External Email - Use Caution       
Dear experts,

mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html, but wasn't able to load the &h.defect_labels as I received the error below.

Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong?
FYI, I'm running recon-all thru the HCP Pipeline. Thanks!

tksurfer avoss_01 lh defect_labels

subject is avoss_01
hemi    is lh
surface is defect_labels
surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf
checking for nofix files in 'defect_labels'
Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01)
Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
nquads=4063237,  nvertices=664
ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

No such file or directory

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer