Hi, Mrinmayi-

Before getting to the technicalities of warp dsets, I have a conceptual question: which native EPI space do you want to map the MNI ROIs to? The succession of stages the EPI could theoretically be in is:
+ raw EPI (subject space, no motion correction/reduction)
+ motion corrected EPI (subject space, but volumes are rigid-bodily aligned to one reference volume)
+ EPI in anatomical space (subject space defined by the anatomical dset, probably an affine transform)
+ warped to standard space (concatenated a nonlinear transform to get to MNI).

Note that there are 3 "native space" options here. In practice, many pieces of this alignment are calculated individually, either "forwards" or "backwards and then inverted" (for the latter, the EPI-anatomical alignment). Then they get concatenated together and applied.

Another practical consideration here is how you have set up your single subject processing (I will humbly guess it was with afni_proc.py....). In such a case, the ordering of blocks we typically recommend is something like (here, from s05* in the AFNI Bootcamp example):

-blocks tshift align tlrc volreg blur mask scale regress \

(And in the large variety of possible afni_proc.py processing, I'm just focusing on the alignment-related blocks here: align, tlrc, and volreg). The important thing to note here is that the volreg block comes after the tlrc block, so in this case the "pb*volreg*" dsets in the results directory (that is, the EPI dsets there that have motion correction applied) include the other warps to anatomical and then to template (MNI, here) space---that is, pb*volreg* will be in MNI space already.

So, the questions are:
+ which EPI dset do you want use with the MNI ROIs?
+ how did you do your processing (namely, with AP, what is the order of blocks)?
+ what is your goal for getting stats of the EPI at the earlier stage using the MNI ROIs (sometimes knowing the specific scientific point of interest affects the recommendations)?
+ if you want stats on the motion-reduced EPI time series, AND your processing block order for warps (align, tlrc and volreg) looks like the example here, then how about if you used the MNI ROIs on the pb*volreg* dset just as it is at present?

--pt