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.
