Fmriprep to censor
Dustin Moraczewski
No response
Brainhack Washington DC
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/
https://github.com/dmoracze/HPC_helper_tools/blob/master/bin/fmriprep-to-censor.py
Expand the functionality of the code I’ve already written to include any number of outlier criteria.
issue one:
issue two:
fmriprep-censor channel on brainhack DC’s slack workspace: https://brainhackdc.github.io/2022/index.html
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849338/
https://fmriprep.org/en/stable/outputs.html#confounds
Participants will learn about fmri censor files, fmriprep’s confounds tables, and basic to intermediate python coding
I will provide some fmriprep derivatives from the open source ABIDE dataset
2
Contributors will be added as collaborators on the project’s repo
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data_management, pipeline_development
1_basic structure
MR_methodologies, reproducible_scientific_methods
BIDS, fMRIPrep
Python, unix_command_line
fMRI
0_no_git_skills, 1_commit_push
No response
Hi @brainhackorg/project-monitors my project is ready!