Hello Tobias,
the demo videos were made in napari, but you can get comparable visualisations in MITK. The lower-right render window of the 2x2 Standard Display in MITK is the 3D window. You can maximize it by hovering your mouse over it and then clicking the middle square of the three options that pop up in the upper right of the render window (between the "+" and tools-icon). Click the "+"-icon and disable "Show crosshair" so that the 2D planes are not in the way. To show your segmentation labels in 3D, you probably want to do a right-click on the corresponding node in the Data Manager and "Create smoothed polygon model". This will create a new node for each label that is shown in 3D. For an exact representation of the label with distinct voxels, you can instead choose "Create polygon model" or select the segmentation node in the "Properties" view and enable the multilabel -> 3D -> visualize option. If you want to overlay the segmentation with a 3D rendering of the base image, you can use the "Volume Visualization" view. There, you can select your image and turn on "Volume rendering". There are several presets available, but you can also fully customize the visualization to your liking (take a look at the F1 help page for more information). I hope this helps you create the visualization you seek. Hint: if you want to save / share the rendering, MITK lets you take snapshots with the "Screenshot Maker" view. Best regards, Stephen ________________________________ Von: Tobias Schmetzer <t.schmet...@tum.de> Gesendet: Dienstag, 2. September 2025 16:49:27 An: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] [Extern] - nnInteractive only for specific DICOM formats? Hello Stephen, apparently something was wrong when I tried it the last time. I think all were greyed out. Today it worked. Maybe the images were not the same ones or something was not aligned and I wasn’t aware. The OpenGL message was exactly that one. I will ignore it then. One last thing that I couldn’t find out so far: How can I activate the 3D view on Windows as in the demo video? Do I manually need to install napari somehow (as described in https://github.com/MIC-DKFZ/napari-nninteractive) or how do I start it? Best regards, Tobias Von: Schaumann, Stephen <s.schaum...@dkfz-heidelberg.de> Gesendet: Dienstag, 2. September 2025 11:12 An: Tobias Schmetzer <t.schmet...@tum.de>; mitk-users@lists.sourceforge.net Betreff: AW: [mitk-users] [Extern] - nnInteractive only for specific DICOM formats? Hello Tobias, do the other segmentation tools work and only nnInteractive is unavailable, or are all tools greyed out? If it's the latter, can you check that the correct image is selected at the top of the Segmentation View and that this image is currently visible + you have performed a reinit on it? If it is not visible / not centered, there should also be a red text below the selection about that. Does the OpenGL warning say "WARNING: An OpenGL Core Profile was requested, but it is not supported on the current platform. Falling back to a non-Core profile. Note that this might cause rendering issues." ? In that case, the warning is known/expected behavior and you can ignore it. Best regards, Stephen ________________________________ Von: Tobias Schmetzer <t.schmet...@tum.de<mailto:t.schmet...@tum.de>> Gesendet: Montag, 1. September 2025 18:37:49 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: Re: [mitk-users] [Extern] - nnInteractive only for specific DICOM formats? Hello Stephen, Sorry for not describing this earlier. I meant in the segmentation menu in the 3d tools I cannot press the button nnInteractive. By the way I get a warning about a unsupported OpenGL profile no matter if the computer has a Nvidia graphics card or not (I tried 3 different computers) Viele Grüße, Tobias Schmetzer ________________________________ Von: Schaumann, Stephen <s.schaum...@dkfz-heidelberg.de<mailto:s.schaum...@dkfz-heidelberg.de>> Gesendet: Montag, 1. September 2025 15:42:00 An: Tobias Schmetzer; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: AW: [Extern] - [mitk-users] nnInteractive only for specific DICOM formats? Hello Tobias, could you elaborate what you mean with it not working? Is the nnInteractive Segmentation of bad quality or does it fail to produce any segmentation at all? Are there any warning / error messages in the MITK Workbench or in the console log? In principle, nnInteractive should work for any image loaded into MITK. Results may vary, of course, based on the image (modality) and how it compares to the training data used for nnInteractive. Best regards, Stephen ________________________________ Von: Tobias Schmetzer <t.schmet...@tum.de<mailto:t.schmet...@tum.de>> Gesendet: Montag, 1. September 2025 12:05:15 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: [Extern] - [mitk-users] nnInteractive only for specific DICOM formats? Hello, I have MRT acquisitions from two different radiologies. Both are in DICOM format. nnInteractive seems to work on only one of them. Is the nnInteractive feature restricted to certain DICOM formats or is there a different problem? Do you want me to post the DICOM specifics here or somewhere else? Viele Grüße, Tobias Schmetzer
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