Updating AFNI dependencies

[mrneont]

Howdy-

I recently checked in on the AFNI install on Neurodesk. I think there are a couple of things to update there:

• We now use the Python modules Flask and Flask-Cors for setting up a local server to interact with afni_proc.py's QC HTML. Those don't appear to be available after ml afni.
• We also use NiiVue as part of the same APQC HTML. We distribute this with our binaries and as part of our build scripts, which basically means building+copying in a compiled niivue_afni.umd.js file in the same location as the main AFNI binaries (i.e., where which afni points). We actually put a copy of the niivue_afni.umd.js file that we build in an openly accessible spot for ease of access, and so it could be gotten with:

   curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/niivue_afni.umd.js
  

It would be great if both of those aspects could be updated.

thanks,
pt

[stebo85]

Dear @mrneont,

Yes, we can make these updates. To clarify what's needed:

1. what are the binary names for this? What is the command you would want to run after a module load to test this?
2. niivue_afni.umd.js is already there:

afni-24.1.02:/opt/afni-latest$ find . | grep niivue
./afnipy/lib_apqc_niivue.py
./niivue_afni.umd.js

What else is needed to make this work? How can I test this?

[mrneont]

Hi, @stebo85 -

Thanks for the quick reply!

1. About Flask and Flask-Cors: these are just Python modules to load. To install these in Ubuntu, say, I would just do:

   sudo apt-get install python3-flask python3-flask-cors
   

   To test this, one would just want to see version numbers for each module detected by the system check:

     afni_system_check.py -disp_ver_pylibs flask flask_cors
   

   A deeper test of functionality would involve running afni_proc.py for a full FMRI processing run, and then opening the created QC HTML with open_apqc.py -infiles ... and seeing that the HTML buttons worked. That might be a more difficult test, but I'm happy to discuss that more if that would be useful.

2. Huh, OK, I tried using Neurodesk from "https://www.neurodesk.org/" -> Play -> Terminal, and then I didn't see it when I module loaded afni (I apologize for copy+pasting a screenshot here, but I couldn't figure out how to copy the text from the terminal):
   
   I guess I am not understanding why this is different.

thanks,
pt

[stebo85]

1. Ok, I will add these and test with afni_system_check.py - currently this outputs in afni 23.3.02:

** error: unknown trailing arguments : ['-disp_ver_pylibs', 'flask', 'flask_cors']

So I guess an update to the latest AFNI version will fix that?

2. the module system only exposes binaries on the top level. The niivue files are inside the container subdirectory:

ls /cvmfs/neurodesk.ardc.edu.au/containers/afni_24.1.02_20240409/afni_24.1.02_20240409.simg/opt/afni-latest/niivue_afni.umd.js 
/cvmfs/neurodesk.ardc.edu.au/containers/afni_24.1.02_20240409/afni_24.1.02_20240409.simg/opt/afni-latest/niivue_afni.umd.js

[mrneont]

1. Indeed, I guess the option -disp_ver_pylibs is newer than that version.

2. Ah, I see---thanks for clarifying that.

[stebo85]

This is now completed in our latest afni container with version 24.3.00

Thank you for flagging this with us:)