I was unable to extract parts of the cortex with the commands you had told me to try last time. I realised then that it was because recon hadn't finished running and I was using partially processed data. So I tried running it again. Here below is what I got. Since I'm using a partitioned machine space may be a problem but it doesn't seem to say so. Thanks in advance for the advice.
#-------------------------------------------- #@# Cortical ribbon mask Sat Mar 20 07:17:29 GMT 2010 /home/s0964091/Desktop/jan/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance jan
mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux
recon-all exited with ERRORS at Sat Mar 20 07:17:29 GMT 2010