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I have a series of DICOM images from a CT scan of a bucket of rocks. I want to systematically measure the size of the interstitial spaces. The reason I'm doing this is to compare it to a simulation I've made to check that my simulation is giving accurate data.

In order for the measurements to be comparable to data from my simulation, I want the method for measuring the gaps to be as follows: define a 3D grid of points within the rocks (say, every 5 mm). At each point that falls within a gap (not in the centre of a rock), measure the gap width from that point in the X, Y, and Z directions.

I've tried messing around with both Horos and ImageJ but I can't work out how to define points (ROIs?) in a systematic way, or to have them show up in all three directional slices of the scan (I'll need to measure two dimensions from one 2D image e.g. X,Y and then switch to the X,Z image to get the third measurement, but use the same defined point).

Ideally once I know how to drop points and understand how they work, I could program the software to automatically do these measurements. Can anyone point me in the right direction?

Thanks!

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