READII RUN WITH IDC DATA

Introduction

This repository contains the code to run the READII pipeline on data available from the Imaging Data Commons (IDC).

The pipeline is designed to extract radiomic features from DICOM images representing CT scans paired with segmentation masks as RTSTRUCTs.;

The python packages used are:

• readii
• med-imagetools

Notebooks

All notebooks are located in the notebooks/ directory.

notebooks/0_DownloadPreparation.ipynb

This will download the data from the IDC dataset and prepare it for the next steps

Directory Structure

notebooks/data/images/nsclc_radiomics//
├── dicoms/
│   ├── Patient-LUNG1-101/
│   │   └── StudyUID-27911/
│   │       ├── CT_SeriesUID-55665/
│   │       └── RTSTRUCT_SeriesUID-25865/
│   ├── Patient-LUNG1-108/
│   │   └── StudyUID-62453/
│   │       ├── CT_SeriesUID-81484/
│   │       └── RTSTRUCT_SeriesUID-99496/
│   └── Patient-LUNG1-162/
│       └── StudyUID-21249/
│           ├── CT_SeriesUID-72433/
│           └── RTSTRUCT_SeriesUID-38612/
└── niftis/
    ├── SubjectID-0_LUNG1-162/
    │   └── StudyUID-21249/
    │       ├── CT_SeriesUID-72433/
    │       │   ├── original.nii.gz
    │       │   ├── randomized_sampled_full.nii.gz
    │       │   ├── randomized_sampled_non_roi.nii.gz
    │       │   ├── randomized_sampled_roi.nii.gz
    │       │   ├── shuffled_full.nii.gz
    │       │   ├── shuffled_non_roi.nii.gz
    │       │   └── shuffled_roi.nii.gz
    │       └── RTSTRUCT_SeriesUID-38612/
    │           └── GTV.nii.gz
    ├── SubjectID-1_LUNG1-101/
    │   └── StudyUID-27911/
    │       ├── CT_SeriesUID-55665/
    │       │   ├── original.nii.gz
    │       │   ├── randomized_sampled_full.nii.gz
    │       │   ├── randomized_sampled_non_roi.nii.gz
    │       │   ├── randomized_sampled_roi.nii.gz
    │       │   ├── shuffled_full.nii.gz
    │       │   ├── shuffled_non_roi.nii.gz
    │       │   └── shuffled_roi.nii.gz
    │       └── RTSTRUCT_SeriesUID-25865/
    │           └── GTV.nii.gz
    └── SubjectID-2_LUNG1-108/
        └── StudyUID-62453/
            ├── CT_SeriesUID-81484/
            │   ├── original.nii.gz
            │   ├── randomized_sampled_full.nii.gz
            │   ├── randomized_sampled_non_roi.nii.gz
            │   ├── randomized_sampled_roi.nii.gz
            │   ├── shuffled_full.nii.gz
            │   ├── shuffled_non_roi.nii.gz
            │   └── shuffled_roi.nii.gz
            └── RTSTRUCT_SeriesUID-99496/
                └── GTV.nii.gz