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, 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.

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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: 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

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terminal options:

   -help                   : show this help

required perameters:

   -anat ANAT              : specify single anatomical dataset
   -epi EPI_r1 EPI_r2 ...  : specify a list of EPI datasets

optional perameters:

   -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

   -verb VERB              : specify verbosity level (3 == -echo)
                             def: 1
   -echo                   : same as -verb 3

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R Reynolds Apr, 2021
version 0.1
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