AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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August 25, 2021 03:34PM
Hi, Mrinmayi-

I'm doing alright, thanks, and I things are good for you, too. That is great that you are running a FMRI processing workshop!

About uber_subject.py---
[caveat---I am not the best person to answer about this, but that person is on leave for a couple days, so I will have a go...]
Firstly, I don't believe that there is currently a way to get it to run in Python 3.*, and many participants might have that, so it might be hard/impossible for them to follow along with it. It requires PyQt4 specifically, I believe, and this might only run in Python 2.7 at the moment.

I see you are using Python 2.7, and then I think the trick would be to have PyQt4 (not PyQt6, as it appears to be showing up). To manage different package things, esp. when Python is involved, I have found Conda (--> and in particular Miniconda) to be the easiest way to go---you can specify the packages+version numbers you want, and in theory they shouldn't interact with each other and you can purge them at your leisure.

Some more notes about (mini)conda specifically are---note there is both a verbose and a quick set of descriptions:
[afni.nimh.nih.gov]

I tried to make a conda environment with PyQt4, which would run uber_subject.py, and here were my results:

Failed and failed (conflict between matplotlib+numpy and PyQt4):
conda create -y -n py27_tiny_pyqt4     -c conda-forge       pyqt=4  python=2.7    matplotlib numpy
conda create -y -n py27_tiny_pyqt4     -c conda-forge       pyqt=4  python=2.7    matplotlib

Failed (Python 3.7 and PyQt4 wouldn't play nicely together):
conda create -y -n py37_tiny_pyqt4     -c conda-forge       pyqt=4  python=3.7

Worked, *but* extremely limited and won't have the nice, "pythonic" QC HTML output from afni_proc.py (just the plainer/less informative will be output---boooo):
conda create -y -n py27_tiny_pyqt4     -c conda-forge       pyqt=4  python=2.7

... so, this provides a way to open the GUI and use it, but I still might go for The Leap to afni_proc.py, parcellating the command into its component parts for understandability.

As an intro to afni_proc.py, there is this presentation given by The Bob from time to time at Bootcamps (also in the afni_handouts/ dir of the Bootcamp tarball):
[afni.nimh.nih.gov]
I have shorter+similar one from talking at the Resting State conference that I can send you, which might be useful.

--pt
Subject Author Posted

unable to run uber_subject.py

avantika July 29, 2020 06:33PM

Re: unable to run uber_subject.py

ptaylor July 30, 2020 09:38AM

Re: unable to run uber_subject.py

mrinmayik August 24, 2021 10:44PM

Re: unable to run uber_subject.py

ptaylor August 25, 2021 03:34PM

Re: unable to run uber_subject.py

mrinmayik August 25, 2021 05:50PM

Re: unable to run uber_subject.py

ptaylor August 25, 2021 06:26PM