[Vv] About RT-Struct

[Thomas BAUDIER]

Hi Neree,


Actually, I don't know if it's possible to save a transformation matrix 
in Dicom tag for RTStruct. But it your case, the rotation matrix is not 
present in the dicom tag.
To open a RTStruct, vv (or clitkDicomRTStruct2Image, the basis are the 
same) considers the CT without the rotation matrix. So the coordinates 
saved in the RTStruct are not correct anymore. It's bug and I'll fix it. 
I want to finish another thing before, because I'm not sure it's 
straightforward to debug that.

Don't hesitate if you have others questions
Thomas


On 2017-08-11 17:27, Neree PAYAN wrote:
> Hi Thomas,
> 
> Thank you for your prompt answer. Indeed you were right, my ROIs were
> saved apparently with the CT characteristics, I have to figure out
> why. I followed your instructions to be able to open the ROIs with the
> PET and CT images, and it works perfectly, thanks for this solution.
> 
> However, I do have some others questions about the RTStruct.
> 
> When I open the RTStruct with the CT which has the identity matrix,
> everything works fine and I can visualize the correct ROIs. If I try
> to do the same with the CT which has a rotation and translation
> matrix, I can’t open the RTStruct. If I understood well, it’s
> because my RTStruct was saved with the rotated Dicom.
> Do the RTStruct and the corresponding image must have necessarily an
> identity matrix or do they must just have the same rotation and
> translation matrix ?
> In our case, couldn't it be possible to pass from the first step
> (clitkDicom2Image) directly to the third (clitkDicomRTStruct2Image) ?
> (by keeping the rotation and translation information in the RTStruct
> instead to transform the CT?)
> 
> Moreover, when I link the two CTs, I noticed that the position of the
> visible ROIs (in the CT transformed) and the positions of the «
> missing ROIs » (in the original CT) are exactly in the same
> coordinates in mm in both CTs. If there is a perfect match (in mm),
> why the rotation and translation matrix prevents for visualizing the
> ROIs ?
> 
> Thank you for your help,
> Best regards,
> 
> Nérée
> 
>> Le 10 août 2017 à 10:34, Thomas BAUDIER
>> <thomas.baudier at creatis.insa-lyon.fr> a écrit :
>> 
>> Hi Neree,
>> 
>> I already encountered your problems:
>> - you can't correctly visualize the ROI with the PET image because
>> the spacing of the 3rd dimension of the ROI is 2.5mm (like the CT)
>> and 4.0mm for the PET.
>> We don't deal with this kind of situation in vv because we expect to
>> open the RTStruct with the corresponding image (here the CT).
>> - the second problem is that the CT has a Rotation and Translation
>> matrix. And in your case the RTStrunt was saved with the rotated
>> Dicom.
>> In vv, we consider the opposite.
>> 
>> I'm sorry, this is choices we've done on the software. I'll talk
>> with David and Simon to improve it.
>> But I have a solution the clitk tools.
>> - The fist step is to transform your dicom into mhd:
>> clitkDicom2Image Body-Low-Dose_CT/*.dcm -o Body-Low-Dose_CT/CT.mhd
>> - You have to transform the CT to have an identity transformed
>> matrix: clitkAffineTransform -i Body-Low-Dose_CT/CT.mhd -o
>> Body-Low-Dose_CT/CT.mhd --transform_grid
>> - Finally, convert your RTStruct into mhd ROI:
>> clitkDicomRTStruct2Image -i ROIs/IM-0001-10000-0001.dcm -j
>> Body-Low-Dose_CT/CT.mhd -o ROIs/ROI
>> 
>> Now you can open the ROIs with the PET ant CT images into vv.
>> 
>> Don't hesitate if you have others questions
>> Thomas
>> 
>> On 2017-08-08 18:40, Neree PAYAN wrote:
>> 
>>> Dear All,
>>> I have DICOM PET images with the associated ROIs (= RT-Struct
>>> DICOM
>>> format). When I try to visualize them on the PET image, I obtain
>>> incorrect ROIs in vv while using 3D Slicer everything seems good.
>>> Moreover, for all my data, ROIs were drawn by merging the PET and
>>> CT
>>> scan images, so I’m expecting to be able to visualize them in
>>> both
>>> CT or PET images (as is the case with Slicer). But I never
>>> succeeded
>>> to visualize the ROIs on the CT with vv.
>>> Have you got any idea why I have these problems ?
>>> You can find the CT, PET and RTStruct DICOM on this download link:
>>> https://cloud.u-bourgogne.fr/index.php/s/EoJ73gwyHmdoEJo [1]
>>> Thank you in advance for your help,
>>> Best Regards,
>>> Nérée
>>> Links:
>>> ------
>>> [1] https://cloud.u-bourgogne.fr/index.php/s/EoJ73gwyHmdoEJo
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