Creating a group-level modeling interface in AFNI using Python

[afni-gangc]

Title

Creating a group-level modeling interface in AFNI using Python

Short description and the goals for the OHBM BrainHack

There are quite a few powerful modeling tools in AFNI that perform group-level analysis. The programs range from simple to complex ones: GLM, ANCOVA with within-subject (or repeated-measures) factors, linear mixed-effects modeling, nonlinear modeling using smooth splines, intraclass correlation, Bayesian multi-level modeling, etc. These programs include 3dttest++, 3dMVM, 3dLMEr, 3dMSS, 3dISC, 3dICC, RBA, etc. Currently there is a Python program, gen_group_command.py, that provides a nice interface for the user to set up group-level analysis for GLM. Two potential projects are

1) create a unified user interface similar to gen_group_command.py that could generate most, if all, of the group-level programs; alternatively,

2) write a user interface for one or a few group-level programs.

Link to the Project

https://github.com/afni/afni/blob/master/src/python_scripts/scripts/gen_group_command.py

Image for the OHBM brainhack website

No response

Project lead

Gang Chen (github: afni-gangc; discord: Gang Chen#1967)

Main Hub

Glasgow

Other Hub covered by the leaders

• [ ] Glasgow
• [ ] Asia / Pacific
• [ ] Europe / Middle East / Africa
• [ ] Americas

Skills

Python Shell scripting

Recommended tutorials for new contributors

• [ ] Set up a brainhack friendly computing environment
• [ ] A introduction to Bash
• [X] Python: Writing a script
• [X] Python: Data analysis with Python
• [ ] Python: Visualisation
• [ ] Machine learning basics
• [ ] BIDS
• [ ] Machine learning for neuroimaging
• [ ] VCS: Using Git and Github
• [ ] VCS: Data management with Datalad
• [ ] Virtualization
• [ ] High Performance Computing: Oracle cloud resource

Good first issues

No response

Twitter summary

No response

Short name for the Discord chat channel (~15 chars)

gen-group

Please read and follow the OHBM Code of Conduct

• [X] I agree to follow the OHBM Code of Conduct during the hackathon

[djarecka]

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides! If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)

[danieltomasz]

hi @afni-gangc I would be interested in working on this projects, especially learning more about porting and interfacing RBA, I am online particant, you can read my DM on discord