| --- |
| license: cc-by-nc-sa-3.0 |
| pretty_name: Mindboggle-101 |
| tags: |
| - medical |
| - mri |
| - brain |
| - t1-weighted |
| - cortical-parcellation |
| - brain-segmentation |
| - neuroimaging |
| task_categories: |
| - image-segmentation |
| size_categories: |
| - n<1K |
| dataset_info: |
| features: |
| - name: subject_id |
| dtype: string |
| - name: cohort |
| dtype: string |
| - name: source_archive |
| dtype: string |
| - name: sex |
| dtype: string |
| - name: age |
| dtype: string |
| - name: image_shape |
| dtype: string |
| - name: num_slices |
| dtype: int32 |
| - name: voxel_spacing |
| dtype: string |
| - name: num_cortical_regions |
| dtype: int32 |
| - name: image |
| dtype: image |
| - name: mask |
| dtype: image |
| - name: overlay |
| dtype: image |
| splits: |
| - name: train |
| num_bytes: 9419820 |
| num_examples: 101 |
| download_size: 9426186 |
| dataset_size: 9419820 |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train-* |
| --- |
| |
| # Mindboggle-101 |
|
|
| Manually-labeled cortical parcellations for **101 healthy-adult T1-weighted brain MRI** volumes, |
| following the Desikan-Killiany-Tourville (DKT) protocol. This is the largest set of consistently, |
| manually labeled human brains and is the reference behind the DKT cortical atlas shipped inside |
| FreeSurfer. |
|
|
| > **Scope of this mirror — read before use.** This repository is the **volumetric** subset of the |
| > full Mindboggle-101 distribution: image volumes + manual **cortical** label volumes. The |
| > FreeSurfer **surface** meshes/labels and the **shape-feature tables** that the official deposit |
| > also contains are **not** included (they are not voxel segmentation masks) — obtain them from the |
| > Harvard Dataverse DOIs below. The **whole-brain (cortex+subcortex) volume labels** for the |
| > OASIS-TRT-20 cohort, and the per-subject `+aseg` (cortical+subcortical) variants, are **excluded** |
| > — see *Licensing*. |
|
|
| ## Contents |
|
|
| **101 subjects**, one T1 brain each, organized by **source cohort** (no train/val/test split): |
|
|
| | Cohort | N | Origin archive | |
| |---|---|---| |
| | NKI-RS-22 | 22 | Nathan Kline Institute – Rockland Sample | |
| | MMRR-21 | 21 | Multi-Modal MRI Reproducibility Resource | |
| | NKI-TRT-20 | 20 | NKI Test–Retest | |
| | OASIS-TRT-20 | 20 | OASIS cross-sectional, test–retest | |
| | Extra-18 | 18 | HLN-12 + MMRR-3T7T-2 + Twins-2 + Colin27-1 + Afterthought-1 | |
| | **Total** | **101** | | |
|
|
| Per subject — `<Cohort>_volumes/<Subject-ID>/`: |
|
|
| | File | Description | |
| |---|---| |
| | `t1weighted.nii.gz` | Native-space T1 (≈256³, 1 mm isotropic, `int16`) | |
| | `t1weighted_brain.nii.gz` | Skull-stripped native T1 | |
| | `t1weighted.MNI152.nii.gz` | T1 affinely registered to MNI152 | |
| | `t1weighted_brain.MNI152.nii.gz` | Skull-stripped T1 in MNI152 | |
| | `t1weighted_brain.MNI152.affine.txt` | Native→MNI152 affine | |
| | **`labels.DKT31.manual.nii.gz`** | **Gold-standard manual DKT31 cortical labels (native space)** | |
| | `labels.DKT31.manual.MNI152.nii.gz` | Same labels in MNI152 space | |
|
|
| Also at the repo root: `subject_sources_Mindboggle101.txt`, `subject_list_Mindboggle101.txt`, |
| `label_definitions.txt`, `label-issues_201903.txt`, `subject_table_Mindboggle101.pdf`, |
| `scans/` (per-cohort acquisition info), and the Apache-2.0 `code_*` helper files. |
|
|
| ## Ground truth & label scheme |
|
|
| **Recommended evaluation reference: `labels.DKT31.manual.nii.gz`** — manually-edited cortical |
| parcellation, **62 cortical regions** (31 per hemisphere) + background. FreeSurfer/`aparc`-style |
