Feedback on using elastix for deformable prostate registration about elastix HOT 7 CLOSED

• FixedImagePyramid should be FixedImageSmoothingPyramid for best results (unless memory is really and issue).
• AutomaticTransformInitialization should be true for rigid and false for affine and bspline.
• 250 number of iterations is also on the low side. If speed is really an issue, 250 is fine, but if you can afford it use at least 512.
• Depending on the problem you might want to use at least 3 resolutions. Some places you use 2 which is on the low side.
• ImageSampler should be RandomSparseMask if users use masks. Otherwise it is fine.
• If you use a BSplineInterplationOrder of 1 you might as well use LinearInterpolator which produces the same results but is faster.

Otherwise it looks good!

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OK great! One comment:

We use external application-specific initializer [...]

OK, then make sure to set AutomaticTransformInitialization to "false" for all parameter maps. It was true for the first one, which will discard your custom initialization.

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@Kmacneil0102 can you please update the configuration as suggested above before running the experiments?

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Sure I can take a look @fedorov, but can you link directly to the parameter files or just post them here? It is not clear to me where to obtain the parameter files in the two discussions you listed. Thanks!

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@kaspermarstal thanks!

You can see the parameter files for rigid/affine/b-spline in this pull request:

• rigid: https://github.com/SlicerProstate/SliceTracker/pull/341/files#diff-35c17ae0c6fc45f6280c8c6719d7c54b
• affine: https://github.com/SlicerProstate/SliceTracker/pull/341/files#diff-04aa48b3655e2714bb803a80c1035da4
• b-spline: https://github.com/SlicerProstate/SliceTracker/pull/341/files#diff-3aa4e49b9ded4e59482b10be9c35f37b

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@kaspermarstal thank you for the feedback! Since my last update, we did more testing, and the elastix registration unfortunately does not always work. But I am sure we will figure it out with your help! @Kmacneil0102 is currently working to reproduce the issues on a public dataset, and we will update this thread as soon as we have results.

See my responses to your suggestions:

AutomaticTransformInitialization should be true for rigid and false for affine and bspline.

We use external application-specific initializer. The initializer we implemented takes the segmentation masks of the prostate in the two images, aligns their centroids, and then does sparse search to optimize the metric by rotating the images over small range (don't remember now in what plane!). This initializer has been working quite well, and I don't think default initializer could replace it. Unless you already have something similar in elastix?

Depending on the problem you might want to use at least 3 resolutions. Some places you use 2 which is on the low side.

We actually started with the default 3, but then reduced, since our region of interest is quite small (could be as small as 5-10% of the total image volume probably), and so there may not be enough data to subsample. Reducing resolutions helped somewhat with making the configuration more reliable.

We will update the rest of the parameters as you advised - it all makes sense to me!

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closing for now, you can reopen when needed.

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