The EMIDEC dataset consists of 100 training (33 normal cases and 67 pathological cases) and 50 testing DE-MRI images. Labels on test set are not provided. The segmentaiton labels of myocardium, cavity, myocardial infarction and no-reflow are provided. Images are stored in NIfTI format. After resampling to 1mm x 1mm x 10mm, images have 5-10 slices.
Note
It is recommended to download the dataset to download the data under ~/.cache/cinema_datasets/emidec as the
integration tests uses this path. Otherwise define the path using environment variable CINEMA_DATA_DIR.
The dataset can be downloaded from https://emidec.com/.
After unzipping, the files will have the following structure:
emidec-dataset-1.0.1.zip
emidec-segmentation-testset-1.0.0.zip
emidec-dataset-1.0.1/
├── Readme.txt
├── Case N006.txt
├── Case N012.txt
├── ...
├── Case_N006/
│ ├── Contours/
│ │ └── Case_N006.nii.gz
│ ├── Images/
│ └── Case_N006.nii.gz
├── Case_N012/
│ ├── Contours/
│ │ └── Case_N006.nii.gz
│ ├── Images/
│ └── Case_N006.nii.gz
├── ...
In the case name, N stands for normal, M for myocardial infarction, P for pathological. The Case N006.txt file
contains the sex, age, and other information about the patient.
Case N006
Gap between slices†: 10 mm
Sex†: F
Age : 70
Tobacco : 3
Overweight : N
Arterial hypertension : Y
Diabetes : N
Familial history of coronary artery disease: N
ECG (ST +) : Y
Troponin : 1.1
Killip Max: 1
FEVG : 60
NTProBNP : 248
The preprocessing is performed with the following steps:
- resampling images to 1.0 x 1.0 x 10.0 mm.
- cropping the images to 192 x 192 for xy, based on the cavity center.
- normalizing the values to [0, 1].
emidec_preprocessThe CLI requires to install the cinema package at the root of repository with pip install -e ..