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 · Harvard Dataverse — individual brains doi: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.