Yes, they should be completely gone. doug
Yang Liu wrote: > Hi Doug, > > The cerebellem and the pons are still in the filled.mgz. Are they > supposed to be completely gone in filled.mgz? > > Thanks, > > Yang > > On Tue, Dec 7, 2010 at 10:48 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Did you look at the filled.mgz? Is it detached there? > > doug > > Yang Liu wrote: > > Hi Doug, > > Thank you for updating the description. > I still got the same problem as before. The processing stream > stopped at "CORRECTING DEFECT 15 (vertices=63586, convex > hull=4120)". > > I followed the instructions to select cutting planes. I > attached the three views when I selecting the cutting plane > for pons. > > The first is h-view-pons.jpg. The horizontal slice shows that > the brain stem is detached from other regions. The red cursor > in the picture is the point I selected from the pons. > The c-view-pons.jpg and the s-view-pons.jpg are the coronal > view and the sagittal view I selected. > > I did not get the point in the instruction that said "verify > with both the horizontal view and the coronal view that your > cursor is central in all three views, adjust as necessary." > I did try to adjust the cursor location in the coronal view > and saggital view to be central. But after I make the > adjustment in the coronal view and sagittal view, I found that > the orignal cursor location in the horizontal view has also > been changed. > > Is my understanding wrong? > > > Yang Liu > > PostDoc > Wellesley College and HMS > > > > > ************************************************************* > 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=-808 (nv=209380, nf=420376, > ne=630564, g=405) > 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 11 iterations > marking ambiguous vertices... > 152885 ambiguous faces found in tessellation > segmenting defects... > 67 defects found, arbitrating ambiguous regions... > analyzing neighboring defects... > -merging segment 1 into 0 > -merging segment 2 into 0 > -merging segment 15 into 0 > -merging segment 7 into 6 > -merging segment 0 into 20 > -merging segment 44 into 25 > -merging segment 38 into 32 > -merging segment 28 into 42 > -merging segment 54 into 52 > -merging segment 60 into 59 > 57 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: -8.7131 (-4.3565) > -vertex loglikelihood: -5.4786 (-2.7393) > -normal dot loglikelihood: -3.3504 (-3.3504) > -quad curv loglikelihood: -5.6067 (-2.8033) > Total Loglikelihood : -23.1488 > > CORRECTING DEFECT 0 (vertices=205, convex hull=133) > After retessellation of defect 0, euler #=-14 > (129395,381695,252286) : difference with theory (-54) = -40 > > CORRECTING DEFECT 1 (vertices=429, convex hull=192) > After retessellation of defect 1, euler #=-13 > (129414,381847,252420) : difference with theory (-53) = -40 > > CORRECTING DEFECT 2 (vertices=100, convex hull=82) > After retessellation of defect 2, euler #=-12 > (129435,381948,252501) : difference with theory (-52) = -40 > > CORRECTING DEFECT 3 (vertices=271, convex hull=174) > After retessellation of defect 3, euler #=-11 > (129487,382198,252700) : difference with theory (-51) = -40 > > CORRECTING DEFECT 4 (vertices=208, convex hull=101) > After retessellation of defect 4, euler #=-10 > (129525,382356,252821) : difference with theory (-50) = -40 > > CORRECTING DEFECT 5 (vertices=68, convex hull=146) > After retessellation of defect 5, euler #=-9 > (129563,382536,252964) : difference with theory (-49) = -40 > > CORRECTING DEFECT 6 (vertices=346, convex hull=162) > After retessellation of defect 6, euler #=-8 > (129639,382836,253189) : difference with theory (-48) = -40 > > CORRECTING DEFECT 7 (vertices=36, convex hull=77) > After retessellation of defect 7, euler #=-7 > (129648,382899,253244) : difference with theory (-47) = -40 > > CORRECTING DEFECT 8 (vertices=141, convex hull=128) > After retessellation of defect 8, euler #=-6 > (129669,383017,253342) : difference with theory (-46) = -40 > > CORRECTING DEFECT 9 (vertices=45, convex hull=79) > After retessellation of defect 9, euler #=-5 > (129687,383104,253412) : difference with theory (-45) = -40 > > CORRECTING DEFECT 10 (vertices=55, convex hull=103) > After retessellation of defect 10, euler #=-4 > (129697,383174,253473) : difference with theory (-44) = -40 > > CORRECTING DEFECT 11 (vertices=6, convex hull=26) > After retessellation of defect 11, euler #=-3 > (129699,383187,253485) : difference with theory (-43) = -40 > > CORRECTING DEFECT 12 (vertices=67, convex hull=105) > After retessellation of defect 12, euler #=-2 > (129708,383259,253549) : difference with theory (-42) = -40 > > CORRECTING DEFECT 13 (vertices=27, convex hull=27) > After retessellation of defect 13, euler #=-1 > (129712,383278,253565) : difference with theory (-41) = -40 > > CORRECTING DEFECT 14 (vertices=6, convex hull=11) > After retessellation of defect 14, euler #=0 > (129712,383280,253568) : difference with theory (-40) = -40 > > CORRECTING DEFECT 15 (vertices=63586, convex hull=4120) > > On Mon, Dec 6, 2010 at 12:34 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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> > <http://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> > > <http://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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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> > <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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > > -- > 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> > > -- 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
