Signy,

This is very easy to do, all you need to do is feed in the anatomical mask into the parameter structure that gets fed into the PPPI command. The gPPI code will extract the voxels with non-zero values in the ROI file. This can all be done in the wrapper. If you are using the same mask in all subjects, its even easier, but if you have a different mask for each subject, then you can create a variable that lists all the masks and then have the wrapper select the correct mask inside the loop over subjects.

There is no need to write a script to extract the data prior to the PPI wrapper.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Jul 7, 2014 at 2:59 PM, S Sheldon <[log in to unmask]> wrote:

Hello,
I am trying to run a gPPI analysis on a set of data that has three task conditions across 5 runs. I would like to see how the hippocampus is funcitonally connected in each of these three tasks using an anatomically defined hippocampal mask. Is there a script that I can use to extract the mean time series from such a mask across subjects to then use in the ppi wrapper?
Thanks,
Signy