Dear James,

You would need to update your configuration file .cshrc or .bashrc (whether you use tcsh or bash), to be able to detect Slicer modules automatically in your terminal, and link as well to their related libraries.
The idea is similar to detect AutoSeg modules and ANTS as well.

Here is an example for bash users - you would need to update accordingly the folders where AutoSeg, ANTS and Slicer are located in YOUR system:

# Autoseg

# Define AUTOSEG_PATH variable

export AUTOSEG_PATH=/usr/local/autoseg

# Add AutoSeg and its related executables to your PATH

export PATH=$PATH:$AUTOSEG_PATH

# Define AUTOSEG_HOME variable

export AUTOSEG_HOME=$AUTOSEG_PATH

#ANTS
# Define ANTSPATH variable


export ANTSPATH=/usr/local/ANTS-1.9.x-Linux/bin


# Add ANTS and its related executables to your PATH


export PATH=$PATH:$ANTSPATH



# Slicer 3

#Define Slicer installation path

export SLICERPATH=/usr/local/Slicer3-3.6.3-2011-03-04-linux-x86_64

#Define Slicer bin and library path variables

export SLICERBINPATH=$SLICERPATH/bin

export SLICERLIBPATH=$SLICERPATH/lib

#Add Slicer binaries to your PATH

export PATH=$PATH:$SLICERPATH:$SLICERLIBPATH/Slicer3/Plugins

# Add Slicer3 libraries to your LD_LIBRARY_PATH environment variable

export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${SLICERLIBPATH}/Slicer3/Plugins:${SLICERLIBPATH}/Teem-1.11.0:${SLICERLIBPATH}/vtk-5.6:${SLICERLIBPATH}:${SLICERLIBPATH}/InsightToolkit:${SLICERLIBPATH}/ModuleDescriptionParser:${SLICERLIBPATH}/vtkITK:${SLICERLIBPATH}/MRML:${SLICERLIBPATH}/MRMLCLI:${SLICERLIBPATH}/MRMLIDImageIO:${SLICERLIBPATH}/SlicerIO:${SLICERLIBPATH}/Slicer3:${SLICERLIBPATH}/FreeSurfer:${SLICERLIBPATH}/vtkTeem:${SLICERLIBPATH}/KWWidgets:${SLICERLIBPATH}/Python/lib:${SLICERLIBPATH}/bmModuleDescriptionParser:${SLICERLIBPATH}/BatchMake:${SLICERLIBPATH}/Slicer3/Plugins

WARNING: the last command (export LD_LIBRARY_PATH...) should be one
single command line...

AutoSeg should then detect all modules succesfully.

Best regards,
Clement.