Documentation/3.4/ReleaseNotes

New Features in Slicer 3.4

Slicer 3.4 has many new features! The list here highlights most major some new features in Slicer 3.4. Please also note that many of these new features are still being developed and will be improved in future releases, so you may encounter some unexpected behavior. If you do encounter unexpected behavior, you can join the Slicer users's mailing by sending email to slicer-users-request@massmail.spl.harvard.edu with the subject "subscribe", and report the behavior there to see if there is a work around (or check the archives), and to the bug tracker if it needs to be solved by the developers.

New Features:

• Welcome Module at Startup
• Improved Save Module
• Improved Editor
• New Registration module
• Fiducial based tractogrphy
• Two Tensor tractography
• Improved SceneSnapshot functionality
• Compare View and Cross Hairs
• Support for Extension Server
• MRML scenes and all data load from and save into XNAT desktop

A summary of new features is also available here: Slicer3:Status

Downloading

Download the release candidates here

Release candidate builds are available for:

• Windows,
• 32-bit Linux
• 64-bit Linux
• Darwin PPC
• Darwin x86

Installing

Linux

tar -xzvf Slicer3-3.4.2009-xx-xx-linux-x86.tar.gz

or, for 64 bit systems

tar -xzvf Slicer3-3.4.2008-xx-xx-linux-x86_64.tar.gz

Mac

Be sure you have X Windows installed.

From a terminal:

tar -xzvf Slicer3-3.4.2009-xx-xx-darwin-x86.tar.gz

or, for older PPC Macs:

tar -xzvf Slicer3-3.2.2009-xx-xx-darwin-ppc.tar.gz

Windows

Double click on:

Slicer3-3.2.2009-xx-xx-win32.exe

Known Issues: Base Operations

• All Platforms:
  • Undo/Redo functionality is available for the Editor Module only at this time.
  • There is currently a 10 stage Undo history in the Editor Module.
  • Procedural color nodes don't display in the Colors Module.
  • Volume rendering transfer functions are not stored in the MRML scene.
  • Grayed-out tool icons reflect functionality not yet available.
  • To load DWI volumes in DICOM format, use the Converters->Dicom DWI loader, with only one volume in the Dicom Directory
  • In Color By Orientation mode, you can't adjust window/level
    • Color By Orientation does not work on tracts
  • If you wish to use the Editor module on DWI or DTI volumes, must create a scalar volume first.

• Linux:
  • You need to have X11 configured to run 3D graphics (opengl/mesa). Confirm that you can run the command

    glxgears

    .
  • For debian/ubuntu you may need to install the libxss1 library in order to run the slicer binary download

    sudo apt-get install libxss1

  • Some versions of linux have an incompatible libssl that generates an error message related to md5 when trying to launch the python console.
• Windows:
  • ...

• Mac:
  • On platforms other than Mac, you can edit an entry in a multi-entry list box (for example, a list of fiducials) by double-clicking on the entry. In order to edit the field on the Mac, you need to click the field and then hit Enter.

For users of Mac OS X 10.5 (Leopard) we suggest replacing the standard X11 application with the latest XQuartz version available here: http://xquartz.macosforge.org/trac/wiki

Known Issues: Modules

As a research platform, Slicer includes several modules that are not yet fully implemented, but which the developers still felt were far enough along in functionality to provide utility for the community. As such, you may find that some operations do not behave as expected, particularly where they interact with other slicer functions. Please let us know about these issues by filing appropriate bug reports.

• Replaced Linear Registration Module with Rigid Registration (the functionality remains the same)
• Replaced DICOM to NRRD with DICOM DWI to NRRD
• Simple Region Growing has been changed to Statistical Region Growing
• DICOM DWI Loader removed, use DWI to NRRD Loader instead

Building

You don't have to build Slicer yourself to use it. If you want a precompiled version, go here.

To build slicer from source, see Slicer3:Build_Instructions

• Windows
  • distributed versions are built with Microsoft Visual Studio .NET in release mode (note that there may be some problems compiling with .NET 2003)

• Linux
  • We are building using g++ version 3.4.3 on RedHat Enterprise Linux 4.

• Mac OSX
  • We are building using gcc version 4.0.1

Reporting Bugs

Please go to http://www.na-mic.org/Bug/ and report bugs for Slicer version 3.

Where to go for Help

Compilation/development questions can be sent to the Slicer Developers Mailing List. Questions about running Slicer can be sent to the Slicer Users Mailing List.

Subscription management tools and archives are available at:

http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel

http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users

Acknowledgements

The Slicer Development Team

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. This work was also supported by NIH grant P41 RR13218 (http://spl.harvard.edu/nac) and the Biomedical Informatics Research Network (http://www.nbirn.net).