[Vv] Fwd: Bug in clitkDicom2Image

[Thomas BAUDIER]

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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