Hi-

First, I would transform the various ROI maps into your EPI space (so, yes, I agree with you, into the 1.4mm space), for example with 3dAllineate.

Then, if all the ROIs are in a single network, I would then combine them into a single volume. If there are multiple networks, you could make each grouping a separate brik in a single file. This can be done using 3dTcat and/or 3dcalc. Probably, you will want to make sure that your ROIs don't overlap at all; if they do, you will need to choose a method for determining which one gets prescribed to a voxel. If they don't overlap or neighbor each other, I guess you could put it through 3dROIMaker in order to assign individual integers to each ROI (the usefulness of this step is dependent upon whether or not you have integers already assigned in your maps).

In 3dNetCorr, the '-in_rois FILE' is a single or multiple brick data set (not text file); each brik is treated as an individual network; an ROI within that network is defined by a set of voxels with a given integer value.

There is some new labeltable functionality available with both 3dNetcorr; if you have a labeltable on your set of ROIs, then those will translate through in the output *.netcc files if you are using the very latest AFNI.

--pt