-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:
foreach run (1 2 3 4 5 6 7 8 9 10)
3dvolreg -base ED_r1+origÕ[2]Õ \
-tshift 0 \
-prefix
ED_r{$run}_vr \
ED_r{$run}+origÕ[2..137]Õ
end
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
