Hi, 

Thank you for the help. I saved it as a plain text. and it did not give me that error again. 

However, even after I saved the new version of the mkbrainmask-sess, i get the same error. 

Tue Jul 22 14:32:30 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata
mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update
----------------------------------------
------------------------------------------------
------------------------------------------------
/Users/balajigoparaju/Desktop/subjectdata/LD-functional 
Tue Jul 22 14:32:30 EDT 2008
/Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold
ls: masks/brain.nii: No such file or directory
-rwxrwxrwx   1 balajigo  admin  523 Jul  7 09:57 006/f.bhdr
Update not needed
Tue Jul 22 14:32:32 EDT 2008
mkbrainmask-sess done
----------------------------------------
Started at Tue Jul 22 14:32:26 EDT 2008
Ended   at Tue Jul 22 14:32:32 EDT 2008
preproc-sess done

Thank you for any help.