Recentering volume

Utilities
1

I am using the volume alignment job to recenter a volume using the center of mass of a provided 3D mask.
I noticed that the resulting re-centered volume is masked. Is it possible to use the mask only as a reference for re-centering but without masking the output volume?

Thanks,

H.

2

Not yet, but it has been requested: Option to output unmasked map in volume alignment tools? (feature request)

3

I run local refinement first (even just for a minute). Then recenter based on the printed coordinates of the center of mask, but don’t provide the mask itself.