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]<mailto:[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]<mailto:[email protected]>]
Sent: Dienstag, 30. April 2013 21:59
To: [email protected]<mailto:[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]<mailto:[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<tel:819.346.1110%20ext%2016634>
--
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<tel:819.346.1110%20ext%2016634>
--
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
------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite
It's a free troubleshooting tool designed for production
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap2
_______________________________________________
mitk-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mitk-users
