Hi Paul,
Thanks a lot for your response!

Yes, I did use afni_proc.py to preprocess these people with the following blocks:

-blocks tshift align volreg mask blur scale regress

So the EPIs are never warped to standard space. The reason for this is because we're looking to do multivariate analyses in small regions that are hand-segmented in individual T1s, and we don't want to warp these to standard space because the non-linear warp applied to the EPIs might introduce distortion in these small regions (which is already probably happening with all the volreg and alignment transforms).

A small correction from my original post: I will be extracting parameter estimates from these ROIs rather than timeseries. So after alignment to native space anatomy (and blurring and scaling) I run 3dDeconvolve on each participant, and use the ROIs as masks to extract from Coeff sub-brick of the Deconvolve output. In order to replicate some past work, I want to run this analysis within ROIs centered around MNI co-ordinates reported in some papers. I need to transform these ROIs from MNI space to the individual's native space EPIs aligned to the native space anatomies (or at least get equivalent co-ordinates in native space so I can make spherical ROIs around them).

Hope this answers your question!
Mrinmayi