Tb.Sp not showing up in Results table

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hb...@cornell.edu

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Sep 16, 2015, 3:39:00 PM9/16/15
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Hi,

This is hopefully be a simple question with a quick answer. I tried googling my problem and searching through the mailing list questions, but I haven't found an answer yet so I've resorted to posting it here.

I am trying to find the Tb.Th and Tb.Sp of trabecular bone cores. My voxel size is 10 um^3 and my stacks have around 1000 images. I select my ROI (a circle because it is a cylindrical core) on a binary image (bone = 255, background = 0) and use the BoneJ plugin Thickness, checking the boxes 'Thickness', 'Spacing', 'Use ROI Manager', and 'Mask thickness map'. (I don't select 'Graphic Result' because it makes the run time too long.) BoneJ runs without issue, however, I don't get an output in the Results table for Tb.Sp - only the Tb.Th results (Tb.Th Mean, Tb.Th Std Dev, and Tb.Th Max) show up.

What am I missing? I have already updated both ImageJ and BoneJ and it didn't seem to fix the problem.

Thank you in advance! It is such a trivial question, but has been quite frustrating.

Heather H

Michael Doube

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Sep 20, 2015, 8:21:04 AM9/20/15
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Hi Heather,

It might be that Spacing is not finishing because there is a lot of empty space outside your core, and the algorithm gets progressively slower as the spheres that are being fitted get bigger. That's particularly bad for sides of images, because the algorithm assumes that outside the image is background. You could check to see if that's the case by looking at your CPU usage (on Mac and Linux, open a command prompt and type 'top', on Windows it will be under system utilities somewhere) and look for Java using all your processors.

You could try cropping your stacks so that the sides nearly touch your core, or cropping down to the largest rectangle that fits within the core, or inverting your ROI and filling the non-core parts of the image with foreground, then running Spacing by itself.

Best regards,

Michael

On Wednesday, 16 September 2015 20:39:00 UTC+1
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