Hi Rick,
Following is the complete code that I used.
foreach fred ( *_t1+orig.HEAD )
set sub = `basename $fred _t1+orig.HEAD`
# transform anat to MNI space
@auto_tlrc -base ~/abin/MNI_avg152T1+tlrc.HEAD -input $fred
# transform EPI to MNI as well (assume anat & EPI are aligned)
adwarp -apar ${sub}_t1+tlrc.HEAD -dpar ${sub}_epi+orig.HEAD -resam Cu -dxyz 2.0
# make individual subject mask
3dAutomask -dilate 1 -prefix ${sub}_amask ${sub}_epi+tlrc.HEAD
end
# Combine individual EPI masks into group mask
3dMean -sum -nscale -prefix ALL_amask *_amask+tlrc.HEAD
foreach fred ( *_epi+tlrc.HEAD )
set sub = `basename $fred _epi+tlrc.HEAD`
#3dBandpass does blurring, filtering, and detrending
3dBandpass -mask ALL_amask+tlrc -blur 6.0 -band 0.01 0.10 -prefix ${sub}_BP -input $fred'[4..$]'
end
# 2 groups of subjects
set SPR = ( 1 2 3 4 5 6 7 8 )
set ggg = ( )
foreach fred ( $SPR )
set ggg = ( $ggg ${fred}_BP+tlrc.HEAD )
end
3dSetupGroupInCorr -mask ALL_amask+tlrc -prefix SPR $ggg
