Documentation/Nightly/FAQ/General

For the latest Slicer documentation, visit the read-the-docs.

General

What is Slicer ?

3D Slicer is:

• A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.
• A free, open source software available on multiple operating systems: Linux, MacOSX and Windows
• Extensible, with powerful plug-in capabilities for adding algorithms and applications.

Features include:

• Multi organ: from head to toe.
• Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy.
• Bidirectional interface for devices.

There is no restriction on use, but Slicer is not approved for clinical use and intended for research. Permissions and compliance with applicable rules are the responsibility of the user. For details on the license see here

Where can I download Slicer?

3DSlicer is available for download by visiting the following link: http://download.slicer.org

You can also get older releases by using the offset parameter in the download page. For example, download page from 7 days ago: http://download.slicer.org/?offset=-7

To get a direct download link of previous revision on a selected operating system: http://download.slicer.org/download?os=macosx&stability=any&offset=-1

Always include these parameters:

• stability, which can be release, nightly, or any
• os, which can be win, macosx, or linux

Additional options:

• revision built before or on the date: date=2015-01-01
• same but checkout date: checkout-date=2015-02-01
• exact revision: revision=27000
• revision less than of equal: closest-revision=26000
• latest revision of 4.3 branch, can include patch as well: version=4.3

Any of these queries can be combined with the offset param, which will step forward or backward a given number of revisions. So, stability=release&version=4.5.0&offset=-1 should give you the revision just before the first 4.5 release.

Where can I download older release of Slicer ?

Older releases of 3DSlicer are available here: https://slicer-packages.kitware.com/#collection/5f4474d0e1d8c75dfc70547e/folder/5f4474d0e1d8c75dfc705482

Extensions can be downloaded for old Slicer releases manually from the Extensions Catalog at the URL: https://extensions.slicer.org/catalog/All/(revision_number)/(operating_system). Revision number is available in Slicer menu: Help / About Slicer (or in the Slicer Releases page). Operating system can be: win, linux, or macosx. For example for Slicer-4.8.0 on Windows extensions are available at: https://extensions.slicer.org/catalog/All/26489/win

Does Slicer work for non-English computing?

At this point no, Slicer uses US English conventions. Specifically this means that directory paths should use ASCII characters only.

There has been some discussion and planning about internationalization but it is not yet available:

• https://www.slicer.org/wiki/Documentation/Labs/I18N
• https://discourse.slicer.org/t/slicer-internationalization/579

How to install Slicer ?

1. Go to http://download.slicer.org
2. Click on the link corresponding to your operating system
3. Replace the version numbers in the commands below as appropriate

   Linux	Windows	Mac OSX
   Start a terminal and type these commands: ''(replace version number as appropriate)'' $ tar xzvf ~/Downloads/Slicer-4.6.2-linux-amd64.tar.gz -C ~/ $ cd ~/Slicer-4.6.2-linux-amd64 $ ./Slicer	Double click on the downloaded Slicer-4.6.2-win-amd64.exe package. Follow instructions displayed on the screen.	Double click on the downloaded Slicer-4.6.2-macosx-amd64.dmg package Drag & drop the Slicer.app onto your Desktop or in your Applications. Need help?

Note on some linux distributions additional packages may be required, e.g. for Slicer 4.9 on Debian Linux 9 if you get errors about missing libraries you may need to run this command:

sudo apt-get install libpulse-dev libnss3 libasound2

Is Slicer really free?

Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).

See the Slicer License page for the legal version of this.

Where can I find someone to help me use Slicer?

We rely on the community of users and developers to share their expertise. Slicer Community support and development discussions are hosted on Discourse, which provides a modern web forum as well as email-only interaction:

   https://discourse.slicer.org

If you post to any public forum, be sure not to include any Protected Health Information (PHI) or any other data that would get you or anyone else in trouble. However, posting example data can be very important to people who are interested in helping you solve your problems. If you can replicate your question using data from the Sample Data or Data Store modules that's the first choice.

The Users Manual gives descriptions for using each module, and you can check out the Training pages for in depth tutorials about workflows.

Mailing list discussions before 2017 April are archived

Can I use slicer for patient care?

Slicer is intended for research work and has no FDA clearances or approvals of any kind. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.

How to cite Slicer?

3D Slicer as a Platform

To acknowledge 3D Slicer as a platform, please cite the Slicer web site and the following publications when publishing work that uses or incorporates 3D Slicer:

• An overview of Slicer and its history
  • Kikinis R, Pieper SD, Vosburgh K (2014) 3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support. Intraoperative Imaging Image-Guided Therapy, Ferenc A. Jolesz, Editor 3(19):277–289 ISBN: 978-1-4614-7656-6 (Print) 978-1-4614-7657-3 (Online)

• About Project Week
  • Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron; 2016. “Increasing the Impact of Medical Image Computing Using Community-Based Open-Access Hackathons: The NA-MIC and 3D Slicer Experience.” Medical Image Analysis 33 (October): 176–80.

• Slicer 4
  • Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network. Magn Reson Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.

• Slicer 3
  • Pieper S, Lorensen B, Schroeder W, Kikinis R. The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community. Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
  • Pieper S, Halle M, Kikinis R. 3D SLICER. Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.

