Setting an MNI origo to a volume

Support
5

Dear Andras,

Thank you very much for your help and the detailed answer, it’s the function I needed!

Still I found some interesting issues regarding which I would like to ask your opinion.
When I first used the shortcut-code, the position of the cursor was out of the volume:

volume_out
volume_out1305×918 72.2 KB

My colleague - who is more expert in programming - found that there is a difference in the qform/sform space, which causes this alteration. I share here the links he sent me in this topic:

Finally he found that if he runs this code below in FSL, then afterwards the shortcut works well on the new volume:

fslorient -copysform2qform sample_file.nii

volume_in
volume_in1305×927 93.2 KB

.
A question: Is there a way that this modification (qform/sform reset) can be done in the Slicer (without having FSL and the required Linux environment)?

Also to share with the community - maybe some could have the same question - Adam made a little modification in the script you’ve sent (as for some reason an error message was received on its initial run), and now everything displayed correctly just as you have said:

def onMouseMoved(observer,eventid):
  mniToWorldTransformNode = getNode('LinearTransform_3')  # replace this by the name of your actual transform
  worldToMniTransform = vtk.vtkGeneralTransform()
  mniToWorldTransformNode.GetTransformToWorld(worldToMniTransform)
  ras=[0,0,0]
  mni=[0,0,0]    
  crosshairNode.GetCursorPositionRAS(ras)
  worldToMniTransform.TransformPoint(ras, mni)
  _ras = "; ".join([str(k) for k in ras])
  _mni = "; ".join([str(k) for k in mni])
  slicer.util.showStatusMessage(f"RAS={_ras}   MNI={_mni}")

crosshairNode=slicer.util.getNode('Crosshair')
observationId = crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionModifiedEvent, onMouseMoved)

MNI
MNI747×159 34.9 KB

I will try the transformations, and if any question rises, I’ll let you know.

1 Like