---
license: other
license_name: mixed-cc-by-4.0-and-cc-by-sa-4.0
license_link: https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/README
pretty_name: SynthStrip
tags:
- medical
- mri
- brain
- skull-stripping
- brain-extraction
- brain-segmentation
- neuroimaging
- multi-contrast
task_categories:
- image-segmentation
size_categories:
- n<1K
configs:
- config_name: default
  data_files:
  - split: validation
    path: data/validation-*
  - split: test
    path: data/test-*
dataset_info:
  features:
  - name: scan_id
    dtype: string
  - name: subset
    dtype: string
  - name: modality
    dtype: string
  - name: modality_full
    dtype: string
  - name: modality_type
    dtype: string
  - name: subject
    dtype: string
  - name: split
    dtype: string
  - name: source_archive
    dtype: string
  - name: license
    dtype: string
  - name: ixi_image_overlap
    dtype: bool
  - name: image_shape
    dtype: string
  - name: num_slices
    dtype: int32
  - name: voxel_spacing
    dtype: string
  - name: brain_voxels
    dtype: int64
  - name: slice_index
    dtype: int32
  - name: image
    dtype: image
  - name: mask
    dtype: image
  - name: overlay
    dtype: image
  splits:
  - name: validation
    num_bytes: 2630827
    num_examples: 24
  - name: test
    num_bytes: 62832682
    num_examples: 558
  download_size: 65436774
  dataset_size: 65463509
---

# SynthStrip

The **SynthStrip** dataset is a collection of full-head brain scans paired with manually-refined
**binary brain masks**, assembled by the FreeSurfer / Martinos Center team to evaluate the
SynthStrip brain-extraction (skull-stripping) tool across a wide range of contrasts, resolutions,
and subject populations (newborns to glioblastoma patients).

> **Scope of this mirror — read before use.** The full SynthStrip release spans 622 MRI, **PET**,
> and **CT** scans. This repository contains the **582 redistributable image + brain-mask pairs**,
> which are **entirely MRI**. The reason is specific: the only PET/CT scans in SynthStrip are the
> **CIM** (CERMEP-IDB-MRXFDG) cases, and the authors may **not** redistribute those images — the
> official release ships CIM as **masks only**. We therefore **exclude all 40 `cim_*` cases** (an
> image-less mask cannot be scored). We also **exclude the anatomical `labels.nii.gz`** maps
> (a different, SynthSeg-style parcellation task — not the binary brain mask). What remains is a
> clean multi-contrast **brain-MRI skull-stripping** benchmark.

## Contents

**582 scans**, organized as `synthstrip_data_v1.5/<SUBSET>_<MODALITY>_<SUBJECT>/` with
`image.nii.gz` + `mask.nii.gz`. No train split (pure evaluation set); the authors' val/test split
is preserved in `scan_metadata.csv` and `synthstrip_data_v1.5/scans_*.txt`.

| Subset | Source archive | Modalities (count) | N | License |
|---|---|---|---|---|
| IXI | Imperial College London | T1w 50 · T2w 50 · PDw 50 · MRA 50 · DWI 32 | 232 | **CC BY-SA 4.0** |
| FSM | FreeSurfer Maintenance (MGH) | T1w 38 · T2w 36 · PDw 32 · qT1 32 | 138 | CC BY 4.0 |
| ASL | HCP-Aging / MGH | T1w 43 · PCASL 43 | 86 | CC BY 4.0 |
| QIN | TCIA QIN-GBM-Treatment-Response | T1w 54 · T2-FLAIR 17 · T2w 39 | 110 | CC BY 4.0 |
| Infant | Boston Children's Hospital | T1w 16 (ages 0–18 mo) | 16 | CC BY 4.0 |
| **Total** | | | **582** | |
| *(excluded)* CIM | CERMEP-IDB-MRXFDG | FDG PET 20 · CT 20 — **masks only, no image** | 40 | CC BY 4.0 |

**Split (authors' publication split):** validation = **24** · test = **558** (the official
`scans_test.txt` lists 598, of which 40 are the excluded `cim_*` cases → 558 here).

