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>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>> 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>>> 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>> >> >> >> 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>> >> >> 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> >> >> >> >> >> 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> >> 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 > >
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