highspeed-fmriprep/README.md

Highspeed fMRIPrep

Overview

This repository contains pre-processed MRI data based on defaced BIDS-data used in Wittkuhn & Schuck, 2020, Nature Communications. Pre-processing was performed using fMRIPrep, version 1.2.2.

Dataset structure

• /code contains all project-specific code with sub-directories /docs for project-specific documentation and /fmriprep for the code relevant to run fMRIPrep on the input /bids dataset
• /bids contains the defaced BIDS-converted MRI dataset as an input to fMRIPrep and is included as an independent sub-datatset
• /tools contains the relevant fMRIPrep container and the necessary Freesurfer license file in the fmriprep sub-directory.
• /logs and /work are empty directories (held in place by .gitkeep files) and contain log files and the (huge) working directory ouput that fMRIPrep produced. They are populated during the execution of highspeed-fmriprep-cluster.sh but not committed to this repo because they will not be used further downstream in the analyses.

Citation

Wittkuhn, L. and Schuck, N. W. (2020). Dynamics of fMRI patterns reflect sub-second activation sequences and reveal replay in human visual cortex. Nature Communications.

A preprint (old version) is available at:

Wittkuhn, L. and Schuck, N. W. (2020). Faster than thought: Detecting sub-second activation sequences with sequential fMRI pattern analysis. bioRxiv. doi:10.1101/2020.02.15.950667

Contact

Please create a new issue if you have questions about the code or data, if there is anything missing, not working or broken.

For all other general questions, you may also write an email to:

• Lennart Wittkuhn
• Nicolas W. Schuck

License

All of the data are licensed under Creative Commons Attribution-ShareAlike 4.0. Please see the LICENSE file and https://creativecommons.org/licenses/by-sa/4.0/ for details.