ISTART-eyeballs: Characterizing the effects of Nyquist ghosting in task-dependent cerebellar connectivity

This repository contains code related to our project investigating the effects of nyquist ghosting from the eyeballs on task-dependent signal in the cerebellum. All hypotheses and analysis plans were pre-registered on osf (https://osf.io/sd395/) in fall semester 2022 and analyses commenced on shortly thereafter. Imaging data will be shared via OpenNeuro when the manuscript is posted on bioRxiv.

A few prerequisites and recommendations

• Understand BIDS and be comfortable navigating Linux
• Install FSL
• Install miniconda or anaconda

Notes on repository organization and files

• Raw DICOMS (an input to heudiconv) are private and only accessible locally (Smith Lab Linux: /data/sourcedata)
• Some of the contents of this repository are not tracked (.gitignore) because the files are large and we do not yet have a nice workflow for datalad. These folders include /data/sourcedata (dicoms) and parts of bids and derivatives.
• Tracked folders and their contents:
  • code: analysis code
  • templates: fsf template files used for FSL analyses
  • masks: images used as masks, networks, and seed regions in analyses
  • derivatives: derivatives from analysis scripts, but only text files (re-run script to regenerate larger outputs)

Basic commands to reproduce our analyses

# get code and data (two options for data)
git clone https://github.com/DVS-Lab/istart-socdoors
cd  istart-socdoors

rm -rf bids # remove bids subdirectory since it will be replaced below
# can this be made into a sym link?

datalad clone https://github.com/OpenNeuroDatasets/ds003745.git bids
# the bids folder is a datalad dataset
# you can get all of the data with the command below:
datalad get sub-*

# run preprocessing and generate confounds and timing files for analyses
bash code/run_fmriprep.sh
python code/MakeConfounds.py --fmriprepDir="derivatives/fmriprep"
bash code/run_gen3colfiles.sh

# run statistics
bash code/run_L1stats.sh
bash code/run_L2stats.sh