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Salience Network Multiscale Switch

Code and data to reproduce the analyses from:

THE MULTISCALE ARCHITECTURE OF THE SALIENCE NETWORK SUPPORTS A BRAIN-WIDE "SWITCH" FUNCTION Author List — Preprint

What this repository does

Integrating in vivo 7T neuroimaging with ultra-high-resolution ex vivo histology and intracranial electrophysiology, this codebase reproduces all figures demonstrating that the salience network (SN) possesses a distinct superior-inferior architectural profile. Specific patterns of laminar differentiation, structural connectivity, and electrophysiology uniquely position the SN to bridge task-negative and task-positive systems.

Quick start

git clone https://github.com/PaulBautin/salience-network-multiscale-switch.git
cd salience-network-multiscale-switch
uv venv env_salience
uv pip install -e . --python env_salience/bin/python
source env_salience/bin/activate

python scripts/figure_1a_t1map.py \
  -pni_deriv /path/to/BIDS_PNI/derivatives/micapipe_v0.2.0 \
  -mics_deriv /path/to/BIDS_MICs/derivatives/micapipe_v0.2.0

Documentation

  • Usage — CLI reference for all figure scripts
  • API Reference — src/ module and function documentation
  • Methods — Acquisition parameters and analysis methods

Repository layout

salience-network-multiscale-switch/
├── data/
│   ├── surfaces/        # fsLR-32k inflated and sphere GIFTIs
│   ├── parcellations/   # Schaefer-400, Von Economo, BigBrain, AHEAD profiles
│   └── dataframes/      # cached intermediate TSV/CSV results
├── docs/                # this documentation
├── results/figures/     # SVG/PNG output figures
├── scripts/             # entry-point scripts, one per figure panel
└── src/                 # reusable processing modules

Requirements