I would like to create (by calculation) an axis in the middle of a cylinder (as seen in the attached file).
Is this something which could be achieved in Slicer?
I thought of performing hole filling in advance and maybe cut the cylinder at the bottom, yet I would like to know if it would be possible to create this axis as I would like to calculate the angle between multiple scans of the same specimen…
Filling the cylinder in Segment Editor is a good idea. You can then use Segment Statistics module to get the position and direction of the cylinder’s long axis.
Thank you!
Can I just choose use any random image data (e.g. from the example data) just to provide RAS coordinates to Segment editor (otherwise it does not work without providing a scalar volume)?
I loaded the MRI head example as scalar volume.
How can I calculate now the angle between the z-axis (this should be the long-axis through the cylinder between those two segments)? (I assume the axes are vectors and represented by the coordinates x y z)
I assume that only the cylinder needs to be depicted without any other structure to make this workflow work?
If you use the GUI then you can use the Specify geometry button to create an empty labelmap volume automatically. Alternatively, you can create a volume from scratch.