Thanks, Bruce. - Don
> -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, November 18, 2015 8:55 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] direction for restart in the middle > > Hi Don > > the defect is too big to fix, and probably means something dramatic is wrong > (e.g. skull or cerebellum attached to the brain component of the wm.mgz). > Check out the ?h.inflated.nofix and see what is going on and correct it before > rerunning > > cheers > Bruce > On Wed, 18 Nov 2015, Krieger, Donald N. wrote: > > > > > I have run freesurfer 6Beta on the scan with very large CSF spaces > > > > With flags: -bigventricles and –notal-check . > > > > I used the latter flag per suggestions in the log as the first run > > failed on a talaraich check. > > > > This second run appears to be hung as it has not written anything new > > into the recon-all.log file for 7 hours. > > > > I would like to restart this at a reasonable point rather than at the > > beginning. > > > > Can you recognize where it is and what is are suggested restart flags? > > > > > > > > Here are the files which have appeared in the mri directory. > > > > aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log > > mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat > > talairach.log transforms wm.mgz > > > > aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz > > brain.mgz filled.mgz norm.mgz orig > > orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz > > wm.seg.mgz > > > > aseg.auto_noCCseg.mgz brainmask.auto.mgz > > ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz > > rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log > > wm.asegedit.mgz > > > > > > > > Here are the last 50 lines or so of the log file: > > > > ProgramName: mri_ca_normalize ProgramArguments: -all- > info ProgramVersion: > > $Name: stable5 $ TimeStamp: 2 > > > > ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: > > 40400 > > > > ...skipping... > > > > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 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 1.48 2011/03/02 00:04:32 nicks Exp $ > > > > $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ > > > > before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, > > g=256) > > > > 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 10 iterations > > > > marking ambiguous vertices... > > > > 111330 ambiguous faces found in tessellation > > > > segmenting defects... > > > > 38 defects found, arbitrating ambiguous regions... > > > > analyzing neighboring defects... > > > > -merging segment 13 into 0 > > > > -merging segment 23 into 0 > > > > -merging segment 29 into 0 > > > > -merging segment 32 into 0 > > > > -merging segment 36 into 0 > > > > -merging segment 16 into 12 > > > > -merging segment 15 into 14 > > > > 31 defects to be corrected > > > > 0 vertices coincident > > > > reading input > > surface/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.q > > sphere.nofix > > ... > > > > reading brain volume from brain... > > > > reading wm segmentation from wm... > > > > Computing Initial Surface Statistics > > > > -face loglikelihood: -9.2710 (-4.6355) > > > > -vertex loglikelihood: -8.2866 (-4.1433) > > > > -normal dot loglikelihood: -3.4816 (-3.4816) > > > > -quad curv loglikelihood: -6.0138 (-3.0069) > > > > Total Loglikelihood : -27.0531 > > > > > > > > CORRECTING DEFECT 0 (vertices=53053, convex hull=8873) > > > > > > > > Thanks for your direction on this. - Don > > > > > > > > > > _______________________________________________ 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. 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