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

[Thomas BAUDIER]

Hi Benoit,

Thank you very much for your contribution. You can submit your code 
directly via Github and pull request.
If you do not know how to do it, send it to me and I will integrate it.

Thank you
Thomas

On 2019-08-10 23:10, Benoît Presles wrote:
> Dear Thomas,
> 
> I successfully managed to update the clitkDicomRTStruct2Image tool so
> that it can take into account images that have a direction cosines
> matrix.
> If you are interested I can send you the source code to your personal 
> e-mail.
> 
> Best regards,
> Ben
> 
> 
> Le 25/07/2019 à 17:30, Thomas BAUDIER a écrit :
>> 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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>>>>>> 
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