[vtkusers] about DICOM orientation and vtk orientation

[Dženan Zukić]

3D Slicer uses RAS coordinate system, unlike DICOM which uses LPS. Thus x
and y coordinates are inverted. Slicer takes care of this inversion for
volume images, but not for polygonal meshes. In other words, you cannot
have a mesh which appears correctly in both Slicer and ParaView.

HTH

On Tue, Nov 17, 2015 at 7:17 AM, David Gobbi <david.gobbi at gmail.com> wrote:

> Hi Jacky,
>
> Can you attach the code that you use to read the image, to create the
> transform, and to apply the transform?
>
> Also note that, for vtk-dicom, there is a method
> vtkDICOMReader::SetMemoryRowOrderToFileNative() that will ensure that the
> layout of pixels in memory is identical to the layout of pixels in the
> file.  And the class vtkDICOMToRAS allows conversion of the image to the
> NIfTI coordinate system, though I'm guessing that you want to work in DICOM
> coordinates.
>
>  - David
>
>
> On Tue, Nov 17, 2015 at 3:44 AM, Jacky Ko <jackkykokoko at gmail.com> wrote:
>
>> Hello,
>>
>> I am using  vtkDICOMImageReader  to  read  dicom  series.  I  need to
>>  export  the  rendered  surface  in stl format  for  further  analysis.
>> However,  I  found  that the exported  surface 's  orientation  is
>>  different  from the  dicom  one  (e.g. loading both  dicom  series and
>>  STL surfaces in 3D slicer).  But  the  case  doesn't  happen in Paraview.
>>
>> I noticed that  there are two options for  extracting scanning  positions
>> and  orientations by  GetImagePositionPatient() and
>>  GetImageOrientationPatient() under  vtkDICOMImageReader class.
>>
>> I also  read  the  code  in  vtk-dicom  as an extension.  However,  some
>> problem occurs  when I am  using the package (I am developing in python).
>> I need to write  my  own transformation matrix and apply  to the image
>> volume to get a spatial corrected surfaces. The problem is ,  how to get
>>  the correct transformation matrix ?
>>
>> Thanks.
>>
>>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/vtkusers/attachments/20151117/34a58af7/attachment.html>