apqc_make_tcsh.py


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.