Interlandmark Distances

[Matt Patterson]

Hi all,

I'm pretty new to using this package (and R in general) so just wanted some help interpreting some results i got. 

I'm looking at the ontogenetic changes in skull size/shape of a particular snake species (Dugite) and i wanted to calculate some linear distances between certain landmark points on the bones of my skulls. My specimens were all scanned using a Skyscan Micro-CT at the same scanning resolution (17.78um). I then processed the scan data through NRecon, then CT-Analyser to obtain the 3D models which i applied the 3D landmarks to.

I used the interlmkdist function to produce the matrix of linear distances, with the following code:

lmks <- data.frame(HL = c(1,2), HW = c(3,4), JL = c(5,6), DQL = c(7,8), MQL = c(9,10), VQL = c(12,14), row.names = c("start", "end"))

A <- dugites

lineardists <- interlmkdist(A, lmks)

##where A is the 3D array containing the landmark coordinates and lmks is the matrix of landmark addresses for the start and end landmarks defining m linear measurements

Other than this i have not done anything else with the landmark data since importing it into R. And these are the results i got below.

I'm finding it hard to interpret these linear distances as i do not know what units these values are in or how to convert them to a unit useful to me. And also the measurements themselves are inconsistent as the value for the head length for a small specimen is larger than the head length of a much larger specimen.

The issue most likely stems from the fact that i haven't given R any information regarding scale or relative size. So i am just wondering how i go about calibrating these measurements. Should i obtain a reference measurement consistent across all specimens and somehow import that information into R so then it can use that to produce more accurate/useful measurements?

I apologise if i haven't explained this well enough, but as i meantioned above, I am quite the novice R user.

Any help someone can provide on this issue would be greatly appreciated.

Cheers,

Matt

[Mike Collyer]

Matt,

The units are the units you use, if you set scale during digitizing.  A distance is the square root of the summed squared distances of the partial coordinates, e.g., x1, y1, z1, x2, y2, z2, …  This puts the distance units in whatever scale you measured, e.g., mm, m, km.  If you did not have a scale, then the units are pixels (2d photos) or whatever field increments that scanner uses.  Check your CT-Analyzer.  It must have a scale feature that allows you to turn those values into something tangible.

Regardless, distances have to be consistent with the Cartesian coordinates in the field of measurement, which has to have some kind of scale.  Often we wish to convert one scale to another (like pixels to mm), but to do that, one needs to know the initial scale.

Cheers!

Mike

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[Matt Patterson]

Thanks Mike,

That helps a lot. I think there is a scaling feature in the processing software (CT-Analyzer), so i'll try incorporating that when digitizing my CT scans.

Cheers,

Matt

Mike

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