And, on the perhaps separate topic of applying @SSwarper's transformation pieces here, you first have (**though, note, I still think using the follower_ROI options with afni_proc.py is a better way to map these ROIs---see my parallel posting):

3dNwarpApply                                                                 \
    -nwarp   'anatQQ.sub1.s1.movie1.SE_WARP.nii anatQQ.sub1.s1.movie1.SE.aff12.1D' \
    -source  GMmask.s1.use+orig

.. and that would indeed, be in the same "+orig" view as the input dset, because nothing is telling it to change.

This command adds a few options that will help you:

3dNwarpApply                                                                 \
    -nwarp   'anatQQ.sub1.s1.movie1.SE_WARP.nii anatQQ.sub1.s1.movie1.SE.aff12.1D' \
    -source  GMmask.s1.use+orig       \
    -master /Users/ramotlab/abin/MNI152_2009_template_SSW.nii.gz     \
    -ainterp NN \
    -prefix GMmask.s1.use_in_MNI.nii.gz

where:
+ "-master .." tells the program what output grid+space to use, which will be MNI here---so your final dset would be on the grid of the MNI template specifically, and it would have "+tlrc" viewing (even with the NIFTI file format I output with here). Though, perhaps you would want to use
-master SOME_PATH/anatQQ.sub1.s1.movie1.SE.nii
... to have the ROIs on the grid of your final anatomical dset, or even:
-master SOME_PATH/errts_*HEAD
... to have it the ROIs on the grid of your final residuals/EPI dset.

+ "-ainterp NN" means to use nearest neighbor (NN) interpolation when mapping the source dset to the output; this will preserve integer values, rather than blurring them, losing hte ROI-ness.

+ "-prefix ..." to specify a desired output dset name.

For AFNI-created ROI dsets that have labeltables in them (like the *REN_* ones mentioned in the parallel post in this thread), you can also re-attach the nice properties of telling the GUI to use an ROI-like colorbar when opening the file as an overlay:

3drefit -cmap INT_CMAP DSET_WARPED

... as well as re-attach the labeltable from the original that had one:

3drefit -copytables DSET_ORIG   DSET_WARPED

This latter one only applies if the original dset *did* have a labeltable or atlaspoints, which you can query with:

3dinfo -is_atlas_or_labeltable DSET_ORIG

-pt