STEP 2: Register the volumes in each 3D+time dataset using AFNI program 3dvolreg.

• STEP 2: Register the volumes in each 3D+time dataset using AFNI program 3dvolreg.

• • All volumes will be registered to the last volume of the last run (i.e., run 9, volume 63). This volume is closest in proximity to the anatomical dataset.
  • • • foreach run ( $runs )
      • • 3dvolreg -verbose -zpad 1 \
        • -base pb01.$subj.r09.tshift+orig'[63]' \
        • -1Dfile dfile.r$run.1D \
        • -prefix pb02.$subj.r$run.volreg \
        • pb01.$subj.r$run.tshift+orig
      • end
      • cat dfile.r??.1D > dfile.rall.1D
    • -verbose : prints out progress report onto screen
    • -zpad : add one temporary zero slice on either end of volume
    • -base : align to last volume, since anatomy was scanned after EPI
    • -1Dfile : save motion parameters for each run (roll, pitch, yaw, dS, dL, dP) into a file containing 6 ASCII formatted columns
    • -prefix : output dataset names reflect processing step 2 (volreg)
    • input datasets are from processing step 1 (tshift)
    • concatenate the motion parameters (dfiles) from all 9 runs into one file