The topology error labels might be be created if it did not finish. YOu
can try just loading the brain.mgz, the wm.mgz, and the orig.nofix and
see if you can find a big topo error
On 5/31/2021 11:16 AM, Ellen Ji wrote:
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
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