STEP 0 (tcat): Apply 3dTcat to copy datasets into the results directory, while removing the first 3 TRs from each run.

• STEP 0 (tcat): Apply 3dTcat to copy datasets into the results directory, while removing the first 3 TRs from each run.

• • The first 3 TRs from each run occurred before the scanner reached a steady state.
  • • 3dTcat -prefix $output_dir/pb00.$subj.r01.tcat \
    • sb23/sb23_r03+orig'[3..$]'
  • The output datasets are placed into $output_dir, which is the results directory.
  • Using sub-brick selector '[3..$]' sub-bricks 0, 1, and 2 will be skipped.
  • • The '$' character denotes the last sub-brick.
    • The single quotes prevent the shell from interpreting the '[' and '$' characters.
  • The output dataset name format is:
  • • • • pb00.$subj.r01.tcat (.HEAD / .BRIK)
    • pb00 : process block 00
    • $subj : the subject ID (sb23, in this case)
    • r01 : EPI data from run 1
    • tcat : the name of this processing block (according to afni_proc.py)
    • • • (other block names are tshift, volreg, blur, mask, scale, regress)