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

[Thomas BAUDIER]

Hi Benoit,

Thank you for your information. I will look into the code of 3DSlice 
when I will have time. I hope it's not a big modification inside vv.

Regards
Thomas

On 2019-07-23 16:15, Benoît Presles wrote:
> Hello Thomas,
> 
> I have just tried to convert the RTStruct.dcm file with 3DSlicer and
> the resulting binary image is an image with the same direction cosines
> matrix as the ImageWithADirectionCosinesMatrix.nii image.
> 
> Best regards,
> Ben
> 
> 
> Le 19/06/2019 à 19:28, Benoît Presles a écrit :
>> 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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