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)
