Run shape analysis runtime indefinite


I’m running the shape analysis module on a hippocampus segmentation mask (.vtk/.nii/*.nrrd) and it does not seem to complete for some reason. I’m following the steps on the documentation (SlicerSALT-SPHARM-PDM-Tutorial - Google Slides). Please let me know if there is something I am missing.



Here are some pointers:

  1. Check the error log. View → Error Log
  2. Check your output folder, has any output data been created?
  3. SPHARM-PDM can check that the topology is spherical, and through an error message out if its not. If the segmentation has an almost-hole (close to closed C-shape boundary) it will run and fail. This will be by either running forever or by causing numeric singularities. You can inspect the 3D shape of your segmentation by generating a 3D model in slicer (ModelMaker Module) and inspecting it in the 3D view. You can correct your segmentations with the Segment Editor Module. I would be happy to have a look if you screenshot your segmentations.

Let us know how it goes after you try these few things.
Thank you for using SALT!