Hi Paul,
Thanks,
Re: multiple brik's, I realized that eventually, LOL

As to registration, I am using a multibrik image as input, but when I use 3dAllineate, which I confess, I'm not that familiar with. I tried with:

3dAllineate -final NN -base masked_mean.nii -automask -cost mi -prefix Yeo_EPI /afs/cabi.rfmh.org/usr/hoptman/scripts/Yeo2011_FSlib_LPI.nii.gz

Previously, I had used FSL (with the NN option for interpolation). For my network map, I'm using Yeo's 7-network parcellation (Yeo et al., 2011). It has 7 integer values, one for each network. I then split each of the networks into a separate image, and merged them to give a 7-BRIK image, with each BRIK having a different integer value (i.e. 1 - 7).

Is there a way for me to tell AFNI to put each value into a separate BRIK (e.g., within 3dAllineate? I'm asking because when I do 3dROIMaker -inset FILE_A -refset FILE_A, I get only a single ROI/BRIK, which is not quite what I want because then I cannot do within network tractography.

Any suggestions would be appreciated.
Thanks!,
Matt