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
