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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. Cluster simulations are run at the end, which take time.
          That might become optional, if there is interest.
       4. 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
    
    required perameters:
    
       -epi EPI_r1 EPI_r2 ...  : specify a list of EPI datasets
    
    optional perameters:
    
       -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                   : same as -verb 3
    
    ------------------------------------------------------------------------------
    R Reynolds Apr, 2021
    version 0.2
    ------------------------------------------------------------------------------