Miscellaneous Tools

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.

Contents

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).

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Neuroimaging Data Processing Snippets:

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.