The OpenMind Dataset: A large-scale Head-And-Neck 3D MRI Dataset for self-supervised learning

Description

The OpenMind Dataset is a large-scale 3D MRI dataset of the head and neck region featuring 114k MRI Images. Its purpose is to provide access of large amounts of 3D medical imaging data to accelerate the development of self-supervised learning methods for 3D medical imaging. This data was pooled from exactly 800 datasets from the OpenNeuro platform and provides 23 different MRI modalities/techniques from over 30 different scanners, representing a highly variable pre-training dataset.

Additional Features

Aside from the 3D MRI Images, we provide stratified metadata for each of the 114k images when made available by the original dataset in a unified format. Moreover, we provide a) deface_masks, which delineate anonymized/defaced regions, allowing to take them into account when developing reconstruction based pre-training methods and b) anatomy_masks, which delineate areas which holds anatomy, e.g. for cases where images were brain extracted. Similarly to the deface_masks this allows to either ignore regions outside of this during reconstruction and allows sampling regions with anatomy, avoiding empty regions for contrastive learning approaches.

Dataset structure

The dataset is structured akin to the original OpenNeuro datasets, following a modified BIDS format, exemplified below. We recommend using the openneuro_metadata.csv which holds the relative paths from the root directory to the images and their associated masks as well as metadata.

-- Readme.md    // this readme 
-- openneuro_metadata.csv  // metadata file containing the relative paths to the images and their metadata
-- openmind_dataset
    |-- openneuro_metadata.csv     # Contains the relative paths to the images and their metadata
    |-- OpenMind
        |-- ds_000001
            |-- sub-01
                |-- anat
                    |-- sub-01_ses-01_T1w.nii.gz  # 3D Image in Nifti format 
                    |-- sub-01_T1w__Data          # Associated Folder holding Masks to Image
                        |-- deface_mask.nii.gz      # deface mask
                        \-- fb_mask.nii.gz          # anatomy mask
                    |-- sub-01_inplaneT2.nii.gz
                    \-- sub-01_inplaneT2__Data   # Associated Folder holding Masks to Image
                        |-- deface_mask.nii.gz
                        \-- fb_mask.nii.gz
                ...
            ...
        ...
        |-- ds_xxxxxx
        ...

Available meta-data tags (Name [Percent of images with this metadata]) within the metadata.csv file are:

• MR Modalitiy/Technique [100%]
• Scanner Manufacturer [100%]
• Scanner Model [100%]
• Scanner Field Strength [100%]
• Age [70%]
• Sex [77.4%]
• Weight [1.5%]
• BMI [15.7%]
• Race [11.7%]
• Handedness (right/left/ambidexterous) [35.4%]
• Health Status (healthy/ill) [26.4%]