[Elastix] RAS or LPS coordiante system?

Kannan U V kannanuv at cshl.edu
Fri Apr 19 14:24:54 CEST 2013


Bilal, did you take into account the fact that the transformation is inverse
On Apr 19, 2013 6:29 AM, "S. Klein" <s.klein at erasmusmc.nl> wrote:

>  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 7043049http://www.bigr.nl/people/StefanKlein
>
>
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