Hi Peter,

You are correct that this follows with the other threads I have posted. For this particular post, I was curious about whether the GCOR command is necessary for anything. I didn't see the output being used for anything and I haven't used in for anything. I wasn't sure if it was neede for any resting-state analyses that my labmate does, so that is why I asked her. If we don't need it, then I won't include it.

I essentially have most of the commands working now. I found that I was making changes to directory paths and defining variables incorrectly (i.e., didn't follow the proc.py output script for some things). It is basically running through the individual subject ClustSim command now.

I have tried the the "-anat_has_skull" option with Qwarp, but the non-brain tissue still is included in the warping process with our dataset. So that is why I am going with FNIRT for the time being until I have more time to play around with skull-stripping and Qwarp.

I like the idea of the empty block function in AFNI_proc.py. That would have saved me some time. But I think what I have going is pretty much working.

Thanks!

Danny