Would you please explain how to convert the coordinates to world coordinate system (X, Y, Z)? Would you be able to provide the script that convert these coordinates (coordinates = np.where(labelArray==labelValue)) which I think ther are in IJK format, to RAS (X, Y, Z)?
I know that vtk.vtkMatrix4x4() will do the job and I’ve already looked into some examples such as Volumes — 3D Slicer documentation, but have not been able to figure out the right code.
First, download MRHead data from Sample Data module
import numpy as np
volumeArray = slicer.util.array("MRHead") # Get the image data in numpy array format
volumeArray[60, 127, 150] = 0 # Make one voxel black, numpy array is in KJI, not IJK.
volumeNode = slicer.mrmlScene.GetFirstNodeByName("MRHead")
volumeNode.Modified() # I think this is needed to let Slicer know the image was modified.
ijkToRasMatrix = vtk.vtkMatrix4x4()
ijkPoint = np.array([150, 127, 60]) # This is IJK, opposite order compared to KJI.
rasPoint = ijkToRasMatrix.MultiplyFloatPoint(np.append(ijkPoint, 1))
If you hover your mouse over the new black point in the image, Data Probe should show the same coordinates that were printed at the end of this script.