Hi Diana
It’s not the number of defects that matters – it is the large ones. The time it takes to correct them is square in the (convex hull of the) number of vertices in the defect. We have a tutorial on our website
about how to find them and fix them. I find it easiest to load the ?h.orig.nofix over the wm.mgz and norm.mgz then load the ?h.defect_labels to onto the ?h.orig.nofix to color the vertices that are in a defect
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of DIANA ORTEGA CRUZ
Sent: Wednesday, June 2, 2021 3:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_fix_topology taking ages
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Dear Douglas and Bruce,
my name is Diana, I am encountering the same issue as Ellen with Fix-topology taking too long. Once we make sense of the origin of the issue (for example, I confirmed that my smoothwm.nofix has a lot of holes), do you know if is there any
way to solve it? Could the data be modified in some way to get through this step?
Thanks a lot for your great help!! Best wishes,
Diana Ortega.
El mié, 2 jun 2021 a las 3:13, Fischl, Bruce (<BFISCHL@mgh.harvard.edu>) escribió:
Or the ?h.inflated.nofix can be helpful as well
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_fix_topology taking ages
I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in surface viewing (not in the volume). You can often see defects better on this surface (they look likes holes or handles; you should at least see some)
On 6/1/2021 4:55 PM, Ellen Ji wrote:
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Hi Doug, when you say it did not finish, could you clarify what process "it" refers to?
I loaded the files you suggested and nothing popped out to me aside from the fact that the wm.mgz didn't seem to cover all the white matter.
Is it possible that topology error labels don't necessarily suggest that something went wrong and I can trust the results?
Thanks.On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
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:
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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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