We are in the process of incorporating elastix into the SliceTracker extension in 3D Slicer that we use to support in-bore targeted prostate biopsy (see publications in the extension documentation for references etc).
The registration problem we need to solve is registration between T2-weighted high-resolution scan of the prostate obtained before the procedure (typically, with the use of endo-rectal coil), and the intra-procedural T2-weighted scan of somewhat lower in-plane resolution (no endo-rectal coil).
Until now, we used registration tools included in 3D Slicer in that extension (details in this publication), but we want the software to be modular so we can experiment with the registration strategies, and we also think elastix registration might be a better registration tool anyway.
To do registration with elastix, we use an application-specific initializer (rigid alignment of the centroids of the segmented masks of the prostate and rough grid search to improve the initial pose), passing the the moving image after applying the rigid transform to elastix, and using one of the default parameter files with minimum changes. You can see the discussion and specifics on how we initialize the parameters here:
Based on the initial testing on a couple of datasets, we are getting good results. We have a reasonable-sized dataset annotated with landmarks that we next planned to use to measure TRE and compare elastix registration with the approach we are using currently for a more principled comparison. Before we do that, we would like to check with the elastix experts on whether the parameterization we use requires any modifications. Would you mind taking a glance at the parameter files, and let us know if you have any recommendations?
To be clear, things seem to work, and we have no specific problem, but we would appreciate if the elastix experts could give us the "blessing", to make sure we use it in the most optimal way, before we do the quantitative evaluation of the registration accuracy.
cc: @che85
We are in the process of incorporating elastix into the SliceTracker extension in 3D Slicer that we use to support in-bore targeted prostate biopsy (see publications in the extension documentation for references etc).
The registration problem we need to solve is registration between T2-weighted high-resolution scan of the prostate obtained before the procedure (typically, with the use of endo-rectal coil), and the intra-procedural T2-weighted scan of somewhat lower in-plane resolution (no endo-rectal coil).
Until now, we used registration tools included in 3D Slicer in that extension (details in this publication), but we want the software to be modular so we can experiment with the registration strategies, and we also think elastix registration might be a better registration tool anyway.
To do registration with elastix, we use an application-specific initializer (rigid alignment of the centroids of the segmented masks of the prostate and rough grid search to improve the initial pose), passing the the moving image after applying the rigid transform to elastix, and using one of the default parameter files with minimum changes. You can see the discussion and specifics on how we initialize the parameters here:
Based on the initial testing on a couple of datasets, we are getting good results. We have a reasonable-sized dataset annotated with landmarks that we next planned to use to measure TRE and compare elastix registration with the approach we are using currently for a more principled comparison. Before we do that, we would like to check with the elastix experts on whether the parameterization we use requires any modifications. Would you mind taking a glance at the parameter files, and let us know if you have any recommendations?
To be clear, things seem to work, and we have no specific problem, but we would appreciate if the elastix experts could give us the "blessing", to make sure we use it in the most optimal way, before we do the quantitative evaluation of the registration accuracy.
cc: @che85