Yes, fix the pons cutting plane. I've modified the text in that link to be clearer. Let me know if you still have trouble.
doug Yang Liu wrote: > Hi Doug, > > Thanks for replying! > I checked the filled.mgz. The cerebellum is still attached. > How can I fix the problem? I am a new user of Freesurfer. > My guess is to select the correct pons cutting plane. But I found that > the instruction on > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting is > a little vague for me. > Are there further instructions (better with figure examples) available? > > Thanks, > > Yang Liu > > PostDoc, > Wellesley College and HMS. > > > > > > > > > On Mon, Dec 6, 2010 at 10:22 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Have you looked at the filled.mgz volume to make sure that > cerebellum is not attached? > > doug > > Yang Liu wrote: > > Hi, > > I am processing the anatomical monkey brain now. > When recon-all runs, it stops at the step of "mris_fix_topology" > > I inserted the last part of my recon-all.log below: > > It stops at "CORRECTING DEFECT 0 (vertices=65691, convex > hull=4296)" > for more than 12 hours. Does this step take that long? Or are > there some problems in the data that make freesurfer idling? > > Thanks, > > Yang > > > #-------------------------------------------- > #...@# Fix Topology lh Sat Dec 4 17:01:16 EST 2010 > > cp ../surf/lh.orig.nofix ../surf/lh.orig > > > cp ../surf/lh.inflated.nofix ../surf/lh.inflated > > /home/yang/091017Castor/scripts > > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 > 091017Castor lh > > reading spherical homeomorphism from 'qsphere.nofix' > using genetic algorithm with optimized parameters > setting seed for random number genererator to 1234 > > ************************************************************* > Topology Correction Parameters > retessellation mode: genetic search > number of patches/generation : 10 > number of generations : 10 > surface mri loglikelihood coefficient : 1.0 > volume mri loglikelihood coefficient : 10.0 > normal dot loglikelihood coefficient : 1.0 > quadratic curvature loglikelihood coefficient : 1.0 > volume resolution : 2 > eliminate vertices during search : 1 > initial patch selection : 1 > select all defect vertices : 0 > ordering dependant retessellation: 0 > use precomputed edge table : 0 > smooth retessellated patch : 2 > match retessellated patch : 1 > verbose mode : 0 > > ************************************************************* > INFO: assuming .mgz format > $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ > before topology correction, eno=-810 (nv=213660, nf=428940, > ne=643410, g=406) > using quasi-homeomorphic spherical map to tessellate cortical > surface... > > Correction of the Topology > Finding true center and radius of Spherical Surface...done > Surface centered at (0,0,0) with radius 100.0 in 9 iterations > marking ambiguous vertices... > 156279 ambiguous faces found in tessellation > segmenting defects... > 64 defects found, arbitrating ambiguous regions... > analyzing neighboring defects... > -merging segment 14 into 0 > -merging segment 11 into 10 > -merging segment 23 into 18 > -merging segment 33 into 22 > -merging segment 40 into 22 > -merging segment 62 into 25 > -merging segment 39 into 34 > -merging segment 35 into 46 > 56 defects to be corrected > 0 vertices coincident > reading input surface > /home/yang/091017Castor/surf/lh.qsphere.nofix... > reading brain volume from brain... > reading wm segmentation from wm... > Computing Initial Surface Statistics > -face loglikelihood: -8.8048 (-4.4024) > -vertex loglikelihood: -5.5855 (-2.7928) > -normal dot loglikelihood: -3.4654 (-3.4654) > -quad curv loglikelihood: -5.6070 (-2.8035) > Total Loglikelihood : -23.4627 > > CORRECTING DEFECT 0 (vertices=65691, convex hull=4296) > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
