The centerline will end near the marked point, so make sure to mark the endpoint of the centerline near the middle of the opening.
You can increase Oversampling to increase accuracy. See documentation:
Oversampling: Specifies resolution during internal remeshing. Higher value results in higher accuracy but longer computation time. Increase this value up to 2-4x if output does not follow the input segmentation accurately enough.
It is very hard to guess how to fine-tune your results and address remaining small issues just by looking at a few screenshots. I would recommend to share a dataset (upload to dropbox, onedrive, etc. and post the link here) or bring your dataset to one of the Slicer meeting:
I tried increasing oversampling from 1.5x to 2.5x, but it doesnāt help at all. I want to close the aperture, then it will probably be okay, but the editing tool in 3D slicer isnāt as flexible as Blender. So, I want to try editing the model in Blender first, then convert it to a series of TIFF photos (but everything will fail in voxelized processes).
Thanks, the data file was very useful. The opening is very large, so it makes sense to close it before you extract the internal volume. You can use āBaffle plannerā module (provided by SlicerHeart extension).
Here is a short video that shows the entire workflow:
Note that the curve provided by Extract Centerline moduleās ācenterlineā method finds the shortest path on the medial surface (approximated by the edges of the Voronoi diagram, purple spiky surface in the screenshot), which is not the geometric center of the cross-section for a spiral shape:
You can use Curved Planar Reformat module (in Sandbox extension) to straighten the spiral and get an idea about the shape and size of the cross-sections in simple 2D images:
Yes, curves have a built-in algorithm for this. More specifically, its GetCurvePointToWorldTransformAtPointIndex method provides transforms that can be used to translate an object (such as the end plate) along the curve, with minimal spinning and rotation.
No graphical user interface is provided for such specialized needs, but you need to write some Python code snippets to describe what you need exactly. Most of the code can be written by AI chatbots, but you need to be able to provide guidance for them. You can start from the Cross-section analysis module, which gets the cross-section that is orthogonal to the centerline, and modify it to use planes that are parallel to the end plate instead.
You can transform the endplate normal directiom from World coordinate system to Curve coordinate system. The plane normal direction remains the same along the curve in he same direction anywhere along the curve in Curve coordinate system. You can get the plane direction in World coordinate system by using the CurvePointToWorld transformation matrix.
Thanks, I tried a lot, however, itās still quite difficult for me. Coding is not that big problem, the main problem is that quite a lot of API Iām not familiar with, many terms, e.g. world etc., I will think about any other solution.
Learning any new API is always time consuming and spending the time on it is a bit of a gamble when you are not sure yet what tools you will use in the end. Fortunately, chatbots are quite good at knowing APIs of open-source tools, such as Slicer, so you donāt have to dig into documentation or examples, just start vibe coding right away. You can also get help from community members who can help out (online, in virtual meetings, and in-person meetings) or get dedicated support from a Slicer Commercial Partner company. You are probably really close to what you need (reslicing the volume with planes parallel to the endplate is about 10 lines of quite simple Python code), but of course you can look around if you can find any tools that work better for you.
