[Vv] Fwd: Bug in clitkDicom2Image

Thomas BAUDIER thomas.baudier at creatis.insa-lyon.fr
Thu Dec 20 13:17:29 CET 2018 

Hi Benoit,

I did a modification:
https://github.com/open-vv/vv/commit/133a3b14fe0d225aff4ea4edd53d61e7f3d063c2

In fact, the processes to open dicom series with vv and with 
clitkDicom2Image are different. Now, clitkDicom2Image does the same 
thing than vv (using itk::GDCMSeriesFileNames).

Does it work for you ?

Thomas

On 2018-12-19 17:58, Benoît Presles wrote:
> 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
>>>>>>>> _______________________________________________
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>>>>>>>> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>> 
>>>>>>> 
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>>>>>> 
>>>>>> 
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>>>> 
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