Enabling QC buttons in QC HTML

[chholak]

AFNI version info (afni -ver): Precompiled binary macos_13_ARM: Feb 20 2025 (Version AFNI_25.0.06 'Severus Alexander')

While trying to rate/comment in the QC HTML file, the QC buttons are inactive. Hovering over the "RATE" button shows that automatic saving is off. How can I turn it on?

Thanks,
Parth

[ptaylor]

Hi, Parth-

Firstly, you have to use open_apqc.py to open the HTML file(s). If you have done that but don't see the buttons working, then you probably need the Flask and Flask-cors Python modules. Is that what the text in the terminal tells you when you run:

open_apqc.py -infiles <PATH>/index.html

? Also note that you can have more than one HTML listed there, and open up multiple ones simultaneously.

We list these as part of the Miniconda install instructions here. Specifically, the current Python package dependencies you should have for using AFNI (though, future readers, this might adapt over time) are:

  - python
  - "matplotlib>=2.2.3"       # minimal ver for 'pythonic' APQC HTML
  - numpy
  - scipy
  - "flask>=2.1.2"            # for local server for APQC HTML 
  - "flask-cors>=3.0.10"      # for local server for APQC HTML 

Note that you do not have to regenerate the APQC HTML or anything. It should just work.

More descriptions of the APQC HTML are provided:

• Reynolds RC, Taylor PA, Glen DR (2023). Quality control practices in FMRI analysis: Philosophy, methods and examples using AFNI. Front. Neurosci. 16:1073800. doi: 10.3389/fnins.2022.1073800

• Taylor PA, Glen DR, Chen G, Cox RW, Hanayik T, Rorden C, Nielson DM, Rajendra JK, Reynolds RC (2024). A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth and interactive QC with afni_proc.py and more. Imaging Neuroscience 2: 1–39. doi: 10.1162/imag_a_00246

• Comment: it is also worth checking out this fun, online demo of the APQC HTML and some of its interactive functionality, described in the above paper.

--pt

[chholak]

Thank you for your detailed response, Paul. I was not using open_apqc.py, but then I got reminded of that while looking at the QC talk you did for the recent AFNI Bootcamp. Everything is working now!

It might be helpful for you to know that this command is not mentioned on the AFNI tutorial on QC (12.4. APQC: afni_proc.py quality control — AFNI, SUMA and FATCAT: v25.0.07) and the (older) AFNI Bootcamp video (https://www.youtube.com/watch?v=mPSH5UROt98&list=PL_CD549H9kgq-_HSwvH5KhFl8A15u6d71&index=46) on the AFNI Academy YouTube channel, which talk about browser restrictions due to security and (in)ability to save local files, and used afni_open -b.

Thanks again,
Parth

[ptaylor]

Hi, Parth-

Those are good suggestions, and we will update the docs, thanks for those pointers!

--pt

[rickr]

That's a good reminder about the docs. The youtube video you reference is about a year older than open_apqc.py, and is due for a remaking...

-rick