were there any errors in the log? Try running it with -make all to have it rebuild missing files On Thu, 28 May 2009, Iwo Bohr wrote:
Dear Freesurfer experts,
When I run recon-all batch command it did not produce all the files normally kept in subject/mri folder. Importantly brainmask.mgz file is missing, so I can't run reg-feat2anat command.
Please advise me what I can do.
Many thanks,
Iwo Bohr, PhD School of Computing Science University of Newcastle, UK