yes, the cortical hemispheres should have separate labels which show up as different colors, and the cerebellum and brainstem below the pons should be erases
On Tue, 7 Dec 2010, 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>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 >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
