Did you check to see whether the cerebellum (or some large bit of skull or brain stem) are still attached? doug
Kevin Liu wrote: > Hi, > > I'm relatively new to the FreeSurfer program and have mostly worked > with processing adult brains. I am currently working on reconstructing > images of young children under 5 and am consistently running into the > same error for the two subjects I am running during mris_fix_topology. > The error is as follows: > > 153 defects found, arbitrating ambiguous regions... > analyzing neighboring defects... > -merging segment 19 into 4 > -merging segment 28 into 7 > -merging segment 44 into 7 > -merging segment 43 into 7 > -merging segment 59 into 7 > -merging segment 63 into 7 > -merging segment 24 into 8 > -merging segment 25 into 17 > -merging segment 21 into 18 > -merging segment 67 into 30 > -merging segment 78 into 30 > -merging segment 38 into 33 > -merging segment 79 into 73 > -merging segment 85 into 77 > -merging segment 113 into 77 > -merging segment 88 into 77 > -merging segment 95 into 77 > -merging segment 97 into 77 > -merging segment 93 into 87 > -merging segment 91 into 90 > -merging segment 135 into 117 > -merging segment 136 into 117 > -merging segment 141 into 126 > -merging segment 146 into 140 > -merging segment 149 into 142 > 128 defects to be corrected > 0 vertices coincident > reading input surface /home/local/SOC/kcl388/wong_ > lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsphere.nofix... > reading brain volume from brain... > reading wm segmentation from wm... > Computing Initial Surface Statistics > -face loglikelihood: -9.7664 (-4.8832) > -vertex loglikelihood: -7.0295 (-3.5147) > -normal dot loglikelihood: -3.5134 (-3.5134) > -quad curv loglikelihood: -6.0484 (-3.0242) > Total Loglikelihood : -26.3577 > > CORRECTING DEFECT 0 (vertices=281, convex hull=141) > After retessellation of defect 0, euler #=-62 (115680,331866,216124) : > difference with theory (-125) = -63 > > CORRECTING DEFECT 1 (vertices=100, convex hull=64) > After retessellation of defect 1, euler #=-61 (115689,331920,216170) : > difference with theory (-124) = -63 > > CORRECTING DEFECT 2 (vertices=12, convex hull=20) > After retessellation of defect 2, euler #=-60 (115690,331929,216179) : > difference with theory (-123) = -63 > > CORRECTING DEFECT 3 (vertices=395, convex hull=187) > After retessellation of defect 3, euler #=-59 (115735,332152,216358) : > difference with theory (-122) = -63 > > CORRECTING DEFECT 4 (vertices=7865, convex hull=2299) > > > > > The defects never completely correct, and the program just hangs on > correcting one of the defects (in this case 'DEFECT 4'). Do you have > any suggestions as to where to go from here? I have checked talairach > and done skull stripping edits, none of which seemed to have worked. > > Best, > Kevin > > > -- > Kevin Liu > MD Candidate 2014 > Feinberg School of Medicine > > > > > -- > Kevin Liu > MD Candidate 2014 > Feinberg School of Medicine > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > 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 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 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.
