I took the time to test it and it doesn't work either. I will test the
branch 15013.
-F
On Wed, May 8, 2013 at 10:57 AM, Félix C. Morency
<[email protected]>wrote:
> Hi Andreas,
>
> Sorry for the late answer. It hasn't come to me to test with
> SetResliceTransformByGeometry() because, IMO, the documentation is not very
> clear about what this method really do. Right now, my workaround works but
> I will try to find some time to test with SetResliceTransformByGeometry()
> for the sake of posterity.
>
> Thanks,
> -F
>
>
> On Fri, May 3, 2013 at 5:14 AM, Fetzer, Andreas <
> [email protected]> wrote:
>
>> Hi Felix,****
>>
>> ** **
>>
>> I am working with the ExtractSliceFilter right now. I had similar
>> problems: It worked well with CT data but MRI made problems. I found a
>> solution by setting:****
>>
>> ** **
>>
>> extractor->SetResliceTransformByGeometry( myImage
>> ->GetTimeSlicedGeometry()->GetGeometry3D( timeStep ) );****
>>
>> ** **
>>
>> Have you tried that?****
>>
>> ** **
>>
>> Best ****
>>
>> Andreas****
>>
>> ** **
>>
>> *From:* Félix C. Morency [mailto:[email protected]]
>> *Sent:* Donnerstag, 2. Mai 2013 16:22
>> *To:* Fetzer, Andreas
>> *Cc:* [email protected]
>>
>> *Subject:* Re: [mitk-users] ExtractSliceFilter geometry issue on 4D data
>> after crop****
>>
>> ** **
>>
>> Andreas,****
>>
>> ** **
>>
>> Thanks for your answer. I perform the cropping using the Image Cropper
>> plugin. It crops each volume of the time series automatically. Afterwards,
>> the slice extraction using a _world geometry_ (say the 2D axial geometry
>> for example) doesn't work. As I said, I think it is related to bug #15013.
>> As a workaround, I adapted my geometry so it's not a world geometry anymore.
>> ****
>>
>> ** **
>>
>> The other bug where the first row and the first column of the image is
>> missing after extraction seems to be bug #11570 [2]. This one is quite old
>> and is still present in the newer MITK versions.****
>>
>> ** **
>>
>> I can send you data for both bugs if it can help you.****
>>
>> ** **
>>
>> [2]: http://bugs.mitk.org/show_bug.cgi?id=11570****
>>
>> ** **
>>
>> Regards,****
>>
>> ** **
>>
>> On Thu, May 2, 2013 at 3:33 AM, Fetzer, Andreas <
>> [email protected]> wrote:****
>>
>> Hi Felix,****
>>
>> ****
>>
>> sorry for the late answer and thank for investigating and reporting this
>> issue! Still the ITK migration is keeping us on the run. However we will
>> have a look at the ExtractSliceFilter issue as soon as possible.****
>>
>> ****
>>
>> Just to get clear about your problem: You perform a cropping on a 4D
>> image. Speaking of cropping, do you extract certain timesteps or is it a
>> geometrical cropping (e.g. using the mitkAutoCropImageFilter?). Afterwards
>> the slice extraction of the cropped image does not work anymore?****
>>
>> ****
>>
>> Best regards****
>>
>> Andreas****
>>
>> ****
>>
>> *From:* Félix C. Morency [mailto:[email protected]]
>> *Sent:* Dienstag, 30. April 2013 21:59
>> *To:* [email protected]
>> *Subject:* Re: [mitk-users] ExtractSliceFilter geometry issue on 4D data
>> after crop****
>>
>> ****
>>
>> Folks,****
>>
>> ****
>>
>> Finally found out that we can't use world geometries with the
>> ExtractSliceFilter. I think it is related to bug #15013 [1] but I can't
>> test because our codebase doesn't build with the ITK4 migration due to the
>> new ITK statistic framework. Also, there seems to be a bug somewhere
>> because my extracted slice is missing the first pixel row and the first
>> pixel column.****
>>
>> ****
>>
>> [1]: http://bugs.mitk.org/show_bug.cgi?id=15013****
>>
>> ****
>>
>> On Mon, Apr 29, 2013 at 9:47 AM, Félix C. Morency <
>> [email protected]> wrote:****
>>
>> Hi list,****
>>
>> ****
>>
>> I have a geometry-related issue with the use of the ExtractSliceFilter.
>> The use case is the following:****
>>
>> ****
>>
>> I have some 4D data that I am cropping using the built-in MITK filter.
>> After the crop, I am using some custom routine to extract 2D slices from
>> the cropped volume using the ExtractSliceFilter. The problem is that the
>> extracted slices are all black.****
>>
>> ****
>>
>> I double checked the PlaneGeometry to extract and everything seem good.
>> I'm using this routine on some other 3D data without any problem. I can
>> also use the routine successfully on the original 4D data. I tested
>> cropping the data in two other softwares, namely Fiji and BrainVisa, and I
>> can use my routine successfully.****
>>
>> ****
>>
>> Does anyone have a clue of what might be the issue?****
>>
>> ****
>>
>> Regards,****
>>
>> -- ****
>>
>> Félix C. Morency, M.Sc.
>> Plateforme d’analyse et de visualisation d’images
>> Centre Hospitalier Universitaire de Sherbrooke
>> Centre de recherche clinique Étienne-Le Bel
>> Local Z5-3031 | 819.346.1110 ext 16634 ****
>>
>>
>>
>> ****
>>
>> ****
>>
>> -- ****
>>
>> Félix C. Morency, M.Sc.
>> Plateforme d’analyse et de visualisation d’images
>> Centre Hospitalier Universitaire de Sherbrooke
>> Centre de recherche clinique Étienne-Le Bel
>> Local Z5-3031 | 819.346.1110 ext 16634 ****
>>
>>
>>
>> ****
>>
>> ** **
>>
>> -- ****
>>
>> Félix C. Morency, M.Sc.
>> Plateforme d’analyse et de visualisation d’images
>> Centre Hospitalier Universitaire de Sherbrooke
>> Centre de recherche clinique Étienne-Le Bel
>> Local Z5-3031 | 819.346.1110 ext 16634 ****
>>
>
>
>
> --
> Félix C. Morency, M.Sc.
> Plateforme d’analyse et de visualisation d’images
> Centre Hospitalier Universitaire de Sherbrooke
> Centre de recherche clinique Étienne-Le Bel
> Local Z5-3031 | 819.346.1110 ext 16634
>
--
Félix C. Morency, M.Sc.
Plateforme d’analyse et de visualisation d’images
Centre Hospitalier Universitaire de Sherbrooke
Centre de recherche clinique Étienne-Le Bel
Local Z5-3031 | 819.346.1110 ext 16634
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