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.. _ahelp_ap_run_simple_rest.tcsh:

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ap_run_simple_rest.tcsh
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    ------------------------------------------------------------------------------
    ap_run_simple_rest.tcsh  - run a quick afni_proc.py analysis for QC
    
       usage: ap_run_simple_rest.tcsh [options] -anat ANAT -epi EPI1 EPI2 EPI3 ...
    
    This program is meant to run a moderately quick single subject analysis,
    treating the EPI as resting state data.
    
    Overview:
    
       0. This program will change over time.  Do not rely on a fixed version.
          See "ap_run_simple_rest.tcsh -ver" for the current version number.
       1. Output files are placed in the current directory, so it is suggested
          to run from a "clean" location, generally away from the raw inputs.
       2. Template registration is merely affine, to be fast.
       3. By default, the first 2 time points are removed as pre-steady state.
          It is a good idea to set -nt_rm appropriately.
    
       inputs   : anat (optional), EPI
    
       controls : recommended opts: -subjid, -nt_rm
    
       outputs  : run_ap_SUBJID   - afni_proc.py command script
                : proc.SUBJID     -_proc script (if AP is run)
                : SUBJID.results  - proc results dir (if run)
                : out.*           - text output files from AP and proc scripts
    
    This program may be devoured by afni_proc.py itself, at some point.
    
    ------------------------------------------------------------------------------
    example 0: just create an afni_proc.py script, run_ap_SUBJ, no data required
    
          ap_run_simple_rest.tcsh -anat anat.nii -epi epi.nii
    
    
    example 1: quickly process EPI (no anat, so no align/tlrc blocks)
    
          ap_run_simple_rest.tcsh -epi epi.nii -run_proc
    
    
    example 2: preferred - run an analysis from a clean directory
    
          cd AFNI_data6/FT_analysis
          mkdir test.ap
          cd test.ap
          ap_run_simple_rest.tcsh -subjid ft.qc \
              -run_proc -nt_rm 2                \
              -anat ../FT/FT_anat+orig          \
              -epi ../FT/FT_epi_r*.HEAD
    
    ------------------------------------------------------------------------------
    terminal options:
    
       -help                   : show this help
       -hist                   : show the program history
       -ver                    : show the version number
    
    required parameters:
    
       -epi EPI_r1 EPI_r2 ...  : specify a list of EPI datasets
    
    optional parameters:
    
       -anat ANAT              : specify single anatomical dataset
    
       -nt_rm NT               : num time points to remove from starts of runs
                                 def: 2
    
       -run_ap                 : actually run the afni_proc.py command
                                 def: do not, just generate AP command script
    
       -run_proc               : do the processing (run the proc script from AP)
                                 def: do not run AP or proc script
    
       -subjid SUBJ_ID         : specify subject ID for file names
                                 def: SUBJ
    
       -template TEMPLATE      : specify template for standard space
                                 def: MNI152_2009_template_SSW.nii.gz
    
       -compressor COMP        : control automatic compression of *.BRIK files.
                                 'COMP' must be one of the allowed keywords for
                                 the AFNI_COMPRESSOR environment variable:
                                    GZIP  COMPRESS  BZIP2  PIGZ
                                 and you must have the associated program for
                                 compression installed (e.g., 'gzip')
                                 def: not set here
    
       -verb VERB              : specify verbosity level (3 == -echo)
                                 def: 1
    
       -echo                   : set 'echo' in the shell, as if run via 'tcsh -x'
                                 (same as '-verb 3')
    
    ------------------------------------------------------------------------------
    R Reynolds Apr, 2021
    version 0.6
    ------------------------------------------------------------------------------