I’m trying to calculate trabecular thickness and spacing to a certain area within my bone. I have generated a series of ROIs (one ROI for each image in my stack) in which I want to limit the thickness and spacing calculations. There was once an option to “Crop to ROI” in the BoneJ thickness menu, but I no longer has that option. My FIJI and BoneJ programs are both up to date. How can I get the Crop to ROI function working again?
As an alternative, I’ve tried “clear outside” or “invert the selection” and “set pixels” outside of the selection to 0, but both options crop or clear every single image in my stack to the same ROI, which is not what I want. I need each image cropped to it’s corresponding ROI. Any tips or tricks on how to achieve this would be helpful.