extract-rsfc-pipeline

A surface-based rs-fMRI preprocessing script for extracting resting-state functional connectivity (RSFC) matrix from raw BOLD timeseries and T1w image.

Requirements

• Python 3.6+
• FreeSurfer
• Connectome Workbench
• AFNI
• FSL with MSM (Multimodal Surface Matching)**
• Ciftify
  • In python 3 environment with several libraries
    • Will be installed via script automatically with several packages

    • pip install ciftify

Provided files

• run_proc.sh
  • Shell-based main script
• ext_rsfc.py
  • Python-based code for extracting RSFC matrix from dtseries.nii (BOLD timeseries)
• Gordon_352_parc.dlabel.nii
  • Parcellation atlas from Gordon et al., 2016
• Slide for detailed description (link)
• Sample data (link)

Reference

[1] Gordon, E. M., Laumann, T. O., Adeyemo, B., Huckins, J. F., Kelley, W. M., & Petersen, S. E. (2016). Generation and evaluation of a cortical area parcellation from resting-state correlations. Cerebral cortex, 26(1), 288-303.

[2] Dickie, E. W., Anticevic, A., Smith, D. E., Coalson, T. S., Manogaran, M., Calarco, N., ... & Voineskos, A. N. (2019). Ciftify: A framework for surface-based analysis of legacy MR acquisitions. Neuroimage, 197, 818-826

Author

Jinwoo Hong / [email protected]