Currently, the masking behaviour in local refinement is that
- The initial mask slices shown at the start of the job stream log are identical to the mask that is provided to the job (aside from them being shifted to have an origin at the fulcrum)
- For each refinement iteration, the actual mask that is used to compute the volumes for alignment is generated by multiplying the current volume with the initial mask, thresholding this using the threshold factor, and dilating using the near and far parameters. This mask is displayed at each iteration in the stream log in the “Real Space Mask Slices Iteration x”.
This behaviour is always the case, so in particular passing ‘static’ to the mask type will still follow this behaviour, which is different from how static masking works in other jobs like new homogeneous refinement for example. In any case, the mask is dynamically updated each iteration using the current volume – but we plan on adding the option for true static masks that don’t change each iteration to future versions of local refinement.
Best,
Michael