[ITK] [ITK-users] rigid landmark registartion simpleITK (python)

[Johnson, Hans J]

Ryan,

Have you tried applying the inverse of the rigid transform defined by landmarks?

A common mistake is apply the transform that works for aligning landmarks points to an image.  They are inverse problems.  The transform that is applied to align landmarks is the inverse of the transform that is needed to resample images.

Hans

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From: Insight-users <insight-users-bounces at itk.org<mailto:insight-users-bounces at itk.org>> on behalf of "Young, Ryan" <Ryan.Young at seattlechildrens.org<mailto:Ryan.Young at seattlechildrens.org>>
Date: Thursday, February 11, 2016 at 7:00 PM
To: "insight-users at itk.org<mailto:insight-users at itk.org>" <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: [ITK-users] rigid landmark registartion simpleITK (python)

Hello,

I am trying to rigidly align a group of landmarked samples.  I have calculated a rigid transformation matrix.  When I apply this to the sample (see code below) is sample is commonly clipped.  It seems like the transformation is pushing the sample out out its physically defined space and the data is lost.  How should I set things up to that large translations and rotations do not result in parts of the image being lost.







affine_center = (0,0,0)
affine_translation =translation

affine_matrix =T.flatten(order='C')
affine = sitk.AffineTransform(affine_matrix, affine_translation, affine_center)

imAffine = sitk.Resample(im, imRef, affine,sitk.sitkLinear, sitk.sitkUInt32)
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