Well, with the 3d interpolation it is difficult. The algorithm is based on having only sparse input. You would have to spend a good amount of time to come up with a smart solution to extract the minimum number of most suitable slices of an existing segmentation that you would then feed into the 3d interpolation to match the original segmentation again to finally have a good starting point for refinement.
Usually the good ol' manual 2d tools are used for high precision refinement. In complexer cases it may be feasible to separately segment the structures you do not want to be part of your segmentation but are prone to be part of your automatic approach (and use 3d interpolation, 2d interpolation, and other tools for it), and then use the boolean segmentation utilities to subtract that from the original segmentations. It's not trivial to set up but you may want to have a look into the Nvidia segmentation tools for MITK. They basically implemented an MITK segmentation tool that automatically segments an organ but also a 2d tool to refine the result with a reduced amount of control points along the edges. This is then used again as input for the automatic 3d segmentation to refine the segmentation. You can see it in action here: https://www.youtube.com/watch?v=T0Pjki4vXx0&t=2m? Best, Stefan ________________________________ Von: José Alonso Solís Lemus <alonso.jasl+...@gmail.com> Gesendet: Freitag, 4. Dezember 2020 13:25 An: Dinkelacker, Stefan Cc: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] [MITKv2018.04.2] MitkWorkspace ability to edit segmentations (I'll repeat my previous email and add to it as I believe it lacked context) Thank you very much for your quick response. This is excellent and should be very helpful moving forward! One more thing, if we have already saved segmentations, the process you described would not be possible. Is there an alternative for those cases? At the moment, our users go back and redo the segmentation, which is not ideal for them. To provide more context, we have an automatic segmentation tool, which is good most of the time, but sometimes the segmentation has some errors. We were wondering if we could edit *those*, instead of having to re-do them manually. Many thanks, José On Fri, 4 Dec 2020 at 12:18, José Alonso Solís Lemus <alonso.jasl+...@gmail.com<mailto:alonso.jasl%2b...@gmail.com>> wrote: Thank you very much for your quick response. This is excellent and should be very helpful moving forward! One more thing, if we have already saved segmentations, the process you described would not be possible. Is there an alternative for those cases? At the moment, our users go back and redo the segmentation, which is not ideal for them. Thank you very much again, José On Thu, 3 Dec 2020 at 20:44, Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> wrote: Hi, to continue 3D interpolations between sessions, (1) Save the project as .mitk file instead of ony the segmentation node, and... (2) ... make sure to check "Show Position Nodes" below the interpolation buttons BEFORE. (3) Only then the Position nodes (only input for 3d interpolation) will be saved and loaded again?. (4) Click on "Reinit Interpolation" after loading the scene again to continue. Best, Stefan ________________________________ Von: José Alonso Solís Lemus <alonso.jasl+...@gmail.com<mailto:alonso.jasl%2b...@gmail.com>> Gesendet: Donnerstag, 3. Dezember 2020 15:57 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: [mitk-users] [MITKv2018.04.2] MitkWorkspace ability to edit segmentations Apologies if this has been asked before. We develop an app on top of MITK (v2018.04.2), where we build upon some of mitk's functionality. This is used by clinicians in their research projects. Regarding the manual segmentation tool, our users raised the concern that editing a loaded segmentation is not possible. The workload for loading the segmentation is as follows: - The user selects the segmentation (.nii) file. - The path of the selected file is then passed on to the mitk::IOUtil::Load command I think they're able to edit each segmented slice, but I believe they would like to use the 3D interpolation tool. Is there a way to get around this? Let me know if you have any questions. Kind regards, José Alonso
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