Line-by-Line Explanation of s1.afni_proc.block command:

• • Line-by-Line Explanation of s1.afni_proc.block command:
  • • -subj_id: Specify a subject ID name for the processing script that will be created by executing the s1.afni_proc.block script. The ID in this example is sb23.blk
    • -dsets : Specify the name of the time series datasets that will be analyzed, as well as the directory path in which they reside. Here, they are called epi_r03+orig .. epi_r11+orig, residing in directory sb23/ (note that .HEAD is required for wildcard matching)
    • -copy_anat: This option will take the anatomical dataset sb23_mpra+orig that currently resides in sb23/ and copy it into the results directory (the results directory will be created once the processing script has been run)
    • tcat_remove_first_trs: This option removes ‘x’ number of timepoints from the beginning of each time series run. Here, we have chosen to remove the first 3 timepoints from each run
    • -volreg_align_to: This volume registration option asks the user to choose which volume will be the base by which all other volumes in the time series runs are aligned. Here we have chosen the last volume from the last epi run (run 9)
    • -regress_make_ideal_sum: Sums the ideal response curves from the regressors and saves as a 1D file, e.g., sum_ideal.1D
    • -regress_stim_times: Specifies the name and location of the stimulus timing files for our experiment. In this example, they are sb23/stim_files/blk_times.*.1D