Hi,
I have upgraded to v5.0 assuming that I'll be in a better shape now. I issued this command:
nohup recon-all -s ../NanditaGoodDataSetSubject5.0_run2 -i ./t1_svs.nii -autorecon-all &
which failed after a while . I used nohup so that I can close shell with terminating the calculation. The tail of recon-all.log is show below (in red ). I do assume that I have no RAM problems as this computer is dedicated for such calculations.
Any hint pls?
Thanks #-------------------------------------------- #@# Smooth2 lh Wed Apr 13 17:48:03 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Apr 13 17:48:12 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.7 mm, total surface area = 85687 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.6 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 321 vertices thresholded to be in k1 ~ [-0.25 0.24], k2 ~ [-0.11 0.05] total integrated curvature = 0.502*4pi (6.303) --> 0 handles ICI = 1.4, FI = 9.5, variation=161.148 170 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.14 0.12] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Wed Apr 13 17:52:48 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm NanditaGoodDataSetSubject5.0_run2 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ NanditaGoodDataSetSubject5.0_run2/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 258 ] WARN: S lookup min: -0.547240 WARN: S explicit min: 0.000000 vertex = 126 #-------------------------------------------- #@# Sphere lh Wed Apr 13 17:53:01 EDT 2011 /home/sramadan/freesurfer/subjects/NanditaGoodDataSetSubject5.0_run2/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 4.62 hours scaling brain by 0.274... pass 1: epoch 1 of 3 starting distance error %20.44 pass 1: epoch 2 of 3 starting distance error %20.39 unfolding complete - removing small folds... starting distance error %20.32 removing remaining folds... final distance error %20.32 284: 0 negative triangles Linux cluster.bwh.harvard.edu 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NanditaGoodDataSetSubject5.0_run2 exited with ERRORS at Wed Apr 13 22:30:15 EDT 2011