[Elastix] RAS or LPS coordiante system?

S. Klein s.klein at erasmusmc.nl
Fri Apr 19 12:29:15 CEST 2013


Hi Bilal, elastix takes into account the direction cosines of the images.
Do you store the landmarks in world coordinates or in voxel coordinates?
Do you use the .vtk format or the input point .txt format to supply the points to transformix?
In your registration, did you set UseDirectionCosines to "true"?
Kind regards,
Stefan

On 18/04/2013 02:52, Bilal Tahir wrote:
Dear All,

I recently moved from VV to Slicer for defining expert landmarks on fixed and moving images prior to registration. I then use transformix to deform the fixed points so I can compare them with original moving points via the target registration error.

One thing I noticed is that Slicer defines the points (via fudicial markers in the annotations module) in the RAS coordinate system as default. Putting these values into transformix gives me completely wrong results. Is Elastix based on the LPS coordinate system as default or another one? Below is part of  my header data for the fixed image:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = -215.592 -417.592 -323.5
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 0.816406 0.816406 1.78125
DimSize = 512 512 160
ElementType = MET_SHORT
ElementDataFile = fixed.raw

Here is the header data for the moving image:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1.52656e-015 -1 0 1 5.55112e-017
Offset = -212.209 -155 200.502
CenterOfRotation = 0 0 0
AnatomicalOrientation = RSA
ElementSpacing = 1.6797 1.6797 10
DimSize = 256 256 24
ElementType = MET_SHORT
ElementDataFile = moving.raw

I look forward to hearing your replies.

Cheers,

Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging



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--
Stefan Klein
+31 10 7043049
http://www.bigr.nl/people/StefanKlein
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