[Vv] About RT-Struct

[Neree PAYAN]

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> 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> 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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