External Email - Use Caution

Recently FSL has changed the location of the bin directory they want you to use.

The FreeSurfer setup script adds the old binary folder to the PATH not the new one. This is causing quite a bit of trouble for me. I made changes to the FreeSurferEnv.sh. I removed lines 440-446 and in its place I put the following. The echo line probably needs to be changed but it works.

if [ -d $FSL_DIR/share/fsl/bin ]; then

    export FSL_BIN=$FSL_DIR/share/fsl/bin
elif [ -d $FSL_DIR/bin ]; then
    export FSL_BIN=$FSL_DIR/bin
else
    if [[ $output == 1 ]]; then
        echo "WARNING: $FSL_BIN does not exist.";
    fi
fi