Hi, Jim-

Glad that the ROIs are being made happily.

Re. the two runs: was masking applied to the EPIs, and do the two runs share the exact same mask? I wonder if the coverage of each FMRI output is the same. Were they processed together?

I imagine that the reason why there are <264 ROIs in each output is that there are some empty ROIs. It doesn't look like you are using a mask explicitly in your 3dNetCorr command. You could add this option to output the internally-determined mask (by where time series are non-constant) in each case, and overlay the ROI map on each, to check if that is what is happening.

-output_mask_nonnull
                     :internally, this program checks for where there are
                      nonnull time series, because we don't like those, in
                      general.  With this flag, the user can output the
                      determined mask of non-null time series.

--pt