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 cycwan@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)

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