Description

This is a groupwise metric for the Elastix registration tool that, given a set of landmarks present in a collection of images, aligns the occurrences of each landmark to their mean position. It targets the following energy

E(mu) = 1/n Σ_i 1/m Σ_j [ p_ij - T( 1/m Σ_k p_ik ) ]

where p_ij is the position of the i-th landmark in the j-th image, n is the number of landmarks, m the number of images, T the transform with parameters mu.

This metric assumes that a BSplineStackTransform is used in the registration.

Structure of the moving points file

Only the moving points file is used, the fixed must be provided only as a dummy to prevent errors, but it is not used in this metric.

It is important to store the moving points in the correct order. Given m moving images (stored in m channels in the time axis), the points must be sorted in the file as

x00 y00 z00 0  // image 0, landmark 0
x01 y01 z01 0  // image 0, landmark 1
     ...
x0n y0n z0n 0  // image 0, landmark n

x10 y10 z10 1  // image 1, landmark 0
x11 y11 z11 1  // image 1, landmark 1
     ...
x1n y1n z1n 1  // image 1, landmark n

  .........

xm0 ym0 zm0 m  // image m, landmark 0
xm1 ym1 zm1 m  // image m, landmark 1
    ...
xmn ymn zmn m  // image m, landmark n

Build

In order to use this metric, it is necessary to include it in an Elastix build. This can be done by passing to CMake the configuration parameter -DELASTIX_USER_COMPONENT_DIRS=$dir, where $dir is the root directory of this repository, when building Elastix.

License

This software is licensed under the Apache License, Version 2.0. For the full license text, see the attached LICENSE file.