Wait, *I* have to do some work now?....
OK, OK, I will look at 3dNetCorr for outputting zeros. This will likely be a behavior that can be flagged with an option.
One thing to note is: this new output (where zero rows/columns representing "missing" ROIs are included) should then probably *not* be put through the current fat_mvm_* pipeline for group analysis, as it currently works. For *.netcc files from 3dNetCorr, the assumption is that all parts of the matrix are "real" values to be processed---and zeros are a possible correlation value. So, you might run 3dNetCorr twice, then: once where the empty ROIs are excluded from the matrix outputs, and once where they are included, depending on what you want to do with them.
--pt
