[Vv] Fwd: Bug in clitkDicom2Image

[Thomas BAUDIER]

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
>>>>>> _______________________________________________
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>>>>>> vv at creatis.insa-lyon.fr
>>>>>> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>> 
>>>>> 
>>>>> _______________________________________________
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>>>> 
>>>> 
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>> 
>> 
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