Slicer:Slicer2.5 Release Notes

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New Features in Slicer 2.5

Slicer 2.5 has many new features! In addition to numerous bug fixes and other improvements, the list here highlights most major some new features in Slicer 2.5. 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 behaviour. Please send questions about unexpected behavior to the Slicer User's mailing list and reports to the bug tracker.

Updates to existing modules:

FMRIEngine
  • new frontend
  • support for block design
  • event releated paradigm
  • peristimulus histogram plotting
  • multirun computation
vtkFreeSurferReaders
  • MGH reader
  • Automated review framework
Ibrowser
  • new functionality for key frame transformation interpolation
DTMRI
  • new clustering tools
  • new ODF tensor glyph
  • new conversion protocols
  • ROI-based fiber classifying/pruning
  • limited support for tensor-to-tensor registration
  • Cleaned up error messages


Additional functionality:

  • New module: vtkAG - nonlinear, multimodal, multichannel registration tool.
  • New module: TransformVolume - arbitrary resampling of volumes with linear transform.
  • New module: QueryAtlas (prototype)
  • Generic readers (using ITK I/O Factories):
    • Sequences of tiffs, jpgs, pngs
    • Analyze VTK, GIPL and others
  • Nrrd reader


System Improvements:

  • Better automated building, especially on OSX
  • Update to commenting script
  • Better exception handling
  • Cleaned up compiler warnings

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 Slicer:Slicer_2.5_Building

  • Windows
    • distributed versions are built with Microsoft Visual Studio .NET in release mode (note that there may be some problems compiling with .NET 2003)
  • Solaris
    • We are building using gcc version 3.0.3.
  • Linux
    • We are building using gcc version 2.96 on RedHat 7, gcc version 3.2.2 on RedHat 9, and gcc 3.2.3 on RedHat Enterprise Linux.
  • Mac OSX
    • These patches must be applied to compile on OSX.

Installing

No special installation is needed -- simply unpack the distribution archive and run the platform-specific executable at the top level (for example, slicer2-win32.exe for the Windows build). The slicer distribution contains all the needed support libraries and has been tested on a variety of system configurations.

Known Issues: Base Operations

  • All platforms
    • Model hierarchies are unreliable - use at your own risk.
  • Linux
    • If you are having problems running Slicer over an ssh connection with X forwarding, the problem may be that you don't have the appropriate OpenGL libraries on the machine you're sshing from.
  • Mac
    • Currently, there is no support for reading DICOM files with the Basic Reader. You can read in DICOMS by clicking Add Volume, then choosing DICOM from the menu, and browsing to the directory containing your DICOM files.
    • Currently, there is no support for building BLT with genlib.tcl, which causes FMRIEngine's UI to fail. See the patch instructions for the Mac under the "Building" section to compile BLT and run FMRIEngine.

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.

  • Mac
    • There is no currently no print header functionality for OSX.
    • See the note under "Base Operations" regarding FMRIEngine functionality.

Reporting Bugs

Please report bugs for Slicer version 2.5.x go to here.

Where to go for Help

Compilation/development questions can be sent to the Slicer Developer's Mailing List. Questions about running Slicer can be sent to the Slicer User's Mailing List.