[Vv] Fwd: Bug in clitkDicom2Image

Thu Dec 20 14:23:40 CET 2018

It seems to work now :-) Thank you very much for your help.

I had the same king of bug with clitkDicom2Image in July 2017 (cf. my 
first email below). Are you doing continuous integration / do you plan 
to do it?

Best regards,
Ben

Le 20/12/2018 à 13:56, Thomas BAUDIER a écrit :
>
> Sorry, it's corrected:
> https://github.com/open-vv/vv/commit/fcbb252eca534687630734b6b0c8b13c799ff282 
>
>
> Thomas
>
> On 2018-12-20 13:34, Benoît Presles wrote:
>> Hi Thomas,
>>
>> I have a segmentation fault error (Segmentation fault: 11) with both
>> the -p option and without.
>>
>> Ben
>>
>>
>> Le 20/12/2018 à 13:17, Thomas BAUDIER a écrit :
>>> 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
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> vv mailing list
>>>>>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>>>>>> http://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> vv mailing list
>>>>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> vv mailing list
>>>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>>> _______________________________________________
>>>>>>>> vv mailing list
>>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> vv mailing list
>>>>>>> vv at creatis.insa-lyon.fr
>>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>> _______________________________________________
>>>>> vv mailing list
>>>>> vv at creatis.insa-lyon.fr
>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>>>
>>>>
>>>> _______________________________________________
>>>> vv mailing list
>>>> vv at creatis.insa-lyon.fr
>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>> _______________________________________________
>>> vv mailing list
>>> vv at creatis.insa-lyon.fr
>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
>>
>>
>> _______________________________________________
>> vv mailing list
>> vv at creatis.insa-lyon.fr
>> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv
> _______________________________________________
> vv mailing list
> vv at creatis.insa-lyon.fr
> https://www.creatis.insa-lyon.fr/mailman/listinfo/vv