The commit message linked below has more of the details. Happy to answer other questions if it’s not clear. It’s a particularly gratifying piece of code because the problem had bothered me for years and finally the nonlinear transform support in Slicer matured to the point that this approach is at least fairly straightforward and I believe it solves the problem the “Right Way”.
Would you mind explaining how to properly harden the volume with the transform that results from the Apply regularization transform option?
As previously mentioned the volume resolution is severely degraded after using the Harden Transform function. I followed the link (resampling documentation) you provided, but could not figure out how to achieve this. Is there a way to do this without degrading resolution?
Harden transform applies the original resolution of the volume to the resampled volume. If the original resolution was low or highly anisotropic then you may see visible degradation. In this case, probably the simplest is to use Crop volume module with “Interpolated cropping” and “Isotropic spacing” enabled and with a “Spacing scale” that is low enough to preserve all relevant details but still large enough so that you don’t end up with a huge image (something between 0.2-0.8 should work).
Thanks for the response! I followed those steps and was able to resample the volume. I am seeking an “automatic” or “one-click” solution to fix this DICOM spacing error as I have a large batch of samples to process with this issue. I see now that it must be manually handled via the Volumes or Crop Volume modules. If I end up programming a simple module to help with this I will reference it here.