Documentation/4.4/FAQ/Viewing and Resampling

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Viewing and Resampling

What coordinate systems does Slicer use?

See this documentation of Slicer coordinate systems.

Is there a global coordinate system ?

There is no coordinate system in Slicer that is called Global. There is one called RAS. When you open Slicer, the middle of the pink wireframe box in the 3D view is at the origin of RAS. When a medical image is loaded in Slicer, it is oriented relative to the RAS coordinate system so the right hand of the patient is towards the R (first coordinate), the front of the patient is towards A (second coordinate). It's a right handed system.

To visualize "something", it is usually most convenient of to transform it to RAS, so it shows up relative to CT or MR images loaded in Slicer. When hovering the mouse over an image slice (2D), the RAS coordinates are displayed in the Data Probe located in lower left corner of the Slicer UI.

Source: http://slicer-devel.65872.n3.nabble.com/Reference-System-tp4031501p4031503.html

How can I use the reformat widget view to resample my images?

You can do something like this in the python console:

red = getNodes('vtkMRMLSliceNode*')['Red']
m = vtk.vtkMatrix4x4()
m.DeepCopy(red.GetSliceToRAS())
m.Invert()

t = slicer.vtkMRMLLinearTransformNode()
t.SetAndObserveMatrixTransformToParent(m)
 

Then put your volume under “t" or provide "t" as the transform to one of the Resample modules.