The problem is solved. Somehow the lh.white file was broken during file transfer.
2012/5/22 Gabor Perlaki <petzinger.ga...@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 >
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