Hi Jürgen,

a defect with 48000 vertices is huge (1/3 of the cortex). Check to make sure that the skull and cerebellum aren't attached to the filled volume and that the hemispheres are properly separated.

cheers, Bruce

On Wed, 11 Feb 2009, Jürgen Hänggi wrote:

Dear FS experts

I tried to reconstruct the surface models of a patient's brain with large anomalies (see attachment). There is a large topological defect which FS cannot fix. FS failed with the following error message:

Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 169740 ambiguous faces found in tessellation segmenting defects... 87 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 0 -merging segment 26 into 0 -merging segment 61 into 3 -merging segment 39 into 31 -merging segment 0 into 36 -merging segment 45 into 37 -merging segment 53 into 37 -merging segment 56 into 37 -merging segment 64 into 54 -merging segment 69 into 66 -merging segment 72 into 70 76 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/altin_pre1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8502 (-4.4251) -vertex loglikelihood: -6.6049 (-3.3024) -normal dot loglikelihood: -3.5099 (-3.5099) -quad curv loglikelihood: -6.1072 (-3.0536) Total Loglikelihood : -25.0721

CORRECTING DEFECT 0 (vertices=29, convex hull=52) After retessellation of defect 0, euler #=-24 (121052,354507,233431) : difference with theory (-73) = -49

CORRECTING DEFECT 1 (vertices=27, convex hull=23) After retessellation of defect 1, euler #=-23 (121054,354521,233444) : difference with theory (-72) = -49

CORRECTING DEFECT 2 (vertices=48634, convex hull=6250) mris_fix_topology(4721) malloc: *** mmap(size=1417760768) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin Freesurfer.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386

recon-all exited with ERRORS at Wed Feb 11 00:01:09 CET 2009

[Freesurfer:/Applications/freesurfer/subjects] Nicki%

Any suggestions? What does bus error mean? How does I can force FS to correct this large defect?

Thanks in advance Regards Jürgen

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Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

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