Day_4.MD

Cont Morphometrics Tools in SlicerMorph from Day 3

• MarkupEditor: to subset or delete points from a dense pointcloud interactively
• Surface Toolbox
• PlaceLMGrid
• Dynamic Modeler
• SlicerMorphR

Exercise for today

• Go through the PlaceLMGrid tutorial above as written. However make sure you use the data link specified for the USP Course for this exercise. Additionally you may have to use the Surface Toolbox module's Smoothing function to place patches more smoothly. Then run your data with the GPA module.

Link to download 4 merged samples to use in the GPA

• Use the SLicerMorphR tutorial above to load your data into R and and geomorph and "slide" the semi landmarks and then bring them back to SlicerMorph for visualization. If you do not already have R and Rstudio on your computer, you can use the MorphoCloud. To do that, first /unshelve your session, and log into it, open a terminal window and type this command and hit enter:

curl https://jetstream2.exosphere.app/exosphere/assets/scripts/mount_ceph.py | sudo python3 - mount \
  --access-rule-name="MorphoCloudCephShare-ro" \
  --access-rule-key="AQAIDi1nKwbRFRAA9KKHUddANj6Ywj8ag7N9pg==" \
  --share-path="149.165.158.38:6789,149.165.158.22:6789,149.165.158.54:6789,149.165.158.70:6789,149.165.158.86:6789:/volumes/_nogroup/60bf684c-51d1-4abb-93f5-188d4d164111/1fe273cd-1e4d-4087-ad2b-01d548a16fe0" \
  --share-name="MorphoCloudCephShare"

this command will make the necessary R libraries availables to you. You only need to do this once. After you completed this step, to launch Rstudio, type these to commands to start Rstudio:

module load rstudio
rstudio

If time permits

• Image Registration Documentation from Slicer
• Slicer Script Repository (Examples are organized by the modules) (scripting)