VMTK extension for PCA

Hello, I’m new to this and so far I’ve been using this tutorial (https://na-mic.org/w/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf). I’ve been trying to do a segmentation for the PCA on a t1 divided by t2 MRI scan. I haven’t been able to get it to work, and I have a few questions.

  1. What would be the optimal amount and optimal placement for the seeds for vesselness and level set segmentation?
  2. When I do vesselness filtering, the preview displays the red parts filtered correctly but the output after the filtering is a black outline around the same parts. Is this an error and does it affect segmentation?
  3. I read that the optimal settings for blood vessel segmentation include reducing blob-like structures threshold and increasing plate-like structures threshold. Are there other alterations I could do to troubleshoot?
  4. Are there more resources where I could read about VMTK in Slicer specifically? The other tutorials I’ve read are about VMTK only.

You could have a look at the project writeup by @haehn https://www.slicer.org/w/images/e/e8/Haehn-Slicer_VMTK_student_research_project.pdf