Hi Ziad,
I have checked again, my subject directory contains all the sub directories and files that you mentioned above but for some reason they didn't copied in last email body here are the contents of the /mri directory
UN:~/CHR01/mri> ls
aparc.a2009s+aseg.mgz orig
aparc+aseg.mgz orig.mgz
aseg.auto.mgz orig_nu.log
aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz
aseg.auto_noCCseg.mgz rawavg.mgz
aseg.mgz rh.ribbon.mgz
brain.finalsurfs.mgz ribbon.mgz
brainmask.auto.mgz segment.dat
brainmask.mgz T1.mgz
brain.mgz talairach.label_intensities.txt
ctrl_pts.mgz talairach.log
error.log talairach_with_skull_2.log
filled.mgz talairach_with_skull.log
lh.ribbon.mgz transforms
mri_nu_correct.mni.log wm.asegedit.mgz
mri_nu_correct.mni.log.bak wm.mgz
norm.mgz wmparc.mgz
nu.mgz wm.seg.mgz
nu_noneck.mgz
UN:~/CHR01/mri>
waiting for your reply
Best Regards
Naveed