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.

#--------------------------------------------
#@# 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