External data

MURLs

 MURLs ()

A class with external medical dataset URLs.

IXI

source

download_ixi_data

 download_ixi_data (path:(<class'str'>,<class'pathlib.Path'>)='../data')

*Download T1 scans and demographic information from the IXI dataset.

Args: path: Path to the directory where the data will be stored. Defaults to ‘../data’.

Returns: The path to the stored CSV file.*

IXITiny

source

download_ixi_tiny

 download_ixi_tiny (path:(<class'str'>,<class'pathlib.Path'>)='../data')

*Download the tiny version of the IXI dataset provided by TorchIO.

Args: path: The directory where the data will be stored. If not provided, defaults to ‘../data’.

Returns: The path to the directory where the data is stored.*

Lower spine data

source

download_spine_test_data

 download_spine_test_data
                           (path:(<class'str'>,<class'pathlib.Path'>)='../
                           data')

*Downloads T2w scans from the study ‘Fully Automatic Localization and Segmentation of 3D Vertebral Bodies from CT/MR Images via a Learning-Based Method’ by Chu et. al.

Args: path: Directory where the downloaded data will be stored and extracted. Defaults to ‘../data’.

Returns: Processed dataframe containing image paths, label paths, and subject IDs.*

source

download_example_spine_data

 download_example_spine_data
                              (path:(<class'str'>,<class'pathlib.Path'>)='
                              ../data')

*Downloads example T2w scan and corresponding predicted mask.

Args: path: Directory where the downloaded data will be stored and extracted. Defaults to ‘../data’.

Returns: Path to the directory where the example data has been extracted.*

MedMNIST3D

source

download_medmnist3d_dataset

 download_medmnist3d_dataset (study:str,
                              path:(<class'str'>,<class'pathlib.Path'>)='.
                              ./data', max_workers:int=1,
                              skip_download:bool=True)

*Downloads and processes a particular MedMNIST3D dataset.

Args: study: MedMNIST dataset (‘OrganMNIST3D’, ‘NoduleMNIST3D’, ‘AdrenalMNIST3D’, ‘FractureMNIST3D’, ‘VesselMNIST3D’, ‘SynapseMNIST3D’) path: Directory to store and extract downloaded data. Defaults to ‘../data’. max_workers: Maximum number of worker processes for data processing. Defaults to 1. skip_download: Flag to indicate if the dataset should be re-downloaded if the dataset exists locally. Default set to False.

Returns: Two pandas DataFrames. The first DataFrame combines training and validation data, and the second DataFrame contains the testing data.*

Endometrical cancer

source

download_example_endometrial_cancer_data

 download_example_endometrial_cancer_data
                                           (path:(<class'str'>,<class'path
                                           lib.Path'>)='../data',
                                           multi_channel:bool=True)

*Download example data for endometrial cancer.

Args: path (str or Path): Path to save the downloaded data. multi_channel (bool): If True, download multi-channel data (Vibe, T2, and ADC). Otherwise, download only Vibe.*