• Slicer 2
  • Gering D.T., Nabavi A., Kikinis R., Hata N., O'Donnell L., Grimson W.E.L., Jolesz F.A., Black P.M., Wells III W.M. An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and an Open MR. J Magn Reson Imaging. 2001 Jun;13(6):967-75. PMID: 11382961.
  • Gering D.T., Nabavi A., Kikinis R., Grimson W.E.L., Hata N., Everett P., Jolesz F.A., Wells III W.M. An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging. Int Conf Med Image Comput Comput Assist Interv. 1999 Sep;2:809-19.

Individual Modules

To acknowledge individual modules

• 

  Each module has an acknowledgment tab in the top section. Information about contributors and funding source can be found there.

• 

  Additional information (including information about the underlying publications) can be typically found on the manual pages accessible through the help tab in the top section

How do I create an account for the Slicer wiki?

Current content of this wiki will be moved to https://slicer.readthedocs.io, https://www.slicer.org, and https://github.com/Slicer/Slicer/wiki websites and legacy content will be archived. New user accounts are no longer offered for this wiki.

Can I install Slicer without administrator rights?

The most convenient way to install Slicer is to run the installer package (Slicer-4.10....exe) as administrator. However, installation is not necessary, you just need to unpack the files in the installer package and copy them to your user directory or a USB drive and start it by running Slicer.exe.

You can unpack the installation package by one of the following methods:

• Install Slicer on any computer where you have administrator access. All the files that you need to run Slicer are in the C:\Program Files\Slicer... directory.
• Unpack the installation package by using 7zip or using the InstallExplorer plugin in Total commander or FAR manager (http://nsis.sourceforge.net/Can_I_decompile_an_existing_installer). All the Slicer files will be in the $_OUTDIR directory, except Slicer.exe, so you have to copy Slicer.exe into $_OUTDIR and run it from there. You can rename the $_OUTDIR directory and discard all the other directories ($COMMONFILES, $PLUGINSDIR, etc).

What if I have problems with Slicer installation?

You can read our guide explaining how to report a problem.

Slicer does not start

"Insufficient graphics capability" popup is displayed

In Slicer-4.9, minimum graphics requirements have been increased compared to earlier versions. Computers running Slicer must support OpenGL 3.2. This OpenGL version was released in 2009 and so all desktop and laptop computers should already support it. However, on virtual machines or when connecting to a computer via remote desktop, this minimum requirements may not be met.

• If you are trying to connect through Windows remote desktop (RDP):
  • Recent Intel integrated GPUs and some NVidia GPUs (Quadro series) running on Windows 10 now support running current OpenGL versions. You may consider upgrading your hardware and operating system.
  • You can use other remote desktop applications, such as RealVNC, AnyDesk, or Google remote desktop (all free, or free for personal use)
  • If your computer can normally run Slicer but when started through remote desktop it displays "Insufficient graphics capability" popup: You need to start Slicer in normal desktop mode and then establish remote connection. You can achieve this by following these steps:
    • Connect to the remote computer using remote desktop
    • Start Slicer on the remote computer
    • Click "Retry" when "Insufficient graphics capability" popup appears
    • Grant administrator access in the displayed user account control popup (administrator access is needed for termination of the current remote desktop session), this will close the remote desktop connection
    • Reconnect to the remote computer using remote desktop - you should see Slicer application started up successfully

Any other issues

See debugging application startup issues.

How to uninstall Slicer?

• On Windows, choose "Uninstall" option from the Start menu.
• On the Mac, remove the Slicer.app file. To clean up settings, remove "~/.config/www.na-mic.org/"
• On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"

See the information about the location of Settings for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.

Where can I find Slicer tutorials?

Slicer tutorials associated with the latest 4.10 stable release are available by visiting the following link: Click Here.

I read errors in the logs complaining about memory

Errors such as “Description: Failed to allocate memory for image.” indicate that you don’t have enough memory space. This can be a common issue if you run a 32-bit version of Slicer. You cannot expect a 32-bit executable to deal with any moderately complex problem. The recommended solution is to download/build/use Slicer in 64-bit mode.

Possible workarounds:

• Use a 64-bit version of Slicer
• You have somewhat more memory if you run the module in a separate process. To do that open Edit / Application Settings / Modules and check the “Prefer Executable CLIs” option, then restart Slicer.
• Decrease the size and/or resolution of the input and output images
  • Consider Crop Volume to focus on just your area of interest.
  • Consider ResampleScalarVectorDWIVolume or ResampleScalarVolume increase the sample spacing (decrease the resolution) of your data.

Which Slicer version should I use: 3.X or 4.X ?

In general slicer3 and slicer4 have roughly similar functionality with respect to registration basics. Probably the most important thing to keep in mind is that slicer3 is no longer actively maintained.

Slicer4, on the other hand, has benefited from literally hundreds of bug fixes over the past several years, and typically has better features and much better performance. Also, the nightly builds of slicer4 are now using ITKv4, which has significantly improved registration code. I am told by active users/developers of ITK that ITKv4 should provide significantly better results in many cases. Also, several new registration techniques are being actively developed for slicer4.

Source: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006190.html

What is my HOME folder ?

Linux or MacOSX	Windows
Start a terminal. $ echo ~ /home/jchris	Start Command Prompt (Start Menu -> All Programs -> Accessories -> Command Prompt) > echo %userprofile% C:\Users\jcfr