The fim ROI, originally drawn in AC-PC view, will not contain any transformation or markers data.

You might be able to use the Nudge Dataset plugin to move a copy of the new AC-PC anat into correct alignment with the ROI dataset, though. Make a copy with "3dcopy anat+acpc anat_copy". Set the plugin up to nudge the anat_copy dataset, view the ROI dataset as the function overlaying the anat, then you can move the anat_copy to be aligned with the function visually.

If you get a good alignment, then you can proceed in one of two ways. You can use the plugin's "Do All" button to save the nudged anat_copy dataset, and then use it. Better, though, might be to move the ROI dataset to be aligned with the new anat. You should be able to do that by using the plugin's "Print" button, which will print the 3drotate command that is equivalent to the movement ordered by the plugin. You can then apply the inverse of that movement to the ROI dataset. For example, if you get

-rotate 3.0I 2.0R -2.0A -ashift 2S 3L 4P

the inverse should be

-rotate 2.0A -2.0L -3.0I -bshift -2S -3L -4P

You use the undocumented "-NN" flag to specify nearest-neighbor interpolation for the ROI dataset. It would maybe be easier to use the nudge plugin to move the ROI dataset into alignment with the new anat, but the nudge plugin doesn't allow NN interpolation at this moment. (I suppose I could fix that.)

bob cox