Hi Peter,
Thanks for the clarification.
I've applied 3dAutoBox to the template that I'm using, so all individuals will be warped to the same cropped space. It's a non-standard MNI brain that has been conformed and interpolated from FreeSurfer.
I've tested various things (like origin, template space markers, voxel size) in the 3dAutoBox-ed image, and they are all as they should be.
It's also reduced my preprocessing time from ~130 to ~45 min, and the saved intermediate files from 6.5 to 2.2 GBs.
In effect, I think 3dAutoBox is the way to go in my case.
If you have any additional comments I'd be curious to hear.
I appreciate your help,
Matthew
