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

Benoît Presles benoit.presles at u-bourgogne.fr
Sat Aug 10 23:10:33 CEST 2019


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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