If you run @SUMA_Make_Spec_FS on all of your Freesurfer folders, you can then take the SUMA folder contents (particularly the aparc+aseg_rank.nii) and use that to identify anatomical regions to pull out activations via a mask. I would probably use 3dcalc to do this for each subject. An example of pulling out the left putamen might go like this:

3dcalc -a 'subj001/SUMA/aparc+aseg_rank.nii' -prefix subj001_putamen.lh -expr 'equals(a,8)'
3dfractionize...
3dmaskave...

The 3dfractionize will resample your mask to the same size as your stats dataset and then you can use 3dmaskave to pull out the actual values. You will want to make sure that your fMRI images were aligned to the same anatomical you ran Freesurfer on. If this isn't the case, things get slightly more complex.

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Edited 1 time(s). Last edit at 09/18/2013 05:10PM by Peter Molfese.