-4-
¥ STEP 1: Volume Register and time shift the voxel time series for each     3D+time dataset using AFNI program 3dvolreg
GWe will also remove the first 2 time points at this step
GUse the ÒforeachÓ loop to do all 10 of EDÕs 3D+time datasets at once:
å
åforeach run (1 2 3 4 5 6 7 8 9 10)
å3dvolreg  -base ED_r1+origÕ[2]Õ\
å     -tshift 0\
å     -prefix ED_r{$run}_vr     \
å     ED_r{$run}+origÕ[2..137]Õ
åend

å-base: Timepoint 2 is our base/target volume to which the remaining timepoints (3-137) will be aligned.  We are ignoring timepoints 0 and 1
å-tshift 0: For each run, the slices within each volume are being time shifted prior to volume registration.  This is done to correct for the different sampling times for each slice
å-prefix gives our output files a new name, e.g., ED_r1_vr+orig
åED_r{$run}+origÕ[2..137]Õ refers to our input datasets (runs 1-10) that will be time shifted and volume registered.  Notice that we are removing timepoints 0 and 1