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

[Benoît Presles]

Hello Thomas,

Thanks for your reply. I will proceed as you suggested.

Is it really impossible to include the transformation? It works with the 
tool clitkDicom2Image.
And with the latest version of VTK?

Best regards,
Ben


Le 19/06/2019 à 11:57, Thomas BAUDIER a écrit :
>
> 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
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>>
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