I’m trying to use the ExtractSkeleton module to find the centreline of an artery. I’m posting to “Support” because I’m currently trying to do it from the GUI. On MacOS 10.12, and I just downloaded the pre-compiled newest nightly to test this.
Steps: I start with a Segmentation of an artery (about 15 pixels diameter, 100 pixels long). Using the Segmentations module, I export it to a label map. In ExtractSkeleton, I request a new Output Image, set skeleton type to 1D, Do not prune branches to True, number of points as default, an output points file name, and request a new markups fiducial node.
Expected: An output image with voxels along the skeleton, a points file with 100 points, and a fiducial node with 100 points.
Actual: An output image with voxels along the skeleton, but an empty points file and no points in the fiducial node.
So, the points file is being created, and the image of the skeleton is being created, but no points are written to the file or to the fiducial node. Am I doing this correctly?
Thanks for your reply. To be honest, I don’t know where the log file is stored, either for the compiled or pre-built application. Where can I find it?
Thanks again.
I just tested ExtractSkeleton with a larger segmented volume, and I was able to get points and markup fiducials. The problem may be with the size and shape of my input label map. For the original, smaller diameter label map, I could only get an output label map if I set Do Not Prune to True. However, I had to set it to False for the larger input.
They’re both roughly cylindrical, and 100 pixels long, but the original “smaller” input was 8 pixels diameter, and the larger input was 23 pixels diameter.
