SLICER - Simple Image Display Utilities - User Guide


Standard 2D picture display programs (like display, bundled with FSL) cannot read 3D / 4D AVW images. Thus FSL includes SLICER, a set of utilities which take 3D AVW files and produce 2D pictures of slices from within these files. These slices can be of axial, coronal or sagittal orientation. If two input images are specified (instead of just one), the first image is used as normal, but overlaid in red on top of this are image edges derived from the second input image. This can be useful for checking the results of registration.

(Note that there is a nice tool (separate from FSL), for viewing AVW images (including colour AVW images generated by FSL) - go to 3D VisionWorks.)

The AVW format does not allow for colour image information to be stored. However, an unused part of the AVW header is used by some FSL programs to store information about suitable colour maps for use with certain images. For example, the colour activation images produced by FEAT contain such information. The programs in SLICER use this to use the right colour map when producing slice pictures.

The different SLICER programs are:


Copyright © 2000, University of Oxford. Written by S. Smith.