Measuring and Landmarking 3D Data with the 3D Slicer Markups Module

3D Slicer can be used to place points, take linear measurements, and create curves from both surface and CT scan data. The Markups module contains these tools, and I show how to use them.
Acknowledgements:
Thanks to the William R. Zooarchaeology Lab (WRAZL) at Indiana University and collections manager Jess Miller-Camp and to the University of Wyoming paleontology collection and collections manager Laura Vietti for access to the specimens seen in this video
Morphosource Links:
Beaver - www.morphosource.org/concern/...
Hoplophoneus - www.morphosource.org/concern/...
0:00 - Introduction to Markups
1:20 - Landmarking on a Mesh
4:42 - Correcting a Landmarking Mistake
5:57 - Linear Measurements
6:28 - Adjusting Display of Markups
6:36 - Understanding Slicers Units
7:58 - Placing Curves
9:43 - Resampling Curves
10:47 - Markups on CT data
15:08 - Exporting Markup data
16:56 - Markup Formats

[@seanhatton73]

Thank you for this excellent presentation, you have saved me a lot of headaches!

[@marioschadel3747]

Wow, this will be super helpful to me and some of my colleagues! The video is very well made, and, except for the analysis part, which I am looking forward to seeing, there is nothing that a new user might miss. Congratulations!

[@nehabhullar913]

Thank-you for the nice tutorial.

[@kathleenrust2599]

Quick question re: closed and open curves. Are the points generated when placing an open or closed curve all considered fixed landmarks for curves? Or are they always considered semi landmarks? I was also wondering if I can start and end an open curve using fixed landmarks from the regular control points? That is, I have 14 fixed landmarks on some fossil teeth, and I'd like to add some curves to the already existing coordinate data from my fixed landmarks to better capture the variation I am interested in. Could I used two landmarks from the already established 14 fixed landmarks as the starting control point and the ending control point for an open curve?

[@JOc17KER]

which one is better making maual landmarking or use pseudoLMGenerartor of slicermorph? Please give some advice

[@VirtPaleo]

My answer is that it greatly depends on your data and there’s a lot of debate about the pros and cons of both. I recommend looking through this paper to get an idea: academic.oup.com/icb/article/59/3/669/5523849

[@JOc17KER]

Thank you very much prof@@VirtPaleo. Looks like i've been lost all this time about this morphometric topic and landmarking. Please give me some advice, i'm doing a thesis about human tibial bone statistical shape model, do you think it is ok to just use pseudoLMGenerator then use PCA of slicermorph?

[@VirtPaleo]

@JOc17KER Any method is going to require some thought and experimentation to capture the variation you're interested and make sure you're seeing actual variation and not mistakes in the data. PseudoLMGenerator would work well for human tibias because there's not a lot of good anatomical landmarks like the skull. I recommend reading Slicermorph's documentation: github.com/SlicerMorph/Tutorials/tree/main/PseudoLMGenerator and paper: besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13669 the later of which has a nice flow chart for how to choose what method will work best for your data.