Surface Area measurements in BoneJ

Hey, I’m a new user to ImageJ and I had a question that I couldn’t find an answer yet to in this Forum. I’m using the BoneJ plugin and 3D viewer to take breast MRI stacks and measure surface area and volume. Using Isosurface and a low threshold, I’m able to generate the 3D object and get surface area but the surface area includes the “back” of the breast. Is there a way to isolate the “skin” surface and ignore the “back” (chest wall) of my 3D object when calculating surface area? I haven’t figured out if there’s a way to use a magic wand or some other plugin to highlight and isolate the two surfaces…
Also, still trying to figure out how to display the object’s volume. I’m sure there’s a way but BoneJ’s documentation is very brief. Any help would appreciated!

I know exactly what you mean and would like to have the same option, to stop surfaces getting generated where the foreground object intersects with the image stack faces (in particular to measure trabecular bone surface area). I’ve talked to @rimadoma about it in the past, although I think that @kephale is doing this stuff now. Until they make an option to do that you will have to somehow estimate the area of the chest wall and subtract it from the total area you’ve measured.

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I’ve started an issue for this in ThreeDViewer. That is where we are most likely to expose this functionality. I will try to update this post when we implement this, but just in case I forget, double check the issue as well.

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@mdoube thank you for your reply. Because the chest wall is not a discrete “slice” of my image stack (from an orthogonal standpoint the slices I’m using are axial, while the chest wall is coronal), I’ve had to use some other software (Vitrea) to measure the 2D surface area of the chest wall footprint and subtract it from the total surface area, as you suggested. It works, but its a little klunky. :wink:

@kephale Thanks for starting an issue for this! For sure, I’m really glad I found BoneJ, but this functionality would make it even better! It already does more than the commercial software (Vitrea) we are using for analysing MRI volumes!

Update: I figured out how to measure the volume, using Moments of Inertia from the BoneJ plugin. Works well!