Post-fMRIPrep ICA-AROMA BIDS-App

[esavary]

Title

Post-fMRIPrep ICA-AROMA BIDS-App

Short description and the goals for the OHBM BrainHack

The aim of this hackathon project is to create an ICA-AROMA post-fMRIPrep pipeline. fMRIPrep is a robust and user-friendly preprocessing tool for diverse fMRI data. ICA-AROMA, on the other hand, is a data-driven method that automatically identifies and removes motion-related independent components from fMRI data.
Prior to fMRIPrep 23.1, ICA-AROMA was an optional component of fMRIPrep, but it was removed as being out-of-scope, as it can be performed on fMRIPrep outputs.
The project focuses on creating an ICA-AROMA pipeline that accepts fMRIPrep outputs as its inputs, in particular MNI152NLin6Asym-resampled BOLD series. The pipeline will apply SUSAN smoothing, run MELODIC, and finally ICA-AROMA. The pipeline will provide options for users to select specific outputs, including noise components and non-aggressively denoised BOLD series, as well as generate reports.
To join the discussion and contribute to this project, you can find more information in the related issue at nipreps/fmriprep#2936.

Link to the Project

https://github.com/nipreps/fmripost-aroma

Image for the OHBM brainhack website

No response

Project lead

Céline Provins, GitHub: @celprov , discord: cprovins

Main Hub

Montreal

Other Hub covered by the leaders

• Montreal
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

Having basic Python knowledge is important, however all levels of experience are welcome.

Recommended tutorials for new contributors

• Set up a brainhack friendly computing environment
• A introduction to Bash
• Python: Writing a script
• 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)

fmriprep_aroma

Please read and follow the OHBM Code of Conduct

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