Hello Alison, Thank you very much for your advice. At least I know where the problem is, even though it doesn't look like I can solve it at the moment, since I have no writing rights to the file and our administrator is ... guess where? away in Boston, at Freesurfer and your home :) Hopefully I'll be able to fix it when he's back early next week. Will let you know
Many thanks again, Iwo
________________________________ From: Allison Stevens astevens@nmr.mgh.harvard.edu To: Iwo Bohr iwobohr@yahoo.co.uk Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Friday, 29 May, 2009 13:58:54 Subject: Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error
Iwo, If you do ls $FREESURFER_HOME/bin
Do you see mri_nu_correct.mni there?
If you do, this message might help you: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
Essentially, you have to make sure the nu_correct uses perl so you need to make sure it knows where it's located.
If you don't have that binary, then you'll need to download it. Let us know, Allison