I can't seem to get AutoSeg to run properly. I followed the advice in the README and installed Slicer 3.6.3 and the latest ANTS (1.9.y), and verified that they work. When I run AutoSeg -gui, I get the GUI and everything seems fine, except that in the output it shows that it's not finding Slicer modules as it goes: e.g.,

  Error: Could not run N4ITKBiasFieldCorrection:
  No such file or directory

The README says that "3D Slicer then needs to be in your PATH, such that its modules are found automatically and thus called properly by AutoSeg". I don't know what specifically that means, and neither the Slicer docs or the AutoSeg ones (which do not include installation, other than the README?) seem to shed any light on this. Searching on the Slicer mailing list archive, advice I saw was to only add the Slicer main directory to the path, and let the Slicer3 program handle setting up its paths... and indeed, when I added additional Slicer directories to my PATH, Slicer3 stopped launching properly until I reverted.

What if anything should be on the PATH to make this work? Since I'm not a regular Slicer user, I'm not sure if I'm having an AutoSeg problem or a Slicer one, but either way it would have been helpful to have a few more details in the README on how to get AutoSeg set up.

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.