[Vv] Fwd: Bug in clitkDicom2Image

[Benoît Presles]

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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>>>
>>>
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>>
>>
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