---
license: cc-by-4.0
language:
- en
- zh
tags:
- medical-imaging
- neuroimaging
- segmentation
- brain
- mri
- ct
task_categories:
- image-segmentation
size_categories:
- 1K<n<10K
---

# Multi-Modal Neuroimaging Segmentation Dataset

This comprehensive dataset contains four major categories of neuroimaging segmentation tasks, designed for developing and evaluating deep learning models in medical image analysis. The dataset includes whole brain segmentation, subcortical structure segmentation, stroke and white matter lesion segmentation, and brain tumor segmentation.

## Dataset Overview

The dataset encompasses multiple imaging modalities and segmentation tasks with standardized formats and consistent quality control. Each category contains preprocessed images with corresponding segmentation masks from various publicly available datasets.

| Category | Task | Imaging Modality | Data Sources | File Format |
|----------|------|------------------|--------------|-------------|
| Whole Brain Segmentation | Full brain tissue segmentation | T1-weighted MRI | CANDI, JHU_Full, Mindboggle  | NIfTI (.nii/.nii.gz) |
| Subcortical Structure Segmentation | Subcortical structures (hippocampus, amygdala, thalamus, etc.) | T1-weighted MRI | ASHSUMC_Merge, MICCAI2012, cerebrum_data  | NIfTI (.nii/.nii.gz) |
| Stroke and White Matter Lesions | Lesion detection and segmentation | T2/FLAIR MRI | ATLAS_2_data, White_Matter | NIfTI (.nii/.nii.gz) |
| Brain Tumor Segmentation | Glioma segmentation | Multi-modal MRI | Brats| NIfTI (.nii/.nii.gz) |

## Data Structure

```
Multi-Modal_Neuroimaging_Segmentation_Dataset/
├── Brain Tumor Segmentation/
│   └── Brats/
│       └── BraTS19_TCIA10_241_1/
│           ├── t1.nii.gz
│           ├── t1ce.nii.gz
│           ├── t2.nii.gz
│           ├── flair.nii.gz
│           └── seg.nii.gz
│       └── BraTS19_TCIA10_261_1/
│           ├── t1.nii.gz
│           ├── t1ce.nii.gz
│           ├── t2.nii.gz
│           ├── flair.nii.gz
│           └── seg.nii.gz
│       └── ...
├── Stroke and White Matter Lesions/
│   ├── ATLAS_2_data/
│   │   ├── image/
│   │   │   - sub-r002s001_ses-1.gz
│   │   │   - sub-r002s002_ses-1.gz
│   │   │   - sub-r002s003_ses-1.gz
│   │   │   - sub-r002s004_ses-1.gz
│   │   │   - sub-r002s005_ses-1.gz
│   │   │   - ... 
│   │   └── label/
│   │       - sub-r002s001_ses-1.nii
│   │       - sub-r002s002_ses-1.nii
│   │       - sub-r002s003_ses-1.nii
│   │       - sub-r002s004_ses-1.nii
│   │       - sub-r002s005_ses-1.nii
│   │       - ... 
│   └── White_Matter/
│       ├── image/
│       │   - Utrecht_0.nii.gz
│       │   - Utrecht_11.nii.gz
│       │   - Utrecht_17.nii.gz
│       │   - Utrecht_19.nii.gz
│       │   - Utrecht_2.nii.gz
│       │   - ... 
│       └── label/
│           - Utrecht_0.nii.gz
│           - Utrecht_11.nii.gz
│           - Utrecht_17.nii.gz
│           - Utrecht_19.nii.gz
│           - Utrecht_2.nii.gz
│           - ... 
├── Subcortical Structure Segmentation/
│   ├── ASHSUMC_Merge/
│   │   └── image/
│   │       - ASHSUMC_000.nii.gz
│   │       - ASHSUMC_001.nii.gz
│   │       - ASHSUMC_002.nii.gz
│   │       - ASHSUMC_003.nii.gz
│   │       - ASHSUMC_004.nii.gz
│   │       - ... 
│   ├── MICCAI2012/
│   │   ├── image/
│   │   │   - 1000_3.nii
│   │   │   - 1001_3.nii
│   │   │   - 1002_3.nii
│   │   │   - 1006_3.nii
│   │   │   - 1007_3.nii
│   │   │   - ... 
│   │   └── label/
│   │       - new_1000_3_glm.nii
│   │       - new_1001_3_glm.nii
│   │       - new_1002_3_glm.nii
│   │       - new_1006_3_glm.nii
│   │       - new_1007_3_glm.nii
│   │       - ... 
│   └── cerebrum_data/
│       ├── image/
│       │   - sub-008_ses-001.gz
│       │   - sub-008_ses-002.gz
│       │   - sub-008_ses-003.gz
│       │   - sub-008_ses-004.gz
│       │   - sub-011_ses-001.gz
│       │   - ... 
│       └── label/
│           - sub-008_ses-001.gz
│           - sub-008_ses-002.gz
│           - sub-008_ses-003.gz
│           - sub-008_ses-004.gz
│           - sub-011_ses-001.gz
│           - ... 
└── Whole Brain Segmentation/
    ├── CANDI/
    │   ├── image/
    │   │   - BPDwPsy_065_MR.nii.gz
    │   │   - BPDwPsy_066_MR.nii.gz
    │   │   - BPDwPsy_067_MR.nii.gz
    │   │   - BPDwPsy_068_MR.nii.gz
    │   │   - BPDwPsy_069_MR.nii.gz
    │   │   - ... 
    │   ├── label/
    │   │   - BPDwPsy_065_MR.nii.gz
    │   │   - BPDwPsy_066_MR.nii.gz
    │   │   - BPDwPsy_067_MR.nii.gz
    │   │   - BPDwPsy_068_MR.nii.gz
    │   │   - BPDwPsy_069_MR.nii.gz
    │   │   - ... 
    │   └── dataset.json
    ├── JHU_Full/
    │   ├── image/
    │   │   - Adt27-55_01_Adt27-55_01.nii.gz
    │   │   - Adt27-55_02_Adt27-55_02.nii.gz
    │   │   - Adt27-55_03_Adt27-55_03.nii.gz
    │   │   - Adt27-55_04_Adt27-55_04.nii.gz
    │   │   - Adt27-55_05_Adt27-55_05.nii.gz
    │   │   - ... 
    │   └── label/
    │       - Adt27-55_01_Adt27-55_01.nii.gz
    │       - Adt27-55_02_Adt27-55_02.nii.gz
    │       - Adt27-55_03_Adt27-55_03.nii.gz
    │       - Adt27-55_04_Adt27-55_04.nii.gz
    │       - Adt27-55_05_Adt27-55_05.nii.gz
    │       - ... 
    └── Mindboggle/
        ├── image/
        │   - Afterthought-1.gz
        │   - HLN-12-1.gz
        │   - HLN-12-10.gz
        │   - HLN-12-11.gz
        │   - HLN-12-12.gz
        │   - ... 
        └── label/
            - Afterthought-1.gz
            - HLN-12-1.gz
            - HLN-12-10.gz
            - HLN-12-11.gz
            - HLN-12-12.gz
            - ... 
```