Does AFNI have plugins to do ICA/PCA on resting state residuals and also for viewing resulting networks?
Not really. You could use 3dpc to do a PCA on a dataset, but it doesn’t do any statistics or clustering. We don’t have any ICA tools.
For viewing “networks”, you can use SUMA – but it is too complex to outline the steps on the message board.
There is a simple ICA program in AFNI for individual subject analysis only: https://afni.nimh.nih.gov/sscc/gangc/ica.html
Thanks Bob and Gang, I will give them a try. Given that these methods are becoming pretty standard for resting state analysis, is there a plan to extend AFNI abilities in this regard near future?
No such plans. We don’t have the time to deal with ICA as well as other stuff. And there are packages well advanced in this area – such as Vince Calhoun’s GIFT – http://mialab.mrn.org/software/gift/index.html