[Vv] Fwd: Bug in clitkDicom2Image

Thomas BAUDIER thomas.baudier at creatis.insa-lyon.fr
Thu Dec 20 13:56:05 CET 2018 

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
>>>>>>>>>> _______________________________________________
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>>>>>>>>> 
>>>>>>>>> 
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>>>>>>>> 
>>>>>>>> 
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>>>>>> 
>>>>>> 
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