Datasets:

Gipsy666
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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
            - ...

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