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.. _ahelp_apqc_make_tcsh.py:

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apqc_make_tcsh.py
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.. contents:: :local:


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.. code-block:: none

    
    
    This program creates the single subject (ss) HTML review script
    '@ss_review_html', which itself generates images and text that form
    the afni_proc.py quality control (APQC) HTML.
    
    It is typically run by the afni_proc.py (AP) proc* script itself.
    
    Options:
    
    -uvar_json  UJ    :(req) UJ is a text file of uvars ("user variables")
                       created by gen_ss_review.py that catalogues important
                       files in the results directory, for the APQC.
    
    -subj_dir   SD    :(req) location of AP results directory (often '.', as
                       this program is often run from within the AP results 
                       directory).
    
    -review_style RS  :(opt) the 'style' of the APQC HTML output HTML.  Allowed
                       keywords are:
                           {basic, none, pythonic}
                       + Using 'pythonic' is the recommended way to go: the
                       1D images are the clearest and most informative.
                       It means you need the Python module Matplotlib
                       (v>=2.2) installed, which should be a light dependency.
                       + Using 'basic' means that no Matplotlib will be
                       used, just 1dplot, and the images will be more,
                       well, basic-looking.
                       + Using 'none' means no APQC HTML is generated (boooooo).
    
    -mot_grayplot_off :(opt) turn off the grayplot generation.  This
                       option was created for a specific case of a user who had
                       a huuuge dataset and the grayplot took annoyingly long
                       to estimate.  Not recommended to use, generally. 
    
    -vstat_list A B C ...
                      :(opt, only applicable if stim timing is used in
                       processing) provide a list of label items to specify
                       which volumes's images should appear in the vstat
                       QC block.  Each item should correspond to subbrick
                       label basename (so not including '_GLT', "#N",
                       'Tstat', 'Fstat', 'Coef', etc.) in the stats_dset.
                       'Full_Fstat' is always added/included, even if not
                       provided in this list. If not used, the program
                       uses default logic to pick up to 5 items to show.
    
    -ow_mode  OM      :(opt) set overwrite mode; choices are
                       backup       -> move old QC dir to QC_<time>; make new QC dir
                       overwrite    -> purge old QC dir and make new QC/
                       shy          -> (def) make new QC dir only if one does not exist
                       See also '-bup_dir ..' for additional backup dir 
                       naming.
    
    -bup_dir  BD      :(opt) if using the '-ow_mode backup' option, then 
                       you can use this opt to provide the desired name of
                       the backup QC directory (def: use QC_<time>).
    
    -do_log           :(opt) flag to turn on making a text log of all the 
                       shell commands that are run when apqc_make_tcsh.py
                       is executed; mainly for debugging purposes, if 
                       necessary.