Thanks Anil! Tudor, sounds like you should give this a try.
I'm re-posting this to the freesurfer list to archive it.
Nick
Hi
I am having the same problem but I have an idea where it's occurring.
I have Windows XP Virtualbox Ubuntu Install where I have an windows share on the Linux using shared folder from windows
When I use the shared folder it gives this error When I use the Bert data set in its original location subjects dir it works fine When I transfer a new subject in virtualuser Freesurfer subjects folder it's works fine I ran it with -debug command to check and I thinks nu_ estimate makes some temp folders which gets messed up when you use shared folders. So to avoid this error transfer the subjects folder to virtualuser subject folder rather than using -sd command to specify a shared folder
Sincerely
Anil