Hello Paul,

I got everything to work and now I understand the pipeline a little better. I am putting the code up on Github and will send the link when it is up. Basically the Lausanne is the freesurfer parcellation, further parcelled into finer bits. So IMO it is a better parcellation because enormous ROIs like superior frontal gyrus are more fine-grained. And of course you can always combine smaller bits to larger ROIs. I used parts of the procedure detailed here: [github.com].

After looking at your code more carefully, I did figure out that it wouldn't output the REN file, but the 3drefit step you suggested worked, and I compared the output with the a2009 REN label. So it seems to work well. I would suggest some additions to AFNI code in the future--maybe a more streamlined, better thought-out process than I came up with (I am not a good programmer). I'll post the link in case others want to use/modify the code in the meantime. Thanks for the help!

Anthony