Per scan — `synthstrip_data_v1.5/<scan_id>/`:

| File | Content | dtype |
|---|---|---|
| `image.nii.gz` | unmodified native-space image (orientation/resolution vary per scan) | int16 / float32 / uint8 |
| `mask.nii.gz` | **binary brain mask (0 = non-brain, 1 = brain)** — same shape & affine as the image | uint8 |

`scan_metadata.csv` (repo root) carries one row per scan: `scan_id, subset, modality,
modality_full, modality_type, subject, split, source_archive, license, ixi_image_overlap`.

## Ground truth

**Single tier** — the manually-refined **binary brain mask**. The reference for each subject was
built by running every classical skull-stripper on the T1w scan and taking the **per-voxel
majority vote**, then **manually refining** it and propagating to the subject's other contrasts by
rigid registration; v1.5 additionally cleaned masks via largest-connected-component + hole-filling.
There are **no competing rater/auto tiers** to choose between. (This is *not* a SAMSEG output —
SAMSEG/SynthSeg is only used for the excluded anatomical `labels.nii.gz`.)

## Cross-dataset overlap (important)

- **IXI (232 scans, ~40% of this mirror) is EXACT source-image overlap with
  [`Angelou0516/ixi-brain`](https://huggingface.co/datasets/Angelou0516/ixi-brain)** — the *same*
  IXI scans, here carrying skull-stripping brain masks instead of ixi-brain's target. They are
  legitimate, distinct benchmark samples (different task), but **do not count IXI as unique images
  when aggregating SynthStrip + ixi-brain** — de-duplicate on the IXI subject id (the `ixi_*`
  `scan_id` token / `subject` column is the join key; `ixi_image_overlap = true` flags every such
  row).
- **QIN (110 scans)** is sourced from **TCIA QIN-GBM-Treatment-Response**, a glioblastoma cohort —
  shared TCIA lineage with the BraTS-family / GBM datasets in the suite. Low leakage concern: the
  task here is **skull-stripping (binary brain mask)**, not tumor segmentation. The `qin_*` token /
  `subject` column traces back to the TCIA subject.
- **ASL (86 scans)** draws in part from the **Human Connectome Project–Aging**.
- No shared lineage with the Medical Segmentation Decathlon.

## Licensing (per subset)

The release uses **two licenses**, so this repo is tagged `license: other` rather than a single CC
tag (tagging the whole repo plain CC BY 4.0 would mis-state the IXI images):

| Component | License |
|---|---|
| IXI images **and** their brain masks (232 scans) | **CC BY-SA 4.0** (share-alike) |
| All other images + masks (FSM, ASL, QIN, Infant) | CC BY 4.0 |

The **share-alike** clause propagates to any derivative of the IXI data — including the IXI rows of
the `data/` parquet preview, which are likewise **CC BY-SA 4.0**. See the official
[license notice](https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/README).

## Provenance & source

Author-hosted by FreeSurfer / Martinos Center (not a third-party re-host): persistent DOI
<https://w3id.org/synthstrip> → <https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/> ·
3D release **v1.5** (2024-06-20). The full release reports **622** scans; **582** are redistributable
and mirrored here (see *Scope*). Each subset must additionally be credited to its original archive
(IXI; FreeSurfer/FSM; HCP-Aging; TCIA QIN-GBM; Boston Children's Hospital) per the README.

## `data/` preview

`data/` holds a Parquet preview for the Hugging Face Dataset Viewer — for each scan, the
brain-mask-centred slice of the image, the binary mask, and an overlay. The authoritative data are
the raw `.nii.gz` files under `synthstrip_data_v1.5/`. IXI-derived preview rows are CC BY-SA 4.0.

## Citation

> Hoopes A, Mora JS, Dalca AV, Fischl B\*, Hoffmann M\*. **SynthStrip: skull-stripping for any brain
> image.** *NeuroImage*, 260:119474, 2022. doi:10.1016/j.neuroimage.2022.119474 (\*equal contribution)

Please also cite the source archive for whichever subset(s) you use (see the bundled
`synthstrip_data_v1.5/README.txt` for the full per-subset reference list).