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 greve@nmr.mgh.harvard.eduwrote:
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 < greve@nmr.mgh.harvard.edu mailto:greve@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 onhttp://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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu mailto:greve@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 greve@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