---
license: cc0-1.0
task_categories:
- image-segmentation
tags:
- medical-imaging
- brain-mri
- parcellation
- quality-control
- neurips-2026
pretty_name: OpenBrain v1.0
configs:
- config_name: sample_manifest
  data_files:
  - split: sample
    path: sample/sample_manifest.csv
  default: true
---

# OpenBrain v1.0

**OpenBrain: An Auditable Generated-Label Release for Whole-Brain MRI Parcellation**  
Accepted to NeurIPS 2026, Evaluations & Datasets Track. [Paper on OpenReview](https://openreview.net/forum?id=dR9OMtUEEC)

Qizhen Lan, Yu-Chun Hsu, Yuxiang Wei, Lijing Zhu, Zenan Sun, Liang He, Lishan Yu, Xiaoqian Jiang.

Maintained by **Qizhen Lan** ([lanqz7766](https://huggingface.co/lanqz7766)).


OpenBrain v1.0 is a public release of brain-extracted T1-weighted MRI
images, SynthStrip-derived brain masks, and automated whole-brain segmentation
labels.

The dataset viewer displays the 64-case sample manifest. The full release contains **35,838 cases** under `cases/`.

## Release Contents

- Cases: 35,838
- Source OpenNeuro datasets: 607
- License: CC0
- Artifacts per case:
  - `image.nii.gz`: revised brain-extracted T1w image
  - `brain_mask.nii.gz`: SynthStrip-derived brain mask
  - `whole_brain_segmentation.nii.gz`: automated whole-brain segmentation label

All released cases are derived from raw T1w images that were exactly matched to
verified public OpenNeuro snapshots with CC0/public-domain-compatible license
metadata. The segmentation labels are algorithmic labels, not manual ground
truth.

## Layout

```text
cases/<case_id>/image.nii.gz
cases/<case_id>/brain_mask.nii.gz
cases/<case_id>/whole_brain_segmentation.nii.gz
metadata/openbrain_v1_0_metadata.csv
metadata/sha256_manifest.csv
sample/cases/<case_id>/...
sample/sample_manifest.csv
sample/README.md
```

## QC Manifest Fields

The QC manifest uses `Q1`--`Q7` for the raw OpenBrain QC-7 values and
`r1`--`r7` for the corresponding source-local percentile risk fields. Larger
`r_k` values indicate higher risk relative to cases from the same OpenNeuro
source dataset; they are not calibrated probabilities of segmentation
correctness. `R` is the aggregate QC-7 risk score, and `tier` is the confidence
tier derived from the fixed release operating points.

The public sample manifest under `sample/sample_manifest.csv` follows the same
QC field convention for the 64-case sample subset.

## Sample

The `sample/` directory is a 64-case preview subset. Every sample case
is drawn from the HighConf tier and includes the same three case artifacts as
the full release: `image.nii.gz`, `brain_mask.nii.gz`, and
`whole_brain_segmentation.nii.gz`. The sample is source-diverse (one case per
source dataset) and selected by low combined risk `R`, with Q1/Q3/Q4
visual-cleanliness tie-breaks.

Use it for visual inspection, download testing, and pipeline smoke tests. The
labels remain algorithmic pseudo-labels, not manual ground truth.

## Exclusions

This release excludes cases with non-CC0 licenses, missing OpenNeuro provenance,
manual-review license status, ambiguous raw BIDS matches, or missing raw T1w
matches. OpenMind-derived quality scores and masks are not included.

## Citation

```bibtex
@inproceedings{lan2026openbrain,
  title = {OpenBrain: An Auditable Generated-Label Release for Whole-Brain MRI Parcellation},
  author = {Lan, Qizhen and Hsu, Yu-Chun and Wei, Yuxiang and Zhu, Lijing and Sun, Zenan and He, Liang and Yu, Lishan and Jiang, Xiaoqian},
  booktitle = {Advances in Neural Information Processing Systems, Evaluations \& Datasets Track},
  year = {2026}
}
```

## Contact

For questions about the release, contact Qizhen Lan at [Qizhen.Lan@uth.tmc.edu](mailto:Qizhen.Lan@uth.tmc.edu).