Hi,
I’m new to 3dSlicer and am trying to understand how to work with the markup function.
My goal is to get the coordinates of three points that I marked up using the “angle” function, so that I can work with them to define a plane when I work with the scan in nifti format in python.
I saw that I can save the markups as .json, and that the file contains positions for each of the points. However I don’t understand how these coordinates translate to the coordinates in the nifti. Is there a way to see the transformation that I need to do? Or an altogether different way of approaching this?
Note that in Slicer you can specify a plane markup using 3 control points, which may be more suitable for representing a plane (as it is visualized as a plane in slice and 3D views, you can more easily shift and rotate it, you can specify boundaries, etc.).
Hi @lassoan, I was wondering what’s the easiest option to get the x, y ,z coordinates of markup points. For the following landmark point, would it be possible to get the number of other two slices? I do not fully understand the slicer’s coordinates, since there are positive and negative values.