Hi Julian, > I am currently importing .nii files from my Python coding into your MITK > Diffusion for motion vector field visualization. Questions that are dedicated to MITK Diffusion specific code (so part of the Diffusion extension, are not my field of expertise. So there people like Peter and Jakob are much better advisers. So I can only tell you who we handle it for image registration vector fields.
> Can you explain how MITK Diffusion encodes colors? > Do my vector lengths also get color encoded? For diffusion code (e.g. tensors) I cannot tell. Sorry. For registration fields: Yes. This is possible. See some details here: https://docs.mitk.org/2021.02/org_mitk_views_matchpoint_visualizer.html > Which options do I have to manipulate the visualization by Python exporting > my .nii files? > Which options do I have in MITK Diffusion directly? The visualization is manipulated by setting the dedicated properties in the data node of the registration object. Example of who this done can be found in the code of the plug in org.mitk.views.matchpoint.visualizer. So the export in python has no impact on how the vector is visualized. You can control it from outside if you generate your own scene file, where you can also define the properties and their values in a file. Hope that helps. Mit besten Grüßen, Ralf P.S.: Please always keep the mailinglist in the loop. 1) the answer might be of interest for others and 2) may be also others know the answer and you do not have to wait till I find time to answer. ;) Please excuse the delay. -----Ursprüngliche Nachricht----- Von: Julian Kuhm [mailto:julian.k...@med.uni-giessen.de] Gesendet: Dienstag, 27. April 2021 18:17 An: Floca, Ralf Omar <r.fl...@dkfz-heidelberg.de> Betreff: Re: [mitk-users] mitk project vector field visualization Dear Ralf Omar Floca, Thanks for the answer. I am currently importing .nii files from my Python coding into your MITK Diffusion for motion vector field visualization. My fields have the format i.e. 10 slices, 250x250 pixels each, where every voxel contains a motion vector of 3 dimensions. Can you explain how MITK Diffusion encodes colors? Do my vector lengths also get color encoded? Which options do I have to manipulate the visualization by Python exporting my .nii files? Which options do I have in MITK Diffusion directly? Thank you very much for an answer in advance, Bests Julian Am 09.04.2021 um 10:47 schrieb Floca, Ralf Omar: > Hi Julian, > > you are right a visualization of vector fields is possible but currently > somewhat hidden. > > You can find the needed code for vector field visualization in the > MatchPointRegistration modul. > > It is done by the mapper classes MITKRegistrationWrapperMapper2D and > MITKRegistrationWrapperMapper3D. > > Those classes visualize instances of mitk::MAPRegistrationWrapper. > mitk::MAPRegistrationWrapper is basically a wrapper around itk::Transforms > with a lot of higher level functionality. > So if you have an itk::Transform (this would also work with an itk::Image > with vectors as there is an itk transform wrapper for that), you could pack > it into a MatchPoint registration instance. > > The very heart of the glyph field generation can be found in mitk:: > Generate3DDeformationGlyph(...) > (../Modules/MatchPointRegistration/src/Rendering/mitkRegVisHelper.cpp). Here, > based on a passed transform and a given geometry, the glyph field is > constructed. > > How you alter/change the visualization is demonstrated in the plugin > org.mitk.ui.qt.matchpoint.visualizer. > > Hope that helps a bit. > > Best, > Ralf > > ---------------------------------- > Message: 2 > Date: Thu, 8 Apr 2021 13:32:40 +0200 > From: Julian Kuhm <julian.k...@med.uni-giessen.de> > To: mitk-users@lists.sourceforge.net > Subject: [mitk-users] mitk project vector field visualization > Message-ID: <de59da6a-f830-cf4f-7431-57c03046d...@med.uni-giessen.de> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi everyone, > > When I look at your project site and specifically inspect the image > here: > https://www.mitk.org/w/images/thumb/3/34/Projects%24Lung.png/225px-Pro > jects%24Lung.png > > I can see you are working on a project (dynamic analysis of > respiratory > movement) to visualize lung motion with a quiver overlay. Is this > functionality of depicting motion vector fields somewhere available? Do you > offer the mapper for the visualization of the vectors? > > Best regards, > > Julian > > > > > ------------------------------ > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > mitk-users mailing list > mitk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mitk-users > > > ------------------------------ > > End of mitk-users Digest, Vol 179, Issue 4 > ******************************************
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