How can I get the coordinates of markups?

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?


The point coordinates in the .json file is in LPS coordinate system, i.e. the DICOM coordinate system.

See the nifti file format specification about how the nifti scanner coordinate system is related to the DICOM coordinate system. For example, you can find a summary here: How are the different head and MRI coordinate systems defined? - FieldTrip toolbox

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.).

1 Like