The problem is solved. Somehow the lh.white file was broken during file transfer.

2012/5/22 Gabor Perlaki petzinger.gabor@gmail.com

Hi all!

I've just ran the preprocessing for TRACULA analysis, with the command "trac-all -prep -c /home/kutato12/Desktop/dmrirc". It works everything fine, and the output files are correct until the following command:

mri_aparc2aseg --s my_subject --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/kutato12/freesurfer/subjects//my_subject/dlabel/anatorig/aparc+aseg+2mm.nii.gz freadFloat: fread failed

SUBJECTS_DIR /home/kutato12/freesurfer/subjects subject my_subject outvol /home/kutato12/freesurfer/subjects//my_subject/dlabel/anatorig/aparc+aseg+2mm.nii.gz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 2.000000 RipUnknown 0

It fails with the following:

freadFloat: fread failed mrisFindNeighbors: /home/kutato12/freesurfer/subjects/my_subject/surf/lh.white: face[1].v[0] = 0, but face 1 not in vertex 0 face list

Segmentation fault Linux kutato12 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

The recon-all finished on the MPRAGE without error before trac-all script was started. I've freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on Ubuntu 11.04, and I use the trac-all update (2012/01/09).

I'd appreciate any help on this issue.

Thanks, Gabor