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OptofMRI_5HT Wiki

Welcome to the OptofMRI_5HT project wiki!

This repository contains analysis code for the optogenetic fMRI study stimulating dorsal raphe serotonin neurons, published in Nature Communications 2024 (Hamada et al.).

Quick Links

• 📖 Project Overview
• 📁 Data Structure
• 🔬 Analysis Pipeline
• 🧠 Regions of Interest (ROIs)
• 📊 Figure Generation Guide

External Resources

• Paper: Hamada et al., Nat Commu 2024
• Dataset: OpenNeuro (ds005077)
• DeepWiki Summary: DeepWiki Overview
• Preprint: bioRxiv

Key Findings

1. Functional activation map - Optogenetic stimulation of DRN serotonin neurons produces brain-wide activation including reward-related networks
2. Anesthesia effects - General anesthetics (isoflurane) reverse the brain-wide activation pattern
3. Structure-function correlation - Functional maps correlate with structural density of serotonergic projections
4. Receptor expression - 5-HT receptor expression and structural density explain the observed functional maps
5. Anesthetic modulation - General anesthetics may modify receptor responses

Getting Started

% Add required toolboxes to path
addpath(genpath('path/to/gramm'))
addpath(genpath('path/to/spm12'))

% Run all analysis codes
run_allcodes

Contact

Hiro Taiyo Hamada
Email: hiroaki.hamada@oist.jp