Fit Sphere - Add to ROI manager

Dear all,

When the Fit Sphere routine exports the circular ROIs to ROI manager, they are all located on the first section of the stack. In order to see the selected sphere on the whole bone – a great idea by the way – each circular ROI should be on the relevant sections, right?
I would also think, just as a suggestion, that adding the option to export ROIs for the inner and outer cubes would be useful as well.


Since “Fit Sphere” is a BoneJ plugin, I added the bonej tag to your post.

Looking at the source code, it appears that the Z position is included in the ROI. So without digging deeper, I do not know why your ROIs do not appear to be associated with the correct Z sections. Maybe @mdoube or @rimadoma can comment further.

Thanks for your answer @ctrueden, it is strange indeed.


To continue on this:
I applied the same routine to another stack (generated by a different source), and the z position was included in the ROI for the first half of the circles. The z position of the rest of the circles were all the middle slice. When the option ‘outer cube’ is unchecked, the z position is not included in any of the circles.
With another stack, the z is included for the first up to the slice 182, which happens to be the number of slices in the outer cube stack. This time, when the option ‘outer cube’ is unchecked, the z position is included up to the point where the z position reached 118, which happens to be the number of slices in the inner cube stack.

It’s unclear to me what differed between the different initial stacks, sorry for not being able to be more explicit.

Hello Eli,

I’m not that familiar with this plugin myself yet, but one thing that could explain this phenomenon is if the stacks had different calibration.

Dear Rimadoma,

Thanks for your answer. The initial stack and the substacks produced by Fit Sphere (i.e., sphere, inner cube, outer cube) have the same resolution…

Ok, by uncliking ‘Copy Sphere’, ‘Inner Cube’, and ‘Outer Cube’ (i.e., just recovering the ROIs from the Fit sphere routine), you do get the ROIs with all z positions included…I guess it’s the exportation of substacks that messes up with the recovering of the z positions.