afni_ci_test_data/AFNI_data6/FT_analysis/s04.cmd.usubj

#!/bin/tcsh

# ----------------------------------------------------------------------
# run uber_subject as would be done in class (see afni16_start_to_finish.pdf)
# 
# notes:
#   - this was generated automatically by uber_subject.py with changes:
#      - top_dir was added for portability across directory trees
#      - the epi and stim inputs were tightened ($top_dir and wildcards)
#      - gui_choice was added to allow running without PyQt4 installed
#
#   - to run with GUI: set gui_choice = ""
#   - for no GUI     : set gui_choice = "-no_gui -save_ap_command cmd.ap.uber"
#
#     (this saves the afni_proc.py command in $HOME/$subj_dir/cmd.ap.uber)
# ----------------------------------------------------------------------

set gui_choice = "-no_gui -save_ap_command cmd.ap.uber"
set subj_dir   = .
set process    = 1

uber_subject.py                                                               \
    $gui_choice                                                               \
    -cvar subj_dir $subj_dir                                                  \
    -svar anat FT/FT_anat+orig.HEAD                                  \
    -svar compute_fitts yes                                                   \
    -svar epi FT/FT_epi_r[123]+orig.HEAD                             \
    -svar gid horses                                                          \
    -svar gltsym 'vis -aud' '0.5*vis +0.5*aud'                                \
    -svar gltsym_label V-A mean.VA                                            \
    -svar regress_jobs 2                                                      \
    -svar run_clustsim no                                                     \
    -svar sid FT                                                              \
    -svar stim FT/AV1_vis.txt FT/AV2_aud.txt                \
    -svar stim_basis 'BLOCK(20,1)' 'BLOCK(20,1)'                              \
    -svar stim_label vis aud                                                  \
    -svar tcat_nfirst 2                                                       \
    -svar volreg_base MIN_OUTLIER


# if process, actually run the analysis
if ( $process ) then
   echo ""
   echo cd $subj_dir
   cd $subj_dir
   echo ""
   sleep 2

   echo 'CREATING PROC SCRIPT:  tcsh -x cmd.ap.uber'
   echo ""
   sleep 3
   tcsh -x cmd.ap.uber |& tee out.cmd.ap.uber
   if ( $status ) then
      exit 1
   endif

   echo ""
   echo 'RUNNING ANALYSIS:  tcsh -xef proc.FT |& tee output.proc.FT'
   echo ""
   sleep 5
   tcsh -xef proc.FT |& tee output.proc.FT
endif