[Vv] clitkDicomRTStruct2Image with an image with a direction cosines matrix

[Thomas BAUDIER]

Hello Benoit,

Sorry for the delay, I worked on different tasks.

It is a problem we already encountered and we did not find a perfect 
solution.
I'm surprised that clitkDicomRTStruct2Image -i RTStruct.dcm -j 
ImageWithADirectionCosinesMatrix.nii -o ROI. works for you with a 
transformed image. In our cases, usually, the output is empty. It's due 
to the fact that the coordinates saved in the RTStruct are based on the 
coordinate system of the ImageWithADirectionCosinesMatrix.nii without 
the transformation matrix. The spacing, size, ... are calculated from 
the inverse tranformation matrix. I already tried to include this 
transformation matrix in the conversion from coordinate point to voxel 
but with VTK it's impossible.

So to realize the conversion, we proceed like this:
- Use clitkAffineTransform with --tranform_grid option and -m to apply 
the opposite transformation on ImageWithADirectionCosinesMatrix.nii
- You can use clitkDicomRTStruct2Image -i RTStruct.dcm -j 
ImageWithoutADirectionCosinesMatrix.nii -o ROI.
- Apply clitkAffineTransform with --tranform_grid option and -m to apply 
the direct transformation on the structures and the nearest neighbour 
interpolator

Thomas

On 2019-06-17 13:39, Benoît Presles wrote:
> Hello Thomas,
> 
> Did you have time to have a look?
> 
> Best regards,
> Ben
> 
> 
> Le 05/06/2019 à 17:38, Benoît Presles a écrit :
>> Dear vv users,
>> 
>> I have tried recently the tool clitkDicomRTStruct2Image to generate a 
>> binary mask with an image with a non-identity direction, i.e. 
>> clitkDicomRTStruct2Image -i RTStruct.dcm -j 
>> ImageWithADirectionCosinesMatrix.nii -o ROI.
>> 
>> The resulting output is a binary image with an identity direction, 
>> with a spacing and size changed compare to the 
>> ImageWithADirectionCosinesMatrix image. According to me, it is a 
>> strange behaviour. Why this choice?
>> 
>> Is it not possible to get an output image with the same spacing, with 
>> the same size and with the same non-identity direction as the 
>> ImageWithADirectionCosinesMatrix image?
>> 
>> 
>> Best regards,
>> Ben
>> _______________________________________________
>> vv mailing list
>> vv at creatis.insa-lyon.fr
>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
> 
> _______________________________________________
> vv mailing list
> vv at creatis.insa-lyon.fr
> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv