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

[Benoît Presles]

Hi Thomas,

I do not use Github but Gitlab. I am going to send you the code directly.

Best regards,
Ben


Le 13/08/2019 à 08:35, Thomas BAUDIER a écrit :
> 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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