If you are attending the tutorial in-person
Step 1: Download the software package for your platform
If you are attending the tutorial in-person: we will be providing USB drives with the software. Copy the package for your platform to your computer.
If you are preparing for the tutorial beforehand, or are following it on your own: use the links below to download the package (all packages are for 64-bit operating systems):
Step 2: Install the software
First, extract the package you downloaded. We will further refer to the location of the extracted folder as DICOM4MICCAI_ROOT.
Next, install the software tools that require installation (3D Slicer and Atom editor), following the platform-specific instructions below.
Note, that if you have an older version of 3D Slicer, you will need to install the one we provide! Although we use a standard 3D Slicer package, we will be using functionality introduced relatively recently.
Windows
Double-click the installers for 3D Slicer and Atom editor to install these tools.
macOS
Open the 3D Slicer package (.dmg file), then drag the 3D Slicer icon in the opened volume to your Applications folder (if you don't do this, Slicer will not function properly!).
To install Atom editor, unzip the Atom.zip file, and drag the Atom icon to your Applications folder.
Linux
Extract the 3D Slicer application from the Slicer-4.9.0-2018-09-10-linux-amd64.tar.gz file.
Install Atom using the .deb or .rpm package.
Step 3: Configure the software
Install 3D Slicer extensions
Launch the 3D Slicer application. Start 3D Slicer and open Extension Manager by clicking this button in the toolbar:
Next, click the "wrench" icon in the upper right corner of the Extension Manager window, and click the "Install Extension from File..."
One by one, install each of the files that are located in the SlicerExtensions folder in DICOM4MICCAI_ROOT.
Install dicom-dump Atom package
Windows: go to menu item File > Settings > Install
Mac: go to menu item Atom > Preferences > Install
Linux: go to menu item Edit > Preferences > Install
Search for dicom-dump package, click "Install" button when found.
Once installed, click dicom-dump "Settings" button, locate the entry with the name "Path to DCMTK installation", and set this path to point to the bin directory in the DICOM4MICCAI_ROOT/dcmtk/bin.
Step 4: Datasets
To keep the data that we will use in the tutorial, make a sub-folder Data in the DICOM-tutorial folder we created earlier.
At the tutorial, we will provide a flash drive with the dataset (see below).
The dataset includes data from 5 collections of The Cancer Imaging Archive (TCIA):
QIN-PROSTATE-Repeatability (not yet released)
NOTE: The image data (CT, MR, PET) used in the tutorial datasets are identical to the TCIA content. The segmentations, measurements and radiomics features stored in DICOM are not yet available on TCIA. We are augmenting those TCIA imaging datasets with the image-derived data in the near future. The dataset we use in the tutorial is a representative example of the data that we expect to make available on TCIA publicly in the near future.
Details on the software used
Software
Information
Home page
3D Slicer
Free open source software platform for medical image informatics, image processing, and three-dimensional visualization.
DCMTK
DCMTK is a free open source collection of libraries and applications implementing large parts the DICOM standard.
dcmqi
Free open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation.
Atom
A hackable text editor for the 21st Century
dicom-dump
An Atom package that simplifies examining the content of DICOM files
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