# Calculating T.Ar and M.Ar on cortical slice stacks

Hi.

We received reviews back on an anlysis and the reviewers asked for T.Ar, Ma.Ar, and Ct.Th in addition to our Ct.Ar, Imax, and Imin measures. I have looked through the different macros listed in BoneJ.

I have found our original stacks (original analysis conducted in 2012!). It appears the original Slice Geometry analysis recorded cortical thickenss (both max. and mean). I am now using the wand tool (at Michael’s recommendation) to get Ma.Ar. I am using the wand tool to threshold (using threshold Set for a multi-stack image) and select the marrow cavity. By adding this to our ancient Ct.Ar measures we can get T.Ar. Our new wand tool selections for M.Ar relative to our original Ct.Ar measures seem to make sense, when checked against the wand tool calculations for T.Ar.

My remaining problem is these are multi-image stacks (about 44 isotropic slices). How do I iterate the wand tool over the 40+ images in each stack to get an average Ma.Ar over the cortical bone volume? And will the threhold remain the same throughout.

Thanks.
Russ

If the marrow cavity is well centred in z you could use the same xy position for all the slices. Something like this macro could work:

``````x = 1; //set your x-value here
y = 1; //set your y-value here
for (z = 1; z <= nSlices(); z++){
doWand(x, y);
area = getValue("Area"); //calibrated area
Roi.remove;
setResult("Slice", z, z);
setResult("M.Ar", z, area);

}
``````

May be safer to first threshold the image into binary, using the “Stack histogram” option in the Threshold tool.