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> 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 <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)

       ------------------------------------------------------------------------

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   --     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>

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   <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




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--
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