Getting Started

Welcome to the 3D Slicer community. This page contains information that you need to get started with 3D Slicer, including how to install and use basic features and where to find more information.

System requirements

3D Slicer runs on any Windows, Mac, or Linux computer that was released in the last 5 years. Older computers may work (depending mainly on graphics capabilites). Slicer can also run on virtual machines and docker containers.

Operating system versions

• Windows: Windows 10, with all recommended updates installed. Windows 10 Version 1903 (May 2019 Update) version is required for support of international characters (UTF-8) in filenames and text. Microsoft does not support Windows 8.1 and Windows 7 anymore and Slicer is not tested on these legacy operating system versions, but may still work.
• macOS: macOS High Sierra (10.13) or later. Latest public release is recommended.
• Linux: Ubuntu 18.04 or later
  CentOS 7 or later. Latest LTS (Long-term-support) version is recommended.

Recommended hardware configuration

• Memory: more than 4GB (8 or more is recommended). As a general rule, have 10x more memory than the amount of data that you load.
• Display: a minimum resolution of 1024 by 768 (1280 by 1024 or better is recommended).
• Graphics: Dedicated graphics hardware (discrete GPU) memory is recommended for fast volume rendering. GPU: Graphics must support minimum OpenGL 3.2. Integrated graphics card is sufficient for basic visualization. Discrete graphics card (such as NVidia GPU) is recommended for interactive 3D volume rendering and fast rendering of complex scenes. GPU texture memory (VRAM) should be larger than your largest dataset (e.g., working with 2GB data, get VRAM > 4GB) and check that your images fit in maximum texture dimensions of your GPU hardware. Except rendering, most calculations are performed on CPU, therefore having a faster GPU will generally not impact the overall speed of the application.
• Some computations in 3D Slicer are multi-threaded and will benefit from multi core, multi CPU configurations.
• Interface device: a three button mouse with scroll wheel is recommended. Pen, multi-touchscreen, touchpad, and graphic tablet are supported. All OpenVR-compatible virtual reality headsets are supported for virtual reality display.
• Internet connection to access extensions, Python packages, online documentation, sample data sets, and tutorials.

Installing 3D Slicer

To download Slicer, click here.

Notes:

• The “Preview Release” of 3D Slicer is updated daily (process starts at 11pm ET and takes few hours to complete) and represents the latest development including new features and fixes.
• The “Stable Release” is usually updated a few times a year and is more rigorously tested.
• Slicer is generally simple to install on all platforms. It is possible to install multiple versions of the application on the same user account and they will not interfere with each other. If you run into mysterious problems with your installation you can try deleting the application settings files.
• Only 64-bit Slicer installers are available to download. Developers can attempt to build 32-bit versions on their own if they need to run Slicer on a 32-bit operating system. That said, this should be carefully considered as many clinical research tasks, such as processing of large CT or MR volumetric datasets, require more memory than can be accommodated with a 32-bit program.

Once downloaded, follow the instructions below to complete installation:

Windows

• Run the installer.
  • Current limitation: Installation path must only contain English (ASCII printable) characters because otherwise some Python packages may not load correctly (see this issue for more details).
• Run Slicer from the Windows start menu
• Use “Apps & features” in Windows settings to remove the application

Mac

• Drag the Slicer application (Slicer.app) to your Applications folder or other location of your choice.
• You cannot install extensions into the read-only volume so you must copy before installing extensions.
• Delete the Slicer.app folder to uninstall

Installing Preview Release: Currently, preview release packages are not signed. Therefore, when the application is started the first time the following message is displayed: “Slicer… can’t be opened because it is from an unidentified developer”. To resolve this error, locate the application in Finder and right-click (two-finger click) and click Open. When it says This app can’t be opened go ahead and hit cancel. Right click again and say Open (yes, you need to repeat the same as you did before - the outcome will be different than the first time). Click the Open (or Open anyway) button to start the application. See more explanation and alternative techniques here.

Linux

• Open the tar.gz archive and copy directory to the location of your choice. Run the Slicer executable.
• Remove the directory to uninstall

Note: Slicer is expected to work on the vast majority of desktop and server Linux distributions. The system is required to provide at least GLIBC 2.17 and GLIBCCC 3.4.19. For more details, read here.

