Hi Alan, If you only have this problem with one or just a few subjects, then I am pretty confident that running recon-all -autorecon2-wm -randomness will solve your problem. Otherwise let me know!
Marie On Jun 28, 2011, at 3:48 PM, Alan Francis wrote: > Hi Marie: > > I have the same problem. I am doing LGI on a group of Genetic High Risk (for > Schizophrenia) subjects (n=77). > > Here is what I got for one brain: > > WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high > (lGI=47.4609)... > ...lGI computation will be stopped. This may be caused by topological > defects, check mris_euler_number on the pial surface. > > ERROR: compute_lgi did not create output file > '/usr/local/freesurfer/subjects/HM5103/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! > Linux NeuroImage-Gamma 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 > UTC 2010 x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011 > > Do I do the same thing that you recommended? > > thanks, > > Alan > > > On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer <marie.sch...@unige.ch> wrote: > > Wayne, > > You can try to rerun the surface reconstruction (recon-all -autorecon2-wm > -randomness, in order to change the number of vertices, and then recon-all > -autorecon3) and then rerun the lgi process (recon-all -lgi), this should > solve the problem. If not, please let me know. > > Marie > > On Jun 27, 2011, at 10:32 PM, Wayne Su wrote: > >> Hello, >> >> I am using FS 5.1 to measure lGI (local Gyrification Index). Only one >> particular scan failed. Here are some messages: >> >> “... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. >> WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high >> (lGI=56.5472)... >> ...lGI computation will be stopped. This may be caused by topological >> defects, check mris_euler_number on the pial surface.” >> >> >> “mris_euler_number ../surf/lh.orig \n >> euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes >> F =2V-4: 287106 = 287110-4 (0) >> 2E=3F: 861318 = 861318 (0) >> >> total defect index = 0” >> >> “mris_euler_number ./lh.pial-outer-smoothed >> ================= >> euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes >> F =2V-4: 131116 = 131120-4 (0) >> 2E=3F: 393348 = 393348 (0) >> >> total defect index = 0” >> >> >> I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 –autorecon3 >> and recon-all -s 01_097_Y0 -localGI >> >> It stopped at the same vertex. >> >> Could you please let me know anything I can do to overcome this issue? Thank >> you very much. >> >> Wayne >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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