hi –
For use with BrainSuite, you can usually skip adding the environment variables to your path. We have done this in the shell scripts that we use to call the compiled MATLAB programs. If you look, for example, at the bdp.sh script, you can see this bit:
# Set up path for MCR applications.
LD_LIBRARY_PATH=.:${BrainSuiteMCR}/runtime/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BrainSuiteMCR}/bin/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BrainSuiteMCR}/sys/os/glnxa64;
MCRJRE=${BrainSuiteMCR}/sys/java/jre/glnxa64/jre/lib/amd64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;
XAPPLRESDIR=${BrainSuiteMCR}/X11/app-defaults ;
export LD_LIBRARY_PATH;
export XAPPLRESDIR;
BDPEXEDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)" ;
export BDPEXEDIR;
"${exe_dir}/bdp" "$@"which sets the library paths before calling bdp. BrainSuiteMCR gets set at the start of the script based on standard installation locations, or you can set it as an environment variable (useful for you install it in a non-default location). This strategy should reduce the impact of the installation.
You can undo the changes you made to your .bashrc file and give it a try.
thanks,
David