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
------------------------------------------------------------------------------
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