Cameron,

This is a known problem with the topology fixer used in the 'dev' (non- public) version of recon-all. We are currently working on a solution. In the meantime, you can either use the 'stable' version of freesurfer (source usr/local/freesurfer/nmr-std-env), or include the -use-old-fixer flag with recon-all, which will revert to using the old topology fixer (the one distributed publicly).

Nick

On Wed, 2007-01-17 at 11:55 -0500, Cameron Ellis wrote:

Hi all, I received the following error while running autorecon. Has anyone come across this before who knows what to do to fix it? Cameron

Command run: recon-all -subjid SM1S17_autoreconall -autorecon2

Error Script: #@# Fix Topology lh Wed Jan 17 04:00:20 EST 2007

cp ../surf/lh.orig.nofix ../surf/lh.orig

cp ../surf/lh.inflated.nofix ../surf/lh.inflated

cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere

cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm

/autofs/space/troy_003/users/retrievalnewest/SM1S17_autoreconall/scripts

mris_topo_fixer -mgz -warnings SM1S17_autoreconall lh

verbose mode on (medium mode): printing warnings Before topology correction, eno=-64 (nv=132420, nf=264968, ne=397452, g=33) Surface Diagnostics: eno=-64 (nv=132420, nf=264968, ne=397452) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold The original surface does not self-intersect The surface has 33 loops (X=-64)

Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 5383 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) -removing defect 0 (overlapping defect 1) INFO: assuming .mgz format reading input surface /autofs/space/troy_003/users/retrievalnewest/SM1S17_autoreconall/surf/lh.orig... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (77.69) < WM (97.20) ] Computing Initial Surface Statistics -face loglikelihood: -6.3839 (-3.1919) -vertex loglikelihood: -6.2470 (-3.1235) -normal dot loglikelihood: -3.6517 (-3.6517) -quad curv loglikelihood: -5.7654 (-2.8827) Total Loglikelihood : -22.0480

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number 3 (-1 loops) computing statistics for defect 1: 55 vertices location: [ (135,115,184) - average intensity = 81.597 ] -gray ( 77.69 , 5.73 ) -white ( 98.05 , 2.73 ) -gray ( 80.21 , 20.72 ) -white ( 98.85 , 18.30 ) -intensity (77.686409 [log = -2.909158 ]- 98.046989 [log = -1.932804 ]) -curv (k1=-0.161 (0.638) , r1 = 6.211 | k2=-0.049 (0.152), r2 = 20.453 ) -curv (k1=-0.130 (0.684) , r1 = 7.700 | k2=-0.023 (0.257), r2 = 43.903 ) MRISalloc(-155, 424): could not allocate vertices Cannot allocate memory Linux node0344 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Jan 17 04:01:31 EST 2007 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer