External Email - Use Caution 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 (<bfis...@mgh.harvard.edu>) escribió: > Or the ?h.inflated.nofix can be helpful as well > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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 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 > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/18DbLFYnkzpL_VG6cCKRH7JNf1r42Clxkaudup1Kh_EGSchdUrdpc-we4LJpSM1WCPet9d251usmpkBDXwVynpCA3mtsn4t3xWp9BZMVxG7sHawhEM9Mi1ghk2PviC4xhEt_vh6c2zHAscS2d7xgul62j5N2_PbC9Kpox0TTiT9WQQo36N8613LTsj6hZesreFdGLrWG5_yOr3056nU-5HpmpKykz6IzdWLtNLK37CtcxwYBLgTyMdSMfIl-ZLCiOqxoY9ZDQ9VWlYFpAkc8lMA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1DI84rKL4SpDdiEv_m65JM6o4rI5AZVlICF1tso_GGIsz103u0f5eJKrymIzWHLYjyJhZ8OPhlD7r1ixMXxhz1Xz4rzrPA15mVVfHip72zyAWRosxKEOiQQzkQeM8llwv2GBAyT8OZgdtM-RAHQfqXClXeu50uqLv1CavAAGVNi2iTEJ8fTTWgOztEQmqU0DxU061XEn2hwSfyTYX_vDvgk2SmjaxOtaH1W2MdXO6Fy9JCvLeP0hjTVMM3VIkgAaqZryn5k7-YEGvP_diJKvhyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/18DbLFYnkzpL_VG6cCKRH7JNf1r42Clxkaudup1Kh_EGSchdUrdpc-we4LJpSM1WCPet9d251usmpkBDXwVynpCA3mtsn4t3xWp9BZMVxG7sHawhEM9Mi1ghk2PviC4xhEt_vh6c2zHAscS2d7xgul62j5N2_PbC9Kpox0TTiT9WQQo36N8613LTsj6hZesreFdGLrWG5_yOr3056nU-5HpmpKykz6IzdWLtNLK37CtcxwYBLgTyMdSMfIl-ZLCiOqxoY9ZDQ9VWlYFpAkc8lMA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1DI84rKL4SpDdiEv_m65JM6o4rI5AZVlICF1tso_GGIsz103u0f5eJKrymIzWHLYjyJhZ8OPhlD7r1ixMXxhz1Xz4rzrPA15mVVfHip72zyAWRosxKEOiQQzkQeM8llwv2GBAyT8OZgdtM-RAHQfqXClXeu50uqLv1CavAAGVNi2iTEJ8fTTWgOztEQmqU0DxU061XEn2hwSfyTYX_vDvgk2SmjaxOtaH1W2MdXO6Fy9JCvLeP0hjTVMM3VIkgAaqZryn5k7-YEGvP_diJKvhyw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > The information in this e-mail is intended only for the person to whom it is > addressed. 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