Hello, that's because the much space of the MYS-SAM9G45 is as user space which has not been mounted. User may need to mount it himself and then it can be used. You can follow below ways:

1. Please use text editor to open the file "at91sam9g45ekes_demo_linux_nandflash.tcl" before the system auto-programming;

2. Go to the location roughly in the 84th line, the contents are as below:

"bootargs=mem=128M console=ttyS0,115200 mtdparts=atmel_nand:5M(bootstrap/uboot/kernel)ro,64M(rootfs),-(data) root=/dev/mtdblock1 rw   rootfstype=jffs2" \

Please change 64M to 200M and note do not change to 256M as part of the space will be used for uboot and system.

"bootargs=mem=128M console=ttyS0,115200 mtdparts=atmel_nand:5M(bootstrap/uboot/kernel)ro,64M(rootfs),-(data) root=/dev/mtdblock1 rw   rootfstype=jffs2" \

3. Re-programming

4. It will be as following if successful.

root@at91sam:~$ df -h
Filesystem                Size      Used Available Use% Mounted on
/dev/mtdblock1          200.0M     31.8M    168.3M  16% /
tmpfs                    40.0k         0     40.0k   0% /mnt/.psplash
/dev/mtdblock1          200.0M     31.8M    168.3M  16% /dev/.static/dev
tmpfs                     2.0M     48.0k      2.0M   2% /dev
tmpfs                    61.5M     92.0k     61.4M   0% /var/volatile
tmpfs                    61.5M         0     61.5M   0% /media/ram