Slicer 2.6 User Information

==Accessing Slicer 2.6==

Obtaining and working with Slicer is easier than you think. Slicer 2.6 is still the most commonly used version of the 3D visualization software. To get up and running, access this

Specifics on Slicer 2.6 with Operating Systems

Generic Instructions (Linux/Unix/Solaris)

For anonymous checkout and build on most Linux and Solaris configurations, you only need to follow the steps below.

Notes:

• You will need a recent cvs client; version 1.12.10 is known to work.
• You will need a recent Subversion (svn) client
• You will need autoconf installed (except on Windows).
• Windows users need to see special download instructions below.
• If you are using gcc, use something around gcc ver. 3.3 vintage. There have been problems compiling various support libraries using gcc ver. 4.0.

1) Get an anonymous checkout

cvs -d :pserver:anonymous@cvs.spl.harvard.edu:/projects/cvs/slicer login

and enter 'bwhspl' as the password and then

cvs -z3 -d :pserver:anonymous@cvs.spl.harvard.edu:/projects/cvs/slicer checkout -r release-2-6 slicer2

Note: to build the current cvs head, omit the '-r release-2-6' argument.

2) Build the required support libraries (Tcl/Tk, VTK, ITK)

cd slicer2
./Scripts/genlib.tcl

• Note: you need svn installed.

3) 'Build slicer'

./Scripts/cmaker.tcl

These steps will build the entire system for you, and you can use this as the basis for further development such as writing your own custom modules.

Windows

Like in releases 2.4 and 2.5, not all the support libraries are easy to build on windows in Slicer 2.6, so you can download a set of precompiled binaries to build against. Insert the following substeps between steps 1) and 2).

1.a) download this file: Slicer2.6-Lib-win32.zip

1.b) unzip the contents into your slicer2 directory. You will end up with the following libraries

Lib/win32/CMake-build
Lib/win32/tcl-build

Then continue with the build steps above, knowing that now you have tclsh executable located in

 Lib/win32/tcl-build/bin

This assumes you are building with the Microsoft Visual Studio .NET version of the development environment. If you need to use a different compiler, you need to change the GENERATOR variable in the 'slicer_variables.tcl' to 'Visual Studio 7.1'. Note that Slicer has not been fully tested on windows environments other than Microsoft Visual Studio .NET. If CMake complains that "cl" can not compile a simple test program, and you are running Visual Studio 7 .NET 2003, you need to change the GENERATOR variable to "Visual Studio 7 .NET 2003".

If you are using MS VisualStudio 6, you can download the building scripts: Slicer2-MSVC6-InstallScripts.zip. (Note that some modules may not build due to library incompatibilities).

Mac OSX

Follow the Generic install steps.

Troubleshooting

These steps are followed as part of the nightly build process for slicer as shown on the slicer dashboard here. Compare the builds shown on the dashboard to the system you are trying to build on.

Features in Slicer 2.6

Slicer 2.6 has many new features! In addition to numerous bug fixes and other improvements, the list here highlights most major some new features in Slicer 2.6. 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.

FMRIEngine

• Supports a common fMRI data analysis workflow;
• Currently is appropriate for preprocessed data (which has been slice-timing corrected and motion corrected);
• Allows the specification of blocked, event-related and mixed designs, and the optional concatenation of runs;
• Allows the saving and loading of paradigms;
• Has a more elaborate set of linear modeling tools, including adding temporal derivatives to capture latency in the response, and trend modeling to remove slowly varying nuissance signals;
• Provides an option to pre-whiten the data to account for temporal correlation structure;
• Displays a 'surfable' visualization of the design matrix and contrasts;
• Permits saving and loading of estimated regression weights for use in GLM-based detection;
• Optionally performs grand mean and global mean scaling on input datasets;
• Allows regions of interest (ROIs) to be defined from brain activation 'blobs';
• Provides tools for selecting one or several ROIs and querying statistics on those regions (pop-up histogram plot, with list of max, min, mean p-value, percent signal change, etc.);
• Label maps can be saved and/or used to create 3D models for visualization with multimodality data;
• Reports uncorrected or corrected p-values (using the False Discovery Rate method);
• Allows voxel timecourses to be plotted in regular long or peristimulus histogram form, along with reference signals from the paradigm;
• Provides pop-up help throughout the interface, to provide information on many topics;
• Has a more modular architecture for adding new kinds of brain activation detectors.

vtkFreeSurferReaders

Features from the previous slicer2.5MGH release have been integrated with the rest of slicer. These features were used in Slicer/Freesurfer Training and a power point presentation can be found here.

