We added a completely new module that makes vessel (or airway or any other tree structure) centerline extraction much faster, flexible, and robust. It can quickly extract a network, determine branch endpoints automatically, allows editing of endpoints, computing centerlines, branches, and quantitative metrics (radius, curvature, torsion, etc). The new “Extract Centerline” module is available in SlicerVMTK extension for latest Slicer-4.11 release (it replaces the old “Centerline Computation” module).
Video demonstrating vessel segmentation, centerline extraction, centerline curve editing, curved planar reformatting (straightening), branch extraction and quantification:
Fabulous, the “curved planar reformat” and “extract centerline” modules are the best, but there is some way to make the “fudicial” that are placed in the “curved planar reformat” be recognized or appear in the centerline of the segmentation ?, this in order to have more accurate measurements, as there are cases in which I need to perform the centerline from the lowest renal artery and for that I rely on the “curved planar reformat” but the fudicials do not appear in the centerline of the segmentation to be able to use the automatic centerline modules with branch recognition.
I followed this video step by step and got stuck at making the centerline. I was unable to select a surface input in the Extract Centerline module. I believe it has something to do with the endpoints and centerline curve shown at 1:02. Can anyone care to explain what step I’m missing? I’m using 3d Slicer 4.11.0-2020-06-27 on Windows 10 and I have MarkupsToModel, SegementEditorExtraEffects, and SlicerVMTK extentions installed.
Dear Mr. Lasso,
I would like to have tested the newest module with the newest 3D-Slicer version (4.11.0), unfortunately the program keeps crashing immediately after starting. I have reinstalled it several times and tested it on different computers (Windows 10).
I hope you can help me.
Excuse me, I have used this method to measure the vessel related morphology, and I feel it is very great. However, I have a question, does the radius measured here refer to the average radius of the vessel in this segment?
how are the “Curvature, Torsion, Tortuosity and StartPointPosition” defined in the “Extract Centerline” module? Which formula is the basis for the measured values?
Unfortunately, I have not found this in my research.
Hi, it seems that “Extract Centerline” has many more options than “Centerline Computation”. Is there a new/updated video available somewhere, presenting the functionalities, and a minimal use-case of the “Extract Centerline” module? I found only a video where “Centerline Computation” is used: Vessel segmentation and centerline extraction using 3D Slicer and VMTK - YouTube . I also asked this question in the section comments of the YouTube video as some people having similar problems may first find the video, then this post/message on the forum.
In short, my problem is that I have what seems like a legitimate segment, but I was unable to generate/extract a centerline.