So for some reason the message board software is refusing to display your last response containing the result of your 'ls' command. But I had a copy emailed to me. It is strange that I do not see an mri/ directory that would contain all of the volumes like "lh.ribbon.mgz", "orig/orig.mgz", and directories such as "orig/" "transforms/" etc. You do have these directories and volumes but they are not under the typical FreeSurfer directory structure. Could it be that they got move accidentally out of the mri/ directory?
Consider recreating ./mri , move ONLY the items you in your posted listing between "lh.ribbon.mgz" and "wm.seg.mgz", including these two limiting files.
Delete the SUMA/ directory and then try rerunning @SUMA_Make_Spec_FS ...
cheers,
Ziad
