This repository contains some miscellaneous utility snippets that may make your life easier.
See the docstring at the beginning of each file for detailed description, usage, examples, etc.
data_conversion_util.py (link)
A few functions to convert data files between json, csv and python dictionary/list, or wide and long format.
randomization.py (link)
A script that randomize stimuli in a weird way (see the docstring in the file).
trigger_sender.py (link)
Automatically send triggers by generating keyboard presses (so you can test an fMRI task script without an MRI scanner).
organize_as_BIDS.py (link)
Rename and reorganize the fMRI data into the Brain Imaging Data Structure (BIDS).
unsteady_volumns.py (link)
Detect the initial unsteady volumns in confounds.tsv, and remove those initial volumns from preproc files. Also check for big head movements and print the info. Run this script before post_fmriprep_lv1.py.
post_fmriprep_lv1.py (link)
An example for level 1 analysis given data preprocessed by FMRIPREP. This script was adapted from this notebook. Run this script after unsteady_volumns.py.
create_masks.sh (link)
Create ROI masks in native space, given images parcellated by FreeSurfer recon-all.