[Elastix] Question regarding Transform Parameter file

M.Staring at lumc.nl M.Staring at lumc.nl
Tue May 20 09:02:14 CEST 2014


Hi Lisa,

Units are in mm.

Regards, Marius

From: elastix-bounces at bigr.nl [mailto:elastix-bounces at bigr.nl] On Behalf Of Lisa Richards
Sent: dinsdag 20 mei 2014 3:57
To: Tom Knoop
Cc: elastix at bigr.nl
Subject: Re: [Elastix] Question regarding Transform Parameter file

Hi Tom,
Thank you for your reply.  I thought that those values must correspond to the x and y offsets, but wanted to get a confirmation.  What are the units on the offset values?  Pixels or mm?  Since my spacing is not 1.0, this would make a difference and I want to make sure that I calculate the maximum offset correctly.
Thank you again for your help,
Lisa

On May 19, 2014, at 3:27 PM, Tom Knoop <t.h.knoop at student.utwente.nl<mailto:t.h.knoop at student.utwente.nl>> wrote:


Hi Lisa,

I might be mistaken, since my experience with elastix somewhat limited. However, I think the information you are looking for is in the manual. According to paragraph 2.6, the translation transform is defined as: Tmu(x)=x+t
in this case the parameter vector mu=t (for exact formatting, see formula 2,11).

That would mean that the TransformParameters are the offsets x and y necessary to map your fixed image to the moving image.  Since you're doing only a translation, I think calculating the maximum shift for an image set could be done by aggregating the transform parameters for all your images, and look for the image with highest values. For the exact meaning and perhaps clearer explanation, the start of paragraph 2.6 is quite informative.

Good luck!

Best,

Tom

On Mon, May 19, 2014 at 10:00 PM, Lisa Richards <lisa.richards at utexas.edu<mailto:lisa.richards at utexas.edu>> wrote:
Hi all,
I have used elastix to perform a Translation transform on a set of images, producing a set of Transform files in the process.  I need to calculate the maximum shift that occurs in the image set.  I am wondering if I can use the TransformParameters output in the parameter file to do this.  For one sample file, the Transform Parameter file is listed below.  What can I infer from this file?  I don't know what the two numbers outputted as the TransformParameters represent and could not find definitions in the documentation.
Thank you for your assistance,
Lisa Richards

-

(Transform "TranslationTransform")
(NumberOfParameters 2)
(TransformParameters -0.129060 0.143669)
(InitialTransformParametersFileName "NoInitialTransform")
(HowToCombineTransforms "Compose")

// Image specific
(FixedImageDimension 2)
(MovingImageDimension 2)
(FixedInternalImagePixelType "float")
(MovingInternalImagePixelType "float")
(Size 477 642)
(Index 0 0)
(Spacing 0.3527777778 0.3527777778<tel:3527777778>)
(Origin 0.0000000000 0.0000000000)
(Direction 1.0000000000 0.0000000000 0.0000000000 1.0000000000)
(UseDirectionCosines "true")

// ResampleInterpolator specific
(ResampleInterpolator "FinalBSplineInterpolator")
(FinalBSplineInterpolationOrder 3)

// Resampler specific
(Resampler "DefaultResampler")
(DefaultPixelValue 0.000000)
(ResultImageFormat "tif")
(ResultImagePixelType "unsigned short")
(CompressResultImage "false")


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