Skull Density Ratio with BoneJ

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Hi has anyone some advice on how to calculate skull density ratio (it is calculated as the ratio between the mean values in Hounsfield units for marrow and cortical bone across multiple points over the skull area) using BoneJ?



You probably don’t need BoneJ’s special features for this.

Just draw ROIs on the marrow and bone areas, and measure the HU-calibrated pixel values in each area. Enter those in a spreadsheet then calculate your ratio.


Thank you a lot Michael for your answer! Sorry to bother you, do you know if there is a faster way of automatizing the roi creation? I have 1024 of them.

Thank you a lot again


There probably is, but you have to consider the cost/benefit. If it takes you ~10 seconds per ROI, then you are looking at ~10,000 seconds, so something like 3 hours’ work. Maybe that’s not too bad for a one-off compared to the time you have to spend developing a custom solution. If there’s a potential repeated, wider, or generalisable benefit then that changes the equation.

Sometimes you can record a macro that at least cuts down the tedious menu-clicking and file open/save stuff, which can speed you up by quite a lot for relatively little development effort.

Plugins > Macros > Record.