| integer codes are stored as `float32` (cast to int on load): |
|
|
| - Left hemisphere `1002–1035`; right hemisphere `2002–2035`. Codes are **non-contiguous** (e.g. |
| 1004/1032/1033 absent — those regions are excluded under DKT31); **remap to a contiguous 0…62 |
| range** for training/scoring. |
| - Region names per code: see **`label_definitions.txt`**. |
| - Cortex is a thin ribbon → ~95 % of voxels are background (label 0); expect strong class imbalance. |
| |
| The reduced **DKT25** scheme and the FreeSurfer-`aseg` whole-brain variants exist only in the |
| surface / `+aseg` products and are **not** in this volumetric mirror. |
| |
| ## Cross-dataset overlap (important) |
| |
| Every Mindboggle-101 subject is **drawn from another public dataset** (OASIS, NKI-RS, NKI-TRT, |
| MMRR, the MNI Colin27 template). Before combining this with any **OASIS- or NKI-derived** benchmark, |
| **de-duplicate** using **`subject_sources_Mindboggle101.txt`** (preserved at the repo root), which |
| maps each Mindboggle ID (e.g. `OASIS-TRT-20-1`) back to its original-archive identifier. The DKT |
| atlas derived from these brains also ships inside FreeSurfer (`aparc.DKTatlas`), and CerebrA is a |
| corrected MNI-registered derivative. No shared lineage with the BraTS family or the Medical |
| Segmentation Decathlon. |
| |
| ## Licensing (per component) |
| |
| This mirror follows the **authors' own copyright notices shipped inside the data**, which are more |
| authoritative than third-party host tags: |
| |
| | Component | License | Where stated | |
| |---|---|---| |
| | T1 images + manual DKT cortical labels (the 101 subjects) | **CC BY-NC-SA 3.0** | `subject_sources_Mindboggle101.txt` (Mindboggle team, 2012) | |
| | Labeling-protocol doc + helper code (`label_definitions.txt`, `code_*`) | Apache-2.0 | bundled file headers | |
| | *(excluded)* OASIS-TRT-20 whole-brain cortex+subcortex labels | CC BY-NC-ND 3.0 | Neuromorphometrics BrainCOLOR-derived | |
| |
| - The repo `license:` tag is **`cc-by-nc-sa-3.0`**, reflecting the image+label data (the primary |
| content): **non-commercial**, **attribution** required, derivatives **shared alike**. |
| - Harvard Dataverse tags the primary image/label files **CC0**; we intentionally adopt the **more |
| restrictive** CC BY-NC-SA 3.0 from the authors' bundled notice as the safer reading of the |
| conflicting signals (NITRC also lists CC BY-NC-SA 3.0). |
| - The CC BY-NC-ND **subcortical** whole-brain labels were dropped so this repository can be cleanly |
| redistributed and previewed; obtain them from the Dataverse DOI below if required. |
| |
| ## Provenance & source |
| |
| Author-maintained: <https://mindboggle.info/data.html> · OSF [`nhtur`](https://osf.io/nhtur/) · |
| Harvard Dataverse — individual brains [`doi:10.7910/DVN/HMQKCK`](https://doi.org/10.7910/DVN/HMQKCK) |
| (**this mirror's source**), atlases `doi:10.7910/DVN/XCCE9Q`, templates `doi:10.7910/DVN/WDIYB5`. |
| Subject count verified against the paper: **101/101**. |
| |
| ## `data/` preview |
| |
| The `data/` directory holds a Parquet preview (middle-axial-slice PNG + cortical-label overlay per |
| volume) for the Hugging Face Dataset Viewer. Previews are rendered **only** from the CC BY-NC-SA |
| cortical labels. The authoritative data are the raw `.nii.gz` files in the `*_volumes/` folders. |
| |
| ## Citation |
| |
| > Klein A, Tourville J. *101 labeled brain images and a consistent human cortical labeling |
| > protocol.* Frontiers in Neuroscience 6:171, 2012. doi:10.3389/fnins.2012.00171 |
| |
| Please also acknowledge the source archives (OASIS, NKI / Rockland, MMRR) per their terms when |
| using the corresponding cohorts. |
| |
