fix anatomical orientation of CCF

[dyf]

Currently the brain is not oriented correctly. The orientation header in the .nrrd files used for the CCF are incorrect. Please use ASL (x=A-to-P, y=S-to-I, z=L-to-R).

[jcfr]

In fact, it is PIR (and not ASL)

Currently, data displayed in Slicer are shown in RAS

Showing the data in in expected coordinate frame can be done applying the following rotation matrix (the value were obtained by manually setting the matrix in the transform module with volume rendering enabled):

0 0 1 -1 
1 0 0 0 
0 1 0 0 
0 0 0 1 

Note that the values above can directly be copy-paste in the matrix widget of the transform module in Slicer.

Here is the transformed volume:

For reference, here is the original un-transformed volume:

Remaining issue is that the direction are inversed, to address this we should look into defining new slice orientation presets. See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Slice_Orientation_Presets

[jcfr]

In addition of applying the transform described above, the Coronal preset should be updated from

-1  0  0
 0  0  1
 0  1  0

to

-1  0  0
 0  0 -1
 0  1  0

Updating the existing preset can be done using:

s = getNode("vtkMRMLSliceNodeGreen")
s.DisableModifiedEventOn()
orientationMatrix = vtk.vtkMatrix3x3()
orientationMatrix.SetElement(0, 0, -1.0)
orientationMatrix.SetElement(1, 0,  0.0)
orientationMatrix.SetElement(2, 0,  0.0)
orientationMatrix.SetElement(0, 1,  0.0)
orientationMatrix.SetElement(1, 1,  0.0)
orientationMatrix.SetElement(2, 1,  1.0)
orientationMatrix.SetElement(0, 2,  0.0)
orientationMatrix.SetElement(1, 2,  -1.0)
orientationMatrix.SetElement(2, 2,  0.0)
s.RemoveSliceOrientationPreset("Coronal")
s.AddSliceOrientationPreset("Coronal", orientationMatrix)
s.DisableModifiedEventOff()