[Vv] About RT-Struct

Mon Nov 13 11:06:01 CET 2017

Hi Thomas,

I'm writting back to you to know if there is any news about the RTStruct's bug ?

Thanks a lot for your help,
Have a nice day,

Nérée

> Le 2 oct. 2017 à 10:53, Neree PAYAN <nerea.payan at u-bourgogne.fr> a écrit :
> 
> Hi Thomas,
> 
> Thank you for your answer. I figured it out how I have to do for saving my RTStruct with the PET characteristics. However, I get back to you to know if you have any news concerning the RTStruct’s bug ?
> 
> Thank you for your help,
> Best regards,
> 
> Nérée 
> 
> 
>> Le 14 août 2017 à 17:26, Thomas BAUDIER <thomas.baudier at creatis.insa-lyon.fr <mailto:thomas.baudier at creatis.insa-lyon.fr>> a écrit :
>> 
>> 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 <mailto: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 <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 <https://cloud.u-bourgogne.fr/index.php/s/EoJ73gwyHmdoEJo>
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