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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.
    
    -can_add_blur CAB :(opt) if the FMRI processing did not use blurring, then
                       the APQC HTML creation can add blurring to a couple steps
                       within the QC generation that might be easier to interpret,
                       such as the seedbased correlation maps, in the TSNR warns
                       levels of any ROI TSNR tables, and in the corr_brain map.
                       This program will check the uvars for whether blurring was
                       used automatically, to know whether it would consider adding
                       extra blur in the QC images; the TSNR warn levels will still
                       be automatically adjusted based on blurring/not.
                       These extra blurs *only* apply in the QC items, not in the
                       final data; this program will check the uvars for whether
                       blurring
                       If you don't want this program to check to add any extra 
                       blur for data processed without blurring, then disable that
                       here.
                       Allowed values of CAB are: Yes or 1, No or 0.
                       (def: Yes)
    
    -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.
    
    -run              :(opt) a trivial option that does nothing, but means you can
                       execute this program, rather than display the help text,
                       when using default -uvar_json and -subj_dir values (which
                       mean running this in the current dir)