# MMB-MRI Dataset

MMB-MRI is a high-resolution multimodal mouse brain MRI dataset organized in a case-wise layout for public release.

The current release contains 75 mouse brains divided into two cohorts:

- `cohort_47mouse`: 47 cases with six MRI modalities and manually corrected 50-region labels.
- `cohort_28mouse`: 28 additional cases with five MRI modalities and atlas-mapped 50-region labels.

All image volumes are provided in NIfTI format. MRI images are stored as `.nii` files and label maps are stored as `.nii.gz` files.

## Directory Layout

```text
dataset_by_case/
  atlas_dorr_114labels.nii
  cohort_47mouse/
    <case_id>/
      images/
        QSMs.nii
        R2s.nii
        T1.nii
        T2.nii
        T2s.nii
        iMag.nii
      labels/
        label_50regions.nii.gz
  cohort_28mouse/
    <case_id>/
      images/
        QSMs.nii
        R2s.nii
        T2.nii
        T2s.nii
        iMag.nii
      labels/
        label_50regions.nii.gz
  metadata/
    case_manifest.csv
    label_mapping.csv
```

## Data Description

- `atlas_dorr_114labels.nii`: shared anatomical reference atlas with the original Dorr atlas labels.
- `cohort_47mouse/<case_id>/images/`: six co-registered MRI modalities (`QSMs`, `R2s`, `T1`, `T2`, `T2s`, `iMag`).
- `cohort_47mouse/<case_id>/labels/label_50regions.nii.gz`: manually corrected 50-region label map.
- `cohort_28mouse/<case_id>/images/`: five co-registered MRI modalities (`QSMs`, `R2s`, `T2`, `T2s`, `iMag`).
- `cohort_28mouse/<case_id>/labels/label_50regions.nii.gz`: atlas-mapped 50-region label map distributed with this release.

## Label Provenance

The shared atlas follows the Dorr mouse brain atlas labeling. The released benchmark label scheme consolidates the atlas annotations into 50 anatomical regions plus background. Labels in `cohort_47mouse` were manually corrected. Labels in `cohort_28mouse` were generated by atlas mapping into native image space and label remapping.

## Metadata

- `metadata/case_manifest.csv`: case-level inventory of cohort membership, modalities, label availability, and label provenance.
- `metadata/label_mapping.csv`: minimal public mapping table from the original atlas labels to the released 50-region label scheme.

## Dataset Summary

- Total cases: 75
- `cohort_47mouse`: 47 cases, 6 modalities per case
- `cohort_28mouse`: 28 cases, 5 modalities per case