# fMRI Dataset for Studying Propofol Anesthesia Mechanisms with Awake Baseline in Mice

## Dataset Overview

This dataset contains resting-state functional MRI (fMRI) data from propofol-induced sleep in mice, organized according to the Brain Imaging Data Structure (BIDS) standard version 1.9.0.

**Data Modality:**
- **fMRI only**: Resting-state functional MRI data from 10 mice (sub-02 to sub-11)

## Dataset Structure

```
fMRI_only_BIDS/
├── dataset_description.json       # BIDS dataset metadata
├── participants.tsv             # Subject metadata (fMRI only)
├── participants.json             # Metadata column descriptions
├── README                       # This file
├── task-rest_bold.json          # Task-specific JSON (inherited)
├── .bidsignore                 # BIDS ignore file
├── sub-02/ to sub-11/         # fMRI subjects (10 subjects)
│   ├── anat/                   # T2-weighted anatomical images
│   │   ├── sub-XX_T2w.nii.gz
│   │   └── sub-XX_T2w.json
│   └── func/                   # Resting-state BOLD fMRI
│       ├── sub-XX_task-rest_bold.nii.gz
│       └── sub-XX_task-rest_bold.json
└── code/                       # Python analysis scripts (see below)
```

## Acquisition Parameters

### fMRI Data
| Parameter | Value |
|-----------|-------|
| Scanner | Bruker BioSpec 94/20, 9.4 T |
| Sequence | Gradient-echo EPI |
| TR | 2000 ms |
| TE | (see individual JSON sidecars) |
| Slices | 30 (axial, interleaved ascending) |
| Slice timing | 0.0 – 1.93 s (30 slices, step = 0.0667 s) |
| Voxel size | (see individual NIfTI headers) |
| Phase encoding direction | j- (anterior–posterior) |
| Subjects | n=10 (sub-02 through sub-11) |

## Subject ID Mapping (Original to BIDS)

| Original ID | BIDS ID | Source Folder |
|-------------|---------|---------------|
| 1 | sub-02 | (from PRO10 dataset) |
| 2 | sub-03 | (from PRO10 dataset) |
| 3b | sub-04 | (from PRO10 dataset) |
| 4 | sub-05 | (from PRO10 dataset) |
| 5c | sub-06 | (from PRO10 dataset) |
| 6 | sub-07 | (from PRO10 dataset) |
| 7b | sub-08 | (from PRO10 dataset) |
| 8 | sub-09 | (from PRO10 dataset) |
| 9 | sub-10 | (from PRO10 dataset) |
| 10 | sub-11 | (from PRO10 dataset) |

## Code Directory (`code/`)

The `code/` directory contains Python 3 scripts used to generate all figures in the manuscript. Each script is prefixed with the figure it corresponds to.

### Requirements
- Python 3.x
- numpy
- scipy
- matplotlib
- nibabel
- nilearn

### Script List
| Script | Description |
|--------|-------------|
| `Fig1F-*` | Fraction of high-motion TRs analysis |
| `Fig3A-*` | Behavioral response rate time course |
| `Fig3DE-*` | Modular brain network metrics |
| `Fig3FH-*` | Graph theory statistics |
| `Fig3G-*` | Graph theory analysis |
| `Fig4ABC-*` | Functional connectivity matrix with significance |
| `Fig4DEF-*` | Connectogram visualization |
| `Fig4G-*` | ROI summary violin plots |
| `Fig5AB-*` | Brain activation maps (mricroGL-friendly) |
| `Fig5C-*` | Binary significance masks |
| `Fig5D-*` | Global signal subject-level analysis |
| `Fig5E-*` | Bubble plot of subjects |
| `Fig5F-*` | Group mask validation |
| `Fig5G-*` | Subject-level amplification analysis |
| `Fig6A-Fig6J*` | Thalamus-specific analyses (connectivity, specificity, dynamics) |
| `S-FigS1C-S-FigS6I-*` | Supplementary figure scripts |

## Validation

This dataset passes `bids-validator` checks. To validate locally:

```bash
npm install -g bids-validator
bids-validator /path/to/fMRI_only_BIDS/
```

## Usage Notes

1. **For fMRI analysis**: Use subjects sub-02 through sub-11
2. **Code execution**: Run Python scripts from the `code/` directory

## License

This dataset is made available under the **Creative Commons Attribution 4.0 International (CC-BY 4.0)** license.

## Citation

If you use this dataset, please cite:

> Ye Yunshuang et al. (2025). fMRI Dataset for Studying Propofol Anesthesia Mechanisms with Awake Baseline in Mice. OpenNeuro.

Also available on Figshare: https://doi.org/10.6084/m9.figshare.32227659

## Contact

For questions about this dataset, please contact: Ye Yunshuang (Shanghai Jiao Tong University)

## Version History

| Version | Date | Changes |
|---------|------|---------|
| v1.0 | 2025-05-10 | Initial release (fMRI only) |