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