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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:
External Email - Use Caution *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:
External Email - Use CautionDear 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_F..., 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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