Slicer 3.0 User Information

Slicer 3.0: Getting Started

Slicer 3 is the latest version of 3D Slicer. It reflects a dedication to the Slicer software platform with an intention to make the software. envisioned as a software platform that is both easy to use for researchers and easy to extend for programmers, while maintaining the high level of functionality needed to support sophisticated science. The NA-MIC engineering core took on the task of designing an architecture for Slicer 3, the broad-strokes requirements of which are:

1. to preserve features of Slicer 2.x that are needed by the user community (comprehensive visualization ability, various modules for segmentation, registration, DTI analysis, volume measurements, ...)
2. to add new functionality desired by the computer science community (ease of adding new modules, ease of interfacing existing to non-slicer software modules, scalability to grid architectures, automated graphical user-interface testing)
3. to design the new platform such that some of the new features requested by the user community (such as undo-redo facility, improved 3D rendered images) are significantly easier to implement.

Some specific features planned in Slicer 3.0 are as follows:

• New 2D GUI widgets with potential for automated testing of GUI functionality, plus high level widgets to support advanced imaging capabilities (e.g., transfer function editor)
• New 3D interaction widgets for direct manipulation and measurement of data
• Lowering the effort to add functionality
• New way to integrate external programs (execution model) as Slicer modules, including ITK
• Improved modularization and plug-in architecture
• Rearchitecture of the data and scene description
• Rearchitecture of the coordinate system structure
• Upwards compatible for the core functionality with Slicer 2.6 from a user perspective
• Easy porting of slicer 2.6 code
• Support Undo/Redo facility for interactive editing
• Usability guidelines to promote software consistency

There are a couple different ways to obtain Slicer3 to run on your own computer. You can either:

• build Slicer 3 yourself from an SVN checkout, or
• download a precompiled Slicer3 installer for your platform, or

Building Slicer

To build Slicer 3 yourself from an SVN checkout, refer to the 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

• For building, g++ version 3.4.3 on RedHat Enterprise Linux 4 is used.

Mac OSX

• For building, gcc version 4.0.1 is used.

Downloading

Deciding to download? Access Slicer 3.0 downloads here

Obtaining a Precompiled Binary

Compiled Slicer3 executables are available here. From the Snapshots directory, select your architecture.

The current supported architectures are:

• darwin-x86: Mac OSX - Darwin x86 Intel
• darwin-ppc: Mac OSX - Darwin Power PC
• linux-x86: Linux-x86 - Linux 32-bit
• linux-x86_64: Linux-x86_64 - Linux 64-bit
• win32: Windows

The Snapshots directory contains both Slicer2 and Slicer3 binaries. For the latest build, select the filename that begins with "Slicer3" and has the most recent date. For the beta binary released prior to the January 2007 All Hands Meeting, choose the file with "PreAHM" in the filename. These are all beta builds, so you might find some bugs. If you do, or are having trouble installing Slicer3, please email slicer-users@bwh.harvard.edu so we can continue to improve Slicer3.

With many modules on Slicer already developed, much of Slicer documentation is modules specific. Consult module documentation to aid you in using Slicer.

Installing on Different Operating Systems

Installing on Mac OSX

The latest Mac OSX builds are either tar.gz files or .sh files. To install Slicer3, open up an X11 terminal window and copy the binary to the location where you want to install. Change the filename in the examples below to reflect the binary you downloaded.

Unpacking .tar.gz Files

To unzip and untar the .tar.gz binary, type:

gunzip ./Slicer3-3.0.2007-01-10-Darwin-x86.tar.gz
tar -xvf ./Slicer3-3.0.2007-01-10-Darwin-x86.tar

Unpacking .sh Files

To unpack the .sh binary, type:

./Slicer3-3.0.2007-01-10-Darwin-x86.sh

You will be prompted to accept the license agreement, and asked where you want to install it. Respond "Y" to both questions.

Running Slicer3

To run Slicer3, cd into the Slicer3-3.0.2007-xx-xx/bin directory and type:

./Slicer3

Installing on Linux

After downloading the file, move it to where you would like to install Slicer3, and then execute the .sh binary. To do this, simply do the following (replace the filename with the one you downloaded):

./Slicer3-3.0.2007-01-08-Linux-x86_64.sh

If the file doesn't execute, make sure that you have execute permission set. To add execute permission, type:

chmod a+x ./Slicer3-3.0.2007-01-08-Linux-x86_64.sh

Some shells have problems executing the script. If so, you might need to specify which shell you want to execute the script, e.g.:

/bin/sh ./Slicer3-3.0.2007-01-08-Linux-x86_64.sh

To run Slicer3, cd into the Slicer3-3.0.2007-xx-xx/bin directory and type:

./Slicer3

Installing on Windows

After downloading the file, simply double-click on it to start the installation process. To uninstall Slicer3, double-click the Uninstall icon in the Slicer3 directory. To run Slicer, go to Start -> Programs -> Slicer3-3.0.2007.xx-xx -> Slicer

Known Issues: Base Operations

All Platforms:

• Slicer 3's interface is optimized for screen resolutions equal to or higher than 1280x1024. While it is useable below that resolution, using the GUI may become less efficient.
• In Slicer 3, fonts currently do not resize, making the text hard to read on extremely large monitors with very high

resolutions.

Linux:

• csh must be installed (it's not on Ubuntu by default).
• the sh shell on some systems is incompatible with the installer (it will work, but with warnings)

Known Issues: Modules

As a research platform, Slicer includes several modules that are not yet fully implemented and yet available because developers felt they were far enough along in functionality to provide utility. As such, you may find that some operations do not behave as expected, particularly at the intersection point with other Slicer functions. To help us improve these modules, please let us know about these issues by filing appropriate bug reports.

Reporting Bugs

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

Finding Help

For help, consult the mailing lists.