Hmmm, a couple things:
In the first command, your input and base are the same:
pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz
pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz
Are you just resampling the data? How did you align it to itself? You could use "3dresample -dxyz .." to resample it (and you can specify the mode.
In the second command, I don't think that just using "-base .." will force the output data to have its grid size; the output will have something close to teh original resolution. Using "-master .." there would, though, make the output be on the grid of the "master" data set.
Also, what is your original 3dAllineate command?
Finally, what is the output of this:
3dinfo -o3 -ad3 -orient -prefix pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_forallineate.nii.gz pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz
--pt
