Skip to content

README.md

Latest commit

 

History

History
58 lines (45 loc) · 2.03 KB

README.md

File metadata and controls

58 lines (45 loc) · 2.03 KB
Raw

Multi-Centre, Multi-Vendor & Multi-Disease Cardiac Image Segmentation Challenge (M&Ms)

Caution

Only 345 images are available without restriction. The remaining 30 images require application.

The M&Ms dataset contains 375 images (175 training, 40 validation and 160 testing) acquired by four different scanner vendors in six hospitals across three countries. The pathologies include hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), hypertensive heart disease (HHD), abnormal right ventricle (ARV), athlete heart syndrome (AHS), ischemic heart disease (IHD), and left ventricle non-compaction (LVNC). The segmentation labels of LV, RV, and MYO are provided for ED and ES phases.

Download Dataset

Note

It is recommended to download the dataset to download the data under ~/.cache/cinema_datasets/mnms as the integration tests uses this path. Otherwise define the path using environment variable CINEMA_DATA_DIR.

Download the dataset from the website and unzip the file.

unzip MnM.zip

After unzipping the file, the files will have the following structure:

MnM.zip
OpenDataset/
├── 211230_M&Ms_Dataset_information_diagnosis_opendataset.csv
├── Training/
│   ├── Labeled/
│   │   ├── A0S9V9/
│   │   │   ├── A0S9V9_sa_gt.nii.gz
│   │   │   ├── A0S9V9_sa.nii.gz
│   │   ├── ...
│   ├── Unlabeled/ # images without segmentation labels despite the presence of _gt.nii.gz files
├── Validation/
│   ├── A5C2D2/
│   ├── ...
├── Testing/
│   ├── A1K2P5/

Preprocessing

The preprocessing is performed on ED and ES images with the following steps:

  • resampling the ED/ES SAX images to 1.0 x 1.0 x 10.0 mm.
  • cropping the images to 192 x 192 for xy, based on the LV center at ED frame.
  • normalizing the values to [0, 1].
mnms_preprocess

The CLI requires to install the cinema package at the root of repository with pip install -e ..