New features include:

• Integrated reading of compresed .mgh files (.mgz)
• Improved scalar overlay display, and clickable models for details of scalar values
• .w surface file reading
• Run-time parsing of colour description text files
• FreeSurfer Group Descriptor file reading and plotting of results
• Imrovements to the quality assurance functionality to load a series of subjects and scan through the selected volumes, using the FreeSurfer subject directory structure

Ibrowser

New functionality in support of the FMRIEngine work described above.

DTMRI

Many new features including:

• Reading dwi and tensors from nrrd files
• Automatic brain mask generated with tensor estimate
• New scale factor control on scalar generation
• Brighter tracts for all scan orientations
• Tract clustering
• Tensor-to-tensor registation (beta feature, not fully supported)
• Tracts can be rasterized into a label map

EMSegmenter and EMAtlasBrainClassifier

Bug fixes and improvements including new algorithms described here

Alignments

• New registration techniques based on ITK registration framework.
• Translation MI: Perorms image registration using 3 translational components based on minimiztion of Mutual Information metric using Regular Step Gradient Descent optimizer.
• Translation Mattes MI: Perorms image registration using 3 translational components based on minimiztion of Mattes Mutual Information metric using Regular Step Gradient Descent optimizer.
• Rigid Mattes MI: Perorms image registration using 3 translational and 3 rotational components based on minimiztion of Mattes Mutual Information metric using Regular Step Gradient Descent optimizer.
• Affine Mattes MI: Perorms image registration using 3 translational, 3 rotational, and 3 scale components based on minimiztion of Mattes Mutual Information metric using Regular Step Gradient Descent optimizer.
• Deformable Demons: Uses Demons algorithm to compute deformation vectors
• Deformable BSpline: Uses BSpline interpolation to compute deformation vectors based on minimiztion of Mattes Mutual Information metric.
• Use TransformVolume module to apply deformation field and linear transformation to resample volumes.

Generic Reader module

• Preserves image orientation and scan order.
• Reads all single component scalar formats supported by ITK I/O factory as of ITK 2.4

Nrrd Reader Module

• Support for DTI images (DWI and Tensors).

Image Export

Image export is re-implemented using ITK image IO mechanism. The following image file formats are supported:

• Analyze (.hdr)
• NRRD(.nrrd) and (.nhrd)
• Meta (.mhd) and (.mha)
• Nifti (.nii), (.img), and (.img.gz)
• VTK (.vtk)

NEW Draw2 Editor

Slicer 2.6 has two manual image editors: Draw (as in Slicer 2.5) and Draw2, which has many new features including:

• High-resolution image editing
• Toggle on/off a cardinal (Catmull-Rom) spline interpolating any control polygon
• Choose sampling density of spline for any polygon
• Select/Move modes automatically toggle based on proximity to selected points, to mimick standard drawing programs; deselect all points by clicking away from the selected points
• Insert mode to allow inserting control points in the middle of a polygon for manual refinement
• Cut, copy, and paste features for control polygons
• Shortcut keys for cut, copy, paste, select all, delete selected, delete all
• Unapply feature: repeatedly click Unapply button to scroll through the applied polygons on any slice at any time and re-edit them
• Can choose whether or not to clear labelmap before each apply operation
• Watch the Simbios Slicer documentation page and Chand's Slicer page for additional information

NEW: Comparison Module

Jermie Anquez of ENST in France contributed a significant set of new functionality for viewing multiple volumes in a coordinated fashion:

• display tab : allows to display up to 9 slices simultaneously (set the

Number of slices using the radio buttons). Use the controls in the top right corner of each slice to set the background, foreground and labelmap displayed. You can fade from background to foreground using the opacity slider. By default, the slices display is independant (linking 'Off' button selected). Each slice has its own orientation, zoom/pan and offset (like in 3D Slicer general framework).

• ** Clicking on Linking 'On' button activates linked display. Specific link

controls are enabled. The orientation, zoom/pan, offset and cursor are then the same on every slice.

• ** The R button resets zoom and pan on every slice (pressing 'r' key over a

slice realizes the same operation)

• mosaik tab : Display a mosaik mixing 2 volumes (useful to check

registration results)

• ** Set the reference and the second volumes to be displayed.
  • Set the number of subdivision, following width and height
  • Set the opacity between the reference and the second volume
  • Set offset, offset increment and orientation of the mosaik.

• flip tab : Flip the volume following the 3 main axes. This operation doesn't generate any transform node, but modifies the Volume node.