Hi Will,

You can do this but you need to specify the appropriate target volume in your call to reformatx.

target would typically be e.g. the template-low-res.nrrd that you used for your registration, but it could be template-full-res.nrrd instead. This will work so long as your images are physically calibrated with consistent coordinate systems. You can also specify a template space using the --target-grid option, but the only wrinkle there is that it will be tagged as being in RAS anatomical space.

Best,

Greg.