@seagulldvm in response to your other questions:
I’m still awaiting whether I check histogram after unchecking pixel. I saw in a post to someone else you said to do that. Also, is platemess not working anymore on Bonesj?
I’m not clear what you mean by “check histogram after unchecking pixel” - in what dialog box are you working when you do that?
Plateness has been deprecated and replaced by Ellipsoid Factor, meaning that Plateness is not working any more.
- How many sampling increments are ideal (using the default of 100 takes a long time, but I’ll do it if that’s ideal)
It depends on your images, and I think you may be referring to the number of vectors ,which defaults to 100. It is worth doing a sensitivity analysis to see how varying sampling increment and number of vectors changes your results.
- On the one I tried, I get a mean of 255 and a St. deviation of 0, when I analyze the histogram, then analyze - set measurements, and then go to image-stacks-statistics.
I think Ale handled this earlier - you have to analyse the histogram of the EF image, not the binary input image.
- The program seems finicky if I put in my own threshold (seems to prefer if I just go to process - make binary) and also if I set the scale.
Setting a scale shouldn’t affect the EF result, because it’s a unitless ratio, unless you set the scale to have anisotropic pixel spacing (i.e. pixel width, height and depth are not all equal) when pixels are actually isotropic. You do need to start with a binary input image. With the Image > Adjust > Threshold command, select the threshold then hit apply.