Hi everyone, I created a symmetric 3D human facial mesh in R (exported as .ply using vcgPlyWrite function in Rvcg) and also digitised 5 midfacial landmarks along the facial axis of symmetry (exported as fcsv using write.fcsv in Morpho). In R, plotting reveals that the 5 landmarks are exactly along facial midline. However, when I load the .ply and .fcsv into Slicer3d, the landmarks no longer lie along facial midline.
Similarly, I noted that although the Sample Data Gorilla_template_LM1.fcsv lie on 3D mesh of Gor_template_low_res.ply, when I import both files into R and plot, the landmarks no longer lie on the surface of the mesh.
This is the R code to load and plot the Gorilla data:
I want to know why the landmarks that are correctly positioned in R appear incorrectly positioned in Slicer3d and vice versa. What should be done to have the facial landmarks lie along facial midline and on the facial surface in Slicer3d?
I am not sure what exactly causes this issue, but it looks like the fiducials/markers are maintaining a relative position/orientation with respect with each other, just not the model… perhaps the model and the fiducials/markers don’t share the same origin?
If I were you, I would start by placing some fiducials on the model using slicer, perhaps on the symmetric face model since there are only 4-5. Then, I would export those landmarks as a .fcsv file and compare the data in the file to the one you generated using R.
Thank you for the reply. I agree that probably the issue is due to different origin. I followed your suggestion to place several fiducials in slicer, exported the landmarks, and plotted in R. The points lie perfect well on facial surface as I have done in R.
However, I really need to import some externally digitized landmarks into slicer. Therefore, I wish to figure out how these externally digitized landamrks, when loaded into slicer, could still be correctly positioned.
I have uploaded my facial .ply and .fscv file into GitHub so that my issue might be better helped.
I can’t comment on why your external landmarks showing up displaced in Slicer, as @Fluvio_Lobo commented there might be other things going on and you will need to troubleshoot it yourself.
As for the gorilla LMs being different in R, I assume that’s because the model was in LPS and R is reading it as if it is RAS. If you negate the first two coordinates of LMs in R, they should line up.
