Documentation/4.3/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.

Where can I download Slicer?

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

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.

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?

Please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates Slicer.

• Slicer 4
  • Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., 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. Magnetic Resonance Imaging 2012; July PMID: 22770690.
• 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, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. An integrated visualization system for surgical planning and guidance using image fusion and an open MR. Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
  • Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging. Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

How do I create an account for the Slicer wiki?

Please note: You only need an account if you want to edit or add pages.

Follow the Log in->Request Account link from the upper right corner of the slicer wiki page. Once the account request is approved, you will be e-mailed a notification message and the account will be usable at log in.

What if I have problems with Slicer installation?

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

How to install Slicer ?

1. Go to http://download.slicer.org
2. Click on the link corresponding to your operating system

3. Linux	MacOSX	Windows
   Start a terminal and type these commands: $ tar xzvf ~/Downloads/Slicer-4.3.0-linux-amd64.tar.gz -C ~/ $ cd ~/Slicer-4.3.0-linux-amd64 $ ./Slicer	Open the Downloads folder and follow these instructions: Double click on the downloaded Slicer-4.3.0-linux-amd64.exe package. Follow instructions displayed on the screen.	Double click on the downloaded Slicer-4.3.0-linux-amd64.dmg package Drag & drop the Slicer.app onto your Desktop or in your Applications. Need help?

   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/"

   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