[Vv] About RT-Struct

[Neree PAYAN]

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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