I created a soft link from the bootloader folder to the different location and that did the trick:
~/Downloads/TK1/Linux_for_Tegra_tk1$ ln -s /media/.../system.img bootloader/system.img
I created a soft link from the bootloader folder to the different location and that did the trick:
~/Downloads/TK1/Linux_for_Tegra_tk1$ ln -s /media/.../system.img bootloader/system.img