Flexibly convert fmriprep confounds to censor files

[dmoracze]

Title

Fmriprep to censor

Leaders

Dustin Moraczewski

Collaborators

No response

Brainhack Global 2022 Event

Brainhack Washington DC

Project Description

Fmriprep gives a smorgasbord of confounds to be used in later processing. While the program provides the option for generating censor files based on a few outlier criteria, I would like to expand on a tool I've written to take in fmriprep derivatives and write new censor files based on new outlier criteria. This tool can be of use to anyone who preprocesses their data with fmriprep and would like to have multiple censor files on hand.

I have already written some basic code, but I'm quickly learning that it should be more flexible.

Knowledge of censoring (aka scrubbing) in fmri is not essential, but for more info you can see this publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849338/

Link to project repository/sources

https://github.com/dmoracze/HPC_helper_tools/blob/master/bin/fmriprep-to-censor.py

Goals for Brainhack Global

Expand the functionality of the code I've already written to include any number of outlier criteria.

Good first issues

1. issue one:

2. issue two:

Communication channels

fmriprep-censor channel on brainhack DC's slack workspace:
https://brainhackdc.github.io/2022/index.html

Skills

Python: beginner to intermediate to expand on the current code
Command line: basic, to help with testing the code and giving feedback about the user experience

Onboarding documentation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849338/

https://fmriprep.org/en/stable/outputs.html#confounds

What will participants learn?

Participants will learn about fmri censor files, fmriprep's confounds tables, and basic to intermediate python coding

Data to use

I will provide some fmriprep derivatives from the open source ABIDE dataset

Number of collaborators

2

Credit to collaborators

Contributors will be added as collaborators on the project's repo

Image

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Type

data_management, pipeline_development

Development status

1_basic structure

Topic

MR_methodologies, reproducible_scientific_methods

Tools

BIDS, fMRIPrep

Programming language

Python, unix_command_line

Modalities

fMRI

Git skills

0_no_git_skills, 1_commit_push

Anything else?

No response

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• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
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