DICOM4MICCAI Hands-on
  • Introduction
  • Prerequisites
    • If you are attending the tutorial in-person
    • If you are following on your own
  • Using DICOM to store your analysis results
    • Using 3D Slicer to convert non-DICOM segmentation results
    • DICOM Structured Reporting for radiomics
    • Using 3D Slicer for storing analysis results in DICOM
      • Step 0: 3D Slicer interface basics
      • Step 1: Import DICOM data
      • Step 2: Load DICOM image
      • Step 3: Segment lesions
      • Step 3.1:QuantitativeReporting interface overview
      • Step 3.2: Create and initialize a new segment
      • Step 3.3: Segment the lesions
      • Step 4: Explore and store the analysis results in DICOM
      • Step 5: Reload the analysis results from DICOM
      • Exporting DICOM data from 3D Slicer
    • Using MITK Workbench for storing segmentation results in DICOM
      • Step 0: MITK interface basics
      • Step 1: Import DICOM data
      • Step 2: Load DICOM image
      • Step 3: Segment lesions
      • Step 4: Explore and store the segmentations in DICOM
      • Step 5: Reload the segmentations from DICOM
  • DICOM data wrangling
  • Further reading
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Prerequisites

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Last updated 6 years ago

In this tutorial we will use several open source software tools, and publicly available datasets.

Many of the tools we install here will be helpful to you in the future when you work with DICOM, so think about this as setting up your lab space for the future work!

We prepared packages with the binaries of some of the tools that are largest in size (to reduce reliance on the network) for each of the platforms. Those are linked from this page together with the platform-specific installation instructions. The list of the tools we will be using is provided in the Details section.

Prerequisites that you will need to install on your own

Some of the components of the tutorial will utilize:

  • , various python packages available via pip install

    • pandas

    • seaborn

You will need to have Python environment, pip, and Jupyter Notebook available on your computer to follow those components of the tutorial.

Python
pyradiomics
Jupyter Notebook
dcm2niix