Hi<br><div id="result_box" dir="ltr">Hopefully my answers can help you.</div><br><br><div class="gmail_quote">2009/9/15 Maximilien Renard <span dir="ltr"><<a href="mailto:iixamaxii@gmail.com">iixamaxii@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
Sorry for my late answer.<br>
<br>
So I've checked the dicom tags of my image using<br>
DicomImageReadPrintTags and I've highlighted these lines :<br>
<br>
(0018|0050) Slice Thickness = 0.75<br>
...<br>
(0020|000e) Series Instance UID = 1.3.12.2.1107.5.1.4.24514.4.0.2018232119198399<br>
...<br>
(0028|0030) Pixel Spacing = 0.41015625\0.41015625<br>
<br>
So I've read a little bit on the internet and it seems that Slice<br>
Thickness is not what I'm searching for.<br>
<br>
The good way seems to be these tags :<br>
<br>
(0020|0032) Image Position (Patient) = -101.79492\-211.79492\-1107.5<br>
(0020|0037) Image Orientation (Patient) = 1\0\0\0\1\0<br>
<br>
and use them in order to :<br>
<br>
1) compute the normal of the planes<br>
2) use the Image Position to compute the position of the current slice<br>
on the axis (and the difference between the position of two adjacent<br>
slices gives the spacing between them).<br>
<br>
( <a href="http://newsgroups.derkeiler.com/Archive/Comp/comp.protocols.dicom/2006-01/msg00055.html" target="_blank">http://newsgroups.derkeiler.com/Archive/Comp/comp.protocols.dicom/2006-01/msg00055.html</a><br>
)<br>
<br>
Since I am kind of a newbie, please forgive me if I asking<br>
stupidities, here are my questions :<br>
<br>
1) How come that despite the fact that there is this Series ID, my<br>
images are not a serie ?<br></blockquote><div><b>The DICOM standard says that a series may be composed of several acquisitions that are identified with the tag (0020.0012) Acquisition Number<br>Acquisition Number: A number identifying the single continuous gathering of data over a period of time that resulted in this image. </b><br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
2) Will the method to compute the Z-Spacing that I describe above work<br>
for all kind of CT Images ?<br></blockquote><div><b>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<br>C.7.6.2.1.1 Image Position And Image Orientation</b> <br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
3) Doesn't ITK have a way to determine this spacing ?<br></blockquote><div><b>Yes, ITK works with the library GDCM correctly determining the Z value of the volume.</b> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thank you very much for your help,<br>
<br>
<br>
Regards,<br>
<br>
<br>
Maximilien Renard<br>
<br>
2009/9/1 Mathieu Malaterre <<a href="mailto:mathieu.malaterre@gmail.com">mathieu.malaterre@gmail.com</a>>:<br>
<div><div></div><div class="h5">> Your image is a CT Image Storage, this is not an RT Struct. Your pixel<br>
> spacing for your 2D image is perfectly fine.<br>
><br>
> $ gdcminfo 20372451<br>
> MediaStorage is 1.2.840.10008.5.1.4.1.1.2 [CT Image Storage]<br>
> TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]<br>
> NumberOfDimensions: 2<br>
> Dimensions: (512,512,1)<br>
> Origin: (-101.795,-211.795,-1107.5)<br>
> Spacing: (0.410156,0.410156,1)<br>
> DirectionCosines: (1,0,0,0,1,0)<br>
> Rescale Intercept/Slope: (-1024,1)<br>
> SamplesPerPixel :1<br>
> BitsAllocated :16<br>
> BitsStored :12<br>
> HighBit :11<br>
> PixelRepresentation:0<br>
> ScalarType found :UINT16<br>
> PhotometricInterpretation: MONOCHROME2<br>
> PlanarConfiguration: 0<br>
> TransferSyntax: 1.2.840.10008.1.2.1<br>
> Orientation Label: AXIAL<br>
><br>
><br>
><br>
> As mentioned by Bradley, you should instantiate a 2D image to your image.<br>
><br>
> HTH<br>
><br>
> On Mon, Aug 31, 2009 at 7:38 PM, Maximilien Renard<<a href="mailto:iixamaxii@gmail.com">iixamaxii@gmail.com</a>> wrote:<br>
>> Hi there,<br>
>><br>
>> I'm having the same problem. Did you found the solution to this<br>
>> problem ? Can someone please explain me what to do ?<br>
>><br>
>> Thank you very much,<br>
>><br>
>> Regards,<br>
>><br>
>><br>
>> Maximilien Renard<br>
>><br>
>> 2009/5/12 Benhacene Boudan Mustafa <<a href="mailto:m.benhacene.boudan@umontreal.ca">m.benhacene.boudan@umontreal.ca</a>>:<br>
>>><br>
>>> Hi all,<br>
>>><br>
>>> When i try to read a dicom structure with InsightToolkit-3.12.0 i get the error :<br>
>>><br>
>>><br>
>>> terminate called after throwing an instance of 'itk::ExceptionObject'<br>
>>> what(): /home/karim/InsightToolkit-3.12.0/Code/Common/itkImageBase.txx:183:<br>
>>> itk::ERROR: Image(0x703510): A spacing of 0 is not allowed: Spacing is [2.5, 2.5, 0]<br>
>>> Abandon<br>
>>><br>
>>><br>
>>> I know that it is due to a bad format of the structure dicom file that doesn't give z spacing.<br>
>>><br>
>>> 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?<br>
>>><br>
>>> thank you<br>
>>><br>
>>><br>
>>> karim<br>
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><br>
><br>
><br>
> --<br>
> Mathieu<br>
><br>
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