512,1)
> > Origin: (-101.795,-211.795,-1107.5)
> > Spacing: (0.410156,0.410156,1)
> > DirectionCosines: (1,0,0,0,1,0)
> > Rescale Intercept/Slope: (-1024,1)
> > SamplesPerPixel    :1
> > BitsAllocated      :16
> > BitsStored         :12
> > HighBit            :11
> > PixelRepresentation:0
> > ScalarType found   :UINT16
> > PhotometricInterpretation: MONOCHROME2
> > PlanarConfiguration: 0
> > TransferSyntax: 1.2.840.10008.1.2.1
> > Orientation Label: AXIAL
> >
> >
> >
> > As mentioned by Bradley, you should instantiate a 2D image to your image.
> >
> > HTH
> >
> > On Mon, Aug 31, 2009 at 7:38 PM, Maximilien Renard<iixamaxii at gmail.com>
> wrote:
> >> Hi there,
> >>
> >> I'm having the same problem. Did you found the solution to this
> >> problem ? Can someone please explain me what to do ?
> >>
> >> Thank you very much,
> >>
> >> Regards,
> >>
> >>
> >> Maximilien Renard
> >>
> >> 2009/5/12 Benhacene Boudan Mustafa <m.benhacene.boudan at umontreal.ca>:
> >>>
> >>> Hi all,
> >>>
> >>> When i try to read a dicom structure with InsightToolkit-3.12.0 i get
> the error :
> >>>
> >>>
> >>> terminate called after throwing an instance of 'itk::ExceptionObject'
> >>>  what():
>  /home/karim/InsightToolkit-3.12.0/Code/Common/itkImageBase.txx:183:
> >>> itk::ERROR: Image(0x703510): A spacing of 0 is not allowed: Spacing is
> [2.5, 2.5, 0]
> >>> Abandon
> >>>
> >>>
> >>> I know that it is due to a bad format of the structure dicom file that
> doesn't give z spacing.
> >>>
> >>> With InsightToolkit-3.0.8 i can bypass that problem using the
> ChangeInformationImageFilter after reading the dicom (no error message) and
> then process it through the other filters. Any way to do something similar
> with InsightToolkit-3.12.0?
> >>>
> >>> thank you
> >>>
> >>>
> >>> karim
> >>> _____________________________________
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> >
> >
> >
> > --
> > Mathieu
> >
> _____________________________________
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