> For the complete documentation index, see [llms.txt](https://qiicr.gitbook.io/dicom4miccai-handson/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://qiicr.gitbook.io/dicom4miccai-handson/prerequisites/if-you-are-attending-the-tutorial-in-person.md). # 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): * [Windows](https://github.com/QIICR/dicom4miccai-handson/releases/download/miccai2017/DICOM4MICCAI-Win64.zip) * [macOS](https://github.com/QIICR/dicom4miccai-handson/releases/download/miccai2017/DICOM4MICCAI-macOS.zip) * [Linux](https://github.com/QIICR/dicom4miccai-handson/releases/download/miccai2017/DICOM4MICCAI-Linux.zip) ## 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: ![](https://qiicr.gitbooks.io/quantitativereporting-guide/docs/screenshots/extension_manager.png) 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). ![](https://1608672434-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LM8e4_Fqz67WxPLjNdd%2F-LMEhqcQYXiWX_3suBNI%2F-LMEk8PEZGUeqWgJ5gC5%2Fimage.png?alt=media\&token=1f34a60b-5491-427f-8113-44b6844d996d) The dataset includes data from 5 collections of [The Cancer Imaging Archive (TCIA)](https://www.cancerimagingarchive.net/): * [TCGA-LGG](https://wiki.cancerimagingarchive.net/display/Public/TCGA-LGG) * [TCGA-GBM](https://wiki.cancerimagingarchive.net/display/Public/TCGA-GBM) * QIN-PROSTATE-Repeatability (not yet released) * [QIN-HEADNECK](https://wiki.cancerimagingarchive.net/display/Public/QIN-HEADNECK) * [LIDC-IDRI](https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI) **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 | |