[Vv] Fwd: Bug in clitkDicom2Image

Wed Dec 19 17:58:43 CET 2018

Dear Thomas,

I have just checked the new version and there is still an error either 
in vv or in clitkDicom2Image (I think in clitkDicom2Image).
First, I convert the dicom image I sent you WITHOUT the -p option and 
open it in vv. Then, I open in vv (vv-->Open Dicom) the dicom image 
without activating the "Patient Coordinate System" checkbox and I link 
the two images. They are NOT aligned.

Thanks for your help,
Best regards,
Ben

Le 19/12/2018 à 16:09, Thomas BAUDIER a écrit :
>
> Hi Benoit,
>
> I think it's ok now with this commit:
> https://github.com/open-vv/vv/commit/5f801bf0b07486889123e941d6913d4369dfc86f 
>
>
> Thank you
> Thomas
>
> On 2018-12-18 08:47, Thomas BAUDIER wrote:
>> Hi Benoit,
>>
>> Ok, I will investigate the problem. Yes, could you send me a dicom
>> image please. You can send it directly to my email if you do not want
>> to send it to the mailing list.
>>
>> Thank you
>> Thomas
>>
>> On 2018-12-17 20:00, Benoît Presles wrote:
>>> Dear Thomas,
>>>
>>> I updated to the latest version of vv.
>>>
>>> About vv, my bad. I did not notice the "Patient Coordinate System"
>>> checkbox in the new version. When I open a dicom with this checkbox
>>> activated, I get the same image orientation as with the old version.
>>>
>>> About clitkDicom2Image, I confirm you that the -p option does not
>>> work. When I use it, the image I generate has no transformation matrix
>>> and it is neither aligned with the image I generated with the old
>>> version of clitkDicom2Image.
>>> Moreover, when I don't use the -p option, the transformation matrix is
>>> the identity but the origin of the generated image is not the same as
>>> the dicom image, so it is not aligned with the dicom image open
>>> without activating the "Patient Coordinate System" checkbox.
>>>
>>>
>>> Do you want me to send you an image in dicom format with a 
>>> transformation ?
>>>
>>>
>>> Best regards,
>>> Ben
>>>
>>>
>>>
>>> Le 17/12/2018 à 17:10, Thomas BAUDIER a écrit :
>>>>
>>>> Hi Benoit,
>>>>
>>>> Sorry for the late reply, I have a lot of work :/
>>>>
>>>> I do not know your previous version of clitk but I did some 
>>>> modification to take into account ITK transformation management 
>>>> modification.
>>>> You can see the commits here:
>>>> https://github.com/open-vv/vv/commits/master/tools/clitkDicom2Image.cxx 
>>>>
>>>> But I do not know why with the -p option it does not work anymore.
>>>>
>>>> But when you open the dicom serie with vv, you can set "Patient 
>>>> Coordinate System" to take the transformation into account when you 
>>>> select the serie. Does it work for you ?
>>>>
>>>> Best regards
>>>> Thomas
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 2018-12-17 12:34, Benoît Presles wrote:
>>>>> Dear Thomas,
>>>>>
>>>>> Did you have time to have a look at the bug ?
>>>>>
>>>>> Best regards,
>>>>> Ben
>>>>>
>>>>>
>>>>> Le 11/12/2018 à 15:25, Benoît Presles a écrit :
>>>>>> Dear Thomas,
>>>>>>
>>>>>> I have updated my version of clitk and a bug I had before 
>>>>>> reappeared!
>>>>>> clitkDicom2Image does not take into account the transformation in 
>>>>>> the dicom header (Image Orientation (Patient) tag in the dicom 
>>>>>> header) even with the -p option (open the image with patient 
>>>>>> coordinate system).
>>>>>> Similarly, when I open the dicom image with vv (vv-->Open Dicom), 
>>>>>> the transformation is not taken into account.
>>>>>>
>>>>>> In a previous version of vv, the transformation was correctly 
>>>>>> taken into account.
>>>>>>
>>>>>>
>>>>>> Thanks for your help,
>>>>>> Best regards,
>>>>>> Ben
>>>>>>
>>>>>>
>>>>>>
>>>>>> Le 24/07/2017 à 16:50, Thomas BAUDIER a écrit :
>>>>>>> Hi Benoit,
>>>>>>>
>>>>>>> I just came back from hollidays and I see your bug.
>>>>>>> Thank you to your support, I checked your files and I validated 
>>>>>>> your modifications.
>>>>>>> So they are available on the git.
>>>>>>>
>>>>>>> Best
>>>>>>> Thomas
>>>>>>>
>>>>>>> On 2017-07-20 20:21, Benoît Presles wrote:
>>>>>>>> Dear vv users,
>>>>>>>>
>>>>>>>> Please find attached the fix I did.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Ben
>>>>>>>>
>>>>>>>>
>>>>>>>> -------- Message transféré --------
>>>>>>>> Sujet :     Bug in clitkDicom2Image
>>>>>>>> Date :     Wed, 12 Jul 2017 09:39:24 +0200
>>>>>>>> De :     Benoît Presles <benoit.presles at u-bourgogne.fr>
>>>>>>>> Pour :     vv at creatis.insa-lyon.fr
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Dear Thomas,
>>>>>>>>
>>>>>>>> I think there is a bug in the clitkDicom2Image tool. 
>>>>>>>> clitkDicom2Image
>>>>>>>> does not take into account the transformation in the dicom header
>>>>>>>> (Image Orientation (Patient) tag in the dicom header).
>>>>>>>> Indeed, the same two images, the first one in "dicom format"
>>>>>>>> (vv-->Open Dicom) and the other in "image format" generated 
>>>>>>>> thanks to
>>>>>>>> clitkDicom2Image, do not overlap.
>>>>>>>>
>>>>>>>> You can download my test data here:
>>>>>>>> https://cloud.u-bourgogne.fr/index.php/s/dNkQJuvXepdmx7e. You will
>>>>>>>> find a dicom image with an orientation and the corresponding image
>>>>>>>> generated thanks to clitkDicom2Image.
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks for your help,
>>>>>>>> Best regards,
>>>>>>>> Ben
>>>>>>> _______________________________________________
>>>>>>> vv mailing list
>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>
>>>>>>
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>>>>>
>>>>>
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