| --- |
| 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). |
| |
