Currently I am trying to segment the cartilages and meniscus. I have already created segments horizontally. however when I tried to fill between slices they are not connecting?
Does anyone knows why?
I really need this to work. I did once before it worked just fine but today i try again its not working
You can fill slices only along one axis at a time. If you painted slices in different orientations then you need to fill between them in several steps. In each step, you show only those segments that have the same orientation and hide all the others (that are in a different orientation or already filled), and then apply “Fill between slices”. Make sure to enable overlapping segments to preserve the segments that are hidden.
If doing this in several steps is not convenient then you may also try methods that work with arbitrarily placed seed regions, such as “Grow from seeds”.
The fill between option is not connecting the gaps between each slices for some reason and i do not know why
I even tried to start a new segmentation for testing and I just did 2 slices from the sagittal view. And tried the fill between, however it is still not connecting thoes 2 slices
Filling only happens between standalone slices (that have completely empty neighbors). Nothing is filled in the image above anymore, because none of the slices look like standalone (there are 2 or more neighbor non-empty slices).
Each slice that you need to fill between has to be a single slice with at least one empty slice on each side.
If two or more neighbor slices are segmented then it will be considered as a complete 3D object and will not be connected to other slices on either side.
Hi I have re-segmented as shown (1) . However when i try fill in between slices it is not working and I am not sure why, the gaps between each slices are not connecting
Sorry for all the troubles. It seems that you segment on oblique slices (you can see that from the warning icon displayed next to the segmentation node selector). This way when you paint on one slice, you actually paint on several slices of the segmentation. Unfortunately, fill between slices algorithm always works on the original slices, cannot work on oblique slices.
You can either try Grow from seeds effect (that does not require this strict slice-by-slice painting), or you can resample the segmentation geometry with rotated axes.
Knee MRI segmentation is hard, but it should be possible to establish a good segmentation workflow.
@carlp I saw some amazingly high quality knee segmentations from you. Could you help with some advice here? Or - it’s soon time for Christmas, so maybe I can ask such things - could you create a screencast video that shows how you segment a knee?
thank you very much. I will explore the grow from seeds effect options as well as rotated axes. But may I know how does the rotated axes work?
Also the screencast will be insanely helpful as i am trying to obtain a geometry for a FEA analysis, meaning that i would require a a decent quality of the knee segmentation.
Hi currently I am just segmenting each slice as I only need the overall geometry and i will redraw the structure in solidworks. However I ran into a problem where if i paint something in one slice it affects its direct neighbour slice,
Hi
Maybe someone knows how to solve the same problem for CT only? Fill between slices does not work. Instead, the slices just get thicker but don’t merge. It’s definitely not a problem with a CT scan, because I tried to do it on another PC and everything was fine. It is also not possible to label other CTs, even in different projections.
I tried to reinstall the application, and reboot the PC - same problem.