Those are giant defects. Check the inflated.nofix to see if the skull or cerebellum is attached
On Aug 19, 2011, at 11:38 AM, Catherine Wan <cyc...@gmail.com> wrote: > Dear List, > > I've been encountering a series of error messages when I did recon-all on a > number of subjects, using Freesurfer v5.1 > > Below are the error messages for 3 different subjects (all with lesions). I > tried them using both dicom and nifti, and on various computers, but the same > messages appeared. > Any advice would be much appreciated. > > Many thanks! > Catherine > > > > SUBJECT 1 > > Correction of the Topology > Finding true center and radius of Spherical Surface...done > Surface centered at (0,0,0) with radius 100.0 in 15 iterations > marking ambiguous vertices... > 188852 ambiguous faces found in tessellation > segmenting defects... > 1 defects found, arbitrating ambiguous regions... > analyzing neighboring defects... > 1 defects to be corrected > 0 vertices coincident > reading input surface > /mnt/nfs/hippo1/freesurfer5/freesurfer/subjects/Aphasia_MIT/DMAR_pre1_nii/surf/lh.qsphere.nofix... > reading brain volume from brain... > reading wm segmentation from wm... > Computing Initial Surface Statistics > -face loglikelihood: -10.1436 (-5.0718) > -vertex loglikelihood: -8.7336 (-4.3668) > -normal dot loglikelihood: -3.6140 (-3.6140) > -quad curv loglikelihood: -7.5212 (-3.7606) > Total Loglikelihood : -30.0124 > > CORRECTING DEFECT 0 (vertices=98583, convex hull=1425) > Excessive topologic defect encountered: could not allocate 1019599903 edges > for retessellation > Cannot allocate memory > > > > > SUBJECT 2 > > mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated > avg radius = 51.9 mm, total surface area = 58524 mm^2 > writing inflated surface to ../surf/lh.inflated > writing sulcal depths to ../surf/lh.sulc > step 060: RMS=0.039 (target=0.015) > inflation complete. > inflation took 0.3 minutes > > mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated > > normalizing curvature values. > averaging curvature patterns 5 times. > sampling 10 neighbors out to a distance of 10 mm > Segmentation fault > > > > SUBJECT 3 (stuck on this step for > 48 hrs) > > > CORRECTING DEFECT 0 (vertices=130, convex hull=179) > After retessellation of defect 0, euler #=-30 (62919,184624,121675) : > difference with theory (-51) = -21 > > CORRECTING DEFECT 1 (vertices=46, convex hull=64) > After retessellation of defect 1, euler #=-29 (62936,184700,121735) : > difference with theory (-50) = -21 > > CORRECTING DEFECT 2 (vertices=75, convex hull=105) > After retessellation of defect 2, euler #=-28 (62974,184859,121857) : > difference with theory (-49) = -21 > > CORRECTING DEFECT 3 (vertices=54486, convex hull=3968) > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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