[Vv] Fwd: Bug in clitkDicom2Image
Thomas BAUDIER
thomas.baudier at creatis.insa-lyon.fr
Thu Dec 20 14:46:06 CET 2018
Thank you for your feedback.
I do continuous integration with travis but just to know if vv compile
or not with different VTK and ITK version
(https://travis-ci.org/open-vv/vv). I do not use test. Maybe one day ...
Best regards
Thomas
On 2018-12-20 14:23, Benoît Presles wrote:
> 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
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>>>>>>>>>>
>>>>>>>>>>
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