I just thought of something...

since all my xyz coordinates and my final processed EPI datasets are all in MNI space, could I create the ROI with 3dUndump directly on the EPI set? Why am I bothering to make the ROI using the anat volume and then resampling to the epi volume if all of them are in the same MNI space? That way I would probably get the same number of voxels in each ROI.

Example:

#find center of mass of subarea and output xyz coordinates to text file
3dCM -set x y z subroi_1_leftSTG.nii.gz > CM_subroi1_leftSTG.txt
#read text file into command to make 6mm ROI using epi dataset as master
3dUndump -prefix leftSTG_sub1_6mmROI -master pc09.${pnum}_rest_run1_MEICA.spc.nii.gz -srad 6 -orient RAI -xyz CM_subroi1_leftSTG.txt