Debian / Ubuntu

The following may be needed on fresh debian or ubuntu:

sudo apt-get install libpulse-dev libnss3 libglu1-mesa
sudo apt-get install --reinstall libxcb-xinerama0

To run Slicer-4.11-2020-09-30 on older debian (e.g. debian 9) you may also need:

sudo apt-get install libxcb-icccm4-dev libxcb-image0-dev libxcb-keysyms1-dev libxcb-randr0 libxcb-render-util0 libxcb-xkb-dev libxkbcommon-x11-dev

ArchLinux

ArchLinux runs the strip utility by default; this needs to be disabled in order to run Slicer binaries. For more information see this thread on the Slicer Forum.

Fedora

Install the dependencies:

sudo dnf install mesa-libGLU libnsl

The included libcrypto.so.1.1 in Slicer-4.11 is incompatible with the system libraries used by Fedora 35. The fix, until it is updated, is to move/remove the included libcrypto files:

$SLICER_ROOT/lib/Slicer-4.11/libcrypto.*

Using Slicer

3D Slicer offers lots of features and gives users great flexibility in how to use them. As a result, new users may be overwhelmed with the number of options and have difficulty figuring out how to perform even simple operations. This is normal and many users successfully crossed this difficult stage by investing some time into learning how to use this software.

How to learn Slicer?

Quick start

You may try to figure out how the application works by loading data sets and explore what you can do.

Load data

Open 3D Slicer and using the Welcome panel either load your own data or download sample data to explore. Sample data is often useful for trying the features of 3D Slicer if you don’t have data of your own.

View data

Data module’s Subject hierarchy tab shows all data sets in the scene. Click the “eye” icon to show/hide an item in all views.

You can customize views (show orientation marker, ruler, change orientation, transparency) by clicking on the push pin in the top left corner of viewer. In the slice viewers, the horizontal bar can be used to scroll through slices or select a slice.

Process data

3D Slicer is built on a modular architecture. Choose a module to process or analyze your data. Most important modules are the followings (complete list is available in Modules section):

• Welcome: The default module when 3D Slicer is started. The panel features options for loading data and customizing 3D Slicer. Below those options are drop-down boxes that contain essential information for using 3D Slicer.
• Data: acts as a central data-organizing hub. Lists all data currently in the scene and allows basic operations such as search, rename, delete and move.
• DICOM: Import and export DICOM objects, such as images, segmentations, strucutre sets, radiation therapy objects, etc.
• Volumes: Used for changing the appearance of various volume types.
• Volume Rendering: Provides interactive visualization of 3D image data.
• Segmentations: Edit display properties and import/export segmentations.
• Segment Editor: Segment 3D volumes using various manual, semi-automatic, and automatic tools.
• Markups: Allows the creation and editing of markups associated with a scene. Currently, lists of fiducially are supported as markups.
• Models: Loads and adjusts display parameters of models. Allows the user to change the appearance of and organize 3D surface models.
• Transforms: This module is used for creating and editing transformation matrices. You can establish these relations by moving nodes from the Transformable list to the Transformed list or by dragging the nodes under the Transformation nodes in the Data module.

Save data

Data sets loaded into the application can be saved using Save data dialog or exported to DICOM format using DICOM module. Detailes are described in Data loading and saving section.

Extensions

3D Slicer supports plug-ins that are called extensions. An extension could be seen as a delivery package bundling together one or more Slicer modules. After installing an extension, the associated modules will be presented to the user as built-in ones. Extensions can be downloaded from the extensions manager to selectively install features that are useful for the end-user.

For details about downloading extensions, see Extensions Manager documentation. Click here for a full list of extensions. The links on the page will provide documentation for each extension.

Slicer is extensible. If you are interested in customizing or adding functionality to Slicer, click here.

Tutorials

You learn both basic concepts and highly specialized workflows from the numerous available step-by-step and video tutorials.

Try the Welcome Tutorial and the Data Loading and 3D Visualization Tutorial to learn the basics.

For more tutorials, visit the Tutorial page.

User manual

Browse the User Guide section to find quick overview of the application user interface or Modules section for detailed description of each module.

Ask for help

3D Slicer has been around for many years and many questions have been asked and answered about it already. If you have any questions, then you may start with a web search, for example Google slicer load jpg to find out how you can import a stack of jpg images.

The application has a large and very friendly and helpful user community. We have poeple who will happy to help with simple questions, such as how to do a specific task in Slicer, and we have a large number of engineering and medical experts who can give you advice with how to solve complex problems.

If you have any questions, go to the Slicer forum and ask us!