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
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