Importing images - rubpergar/3D-Slicer-guide GitHub Wiki

📥 Importing Images

In this section, you will learn how to import medical images into 3D Slicer, using DICOM images from patients with non-small cell lung cancer (NSCLC).

🔍 Patient Data

In the images folder of this repository, you will find images corresponding to two patients from the public NSCLC-Radiomics dataset, available on The Cancer Imaging Archive (TCIA).

These images were extracted from the following study:

Aerts, H. J. W. L., Wee, L., Rios Velazquez, E., Leijenaar, R. T. H., Parmar, C., Grossmann, P., Carvalho, S., Bussink, J., Monshouwer, R., Haibe-Kains, B., Rietveld, D., Hoebers, F., Rietbergen, M. M., Leemans, C. R., Dekker, A., Quackenbush, J., Gillies, R. J., Lambin, P. (2014). Data From NSCLC-Radiomics (version 4) [Data set]. The Cancer Imaging Archive.
📎 https://doi.org/10.7937/K9/TCIA.2015.PF0M9REI

This dataset contains images of 422 patients with NSCLC, including pre-treatment CT scans along with manually segmented tumor volumes by a radiation oncologist.

⚠️ Data Usage

The NSCLC-Radiomics dataset is licensed under Creative Commons Attribution-NonCommercial 3.0 (CC BY-NC 3.0). This means that:

✔️ Use, distribution, and modification of the content are allowed, as long as proper credit is given to the original authors.
❌ Commercial use is not permitted without explicit permission from the dataset owners.

This material has been used exclusively for educational and research purposes within the scope of this guide.

📜 More information about the license:
🔗 Creative Commons BY-NC 3.0

📂 Folder Structure

Inside the images folder, you will find two subfolders: LUNG1-001 and LUNG1-006, each corresponding to a different patient. Each of these folders contains three directories:

  • CT/ 📸 → Contains the CT scan images in DICOM format.
  • RTSTRUCT/ 🎯 → DICOM files that store anatomical structures and manually segmented tumors.
  • SEG/ 🧩 → DICOM SEG files containing structured segmentations.

Additionally, a ZIP file is included, compressing these three folders for easier download.

📜 What is DICOM?

DICOM (Digital Imaging and Communications in Medicine) is the standard format for storing and transmitting medical images. It allows the inclusion of patient information, acquisition metadata, and segmentations within a single file.

3D Slicer includes a built-in DICOM manager, which facilitates the import and visualization of these images.

🖥️ Importing Images into 3D Slicer

To correctly import the images into 3D Slicer, follow these steps:

📂 1. Download and Extract the Files

  1. Download the ZIP file for the desired patient (e.g., LUNG1-006.zip).
  2. Extract the ZIP content, obtaining the three folders: CT, RTSTRUCT, and SEG.

📥 2. Import DICOM Files into 3D Slicer

  1. Open 3D Slicer.

  2. In the top menu, select DICOM to access the image manager.

  3. Click Import DICOM files... and select the DICOM files from each folder.

✅ 3. Verify the Import

  1. In the DICOM Database section, you should see the imported images correctly listed.

  2. Once verified, you can proceed with visualization and analysis in 3D Slicer.

🎯 Now you're ready to explore and analyze medical images in 3D Slicer! 🚀

⏮️ 🚀 Start

⬅️ Previous: 🛠️ Environment Setup

➡️ Next: 👀 Visualization