Re: [Freesurfer] recon-all

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)

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

    _______________________________________________
    Freesurfer mailing list
    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>
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>



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.