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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