Dear all
Came across a segmentation fault while running recon-all, specifically
during mris_make_surfaces... Output pasted below...
Any ideas/help greatly appreciated!
Adrian.
--
Adrian L. Williams, PhD
Centre for Cognition & Neuroimaging
Brunel University
Uxbridge
Middlesex
UB8 3PH
#--------------------------------------------
#@# Make Final Surf rh Sun Jan 11 09:11:39 GMT 2009
/Volumes/DataDisk/freesurf/adrian/scripts
\n mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh \n
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $
$Id: mrisurf.c,v 1.557.2.15 2008/07/30 17:54:19 greve Exp $
reading volume /Volumes/DataDisk/freesurf/adrian/mri/filled.mgz...
reading volume /Volumes/DataDisk/freesurf/adrian/mri/brain.finalsurfs.mgz...
reading volume /Volumes/DataDisk/freesurf/adrian/mri/wm.mgz...
19879 bright wm thresholded.
4 bright non-wm voxels segmented.
reading original surface position from
/Volumes/DataDisk/freesurf/adrian/surf/rh.orig...
computing class statistics...
border white: 277588 voxels (1.65%)
border gray 287750 voxels (1.72%)
WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0]
GM (88.0) : 86.5 +- 9.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 75.9 (was 70)
setting MAX_BORDER_WHITE to 111.6 (was 105)
setting MIN_BORDER_WHITE to 85.0 (was 85)
setting MAX_CSF to 66.8 (was 40)
setting MAX_GRAY to 100.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 80.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 57.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.02-->6.25) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.12 (0.00-->4.95)
mean absolute distance = 0.84 +- 1.11
3662 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
intensity peaks found at WM=106, GM=85
using class modes intead of means....
mean inside = 100.7, mean outside = 89.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=92.7, 106 (106) missing vertices, mean dist 0.2 [0.8
(%36.9)->0.8 (%63.1))]
%59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=ALW-A, nav=4, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
vertex spacing 0.90 +- 0.24 (0.10-->7.73) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.12 (0.00-->4.09)
vertex spacing 0.91 +- 0.25 (0.08-->8.87) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.13 (0.00-->4.04)
smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.06-->8.92) (max @ vno 57593 --> 140123)
face area 0.28 +- 0.13 (0.00-->4.04)
mean absolute distance = 0.46 +- 0.83
3512 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3631140.5, rms=6.62
001: dt: 0.5000, sse=4303983.5, rms=4.71
002: dt: 0.5000, sse=4324421.5, rms=3.47
003: dt: 0.5000, sse=4337002.0, rms=2.68
004: dt: 0.5000, sse=4291947.5, rms=2.21
005: dt: 0.5000, sse=4263108.5, rms=1.94
006: dt: 0.5000, sse=4212978.0, rms=1.80
007: dt: 0.5000, sse=4200574.0, rms=1.72
rms = 1.68, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=4191339.5, rms=1.68
009: dt: 0.2500, sse=3181011.8, rms=1.44
rms = 1.42, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=3087899.5, rms=1.42
rms = 1.41, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=3061586.0, rms=1.41
positioning took 75.5 minutes
inhibiting deformation at non-cortical midline structures...
mean border=94.2, 141 (49) missing vertices, mean dist -0.2 [0.6
(%61.8)->0.3 (%38.2))]
%65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=ALW-A, nav=2, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
vertex spacing 0.90 +- 0.24 (0.03-->9.51) (max @ vno 57593 --> 140123)
face area 0.34 +- 0.16 (0.00-->5.05)
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.07-->9.67) (max @ vno 57593 --> 140123)
face area 0.34 +- 0.16 (0.00-->5.09)
mean absolute distance = 0.39 +- 0.57
4028 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3383843.2, rms=3.03
012: dt: 0.5000, sse=3668512.5, rms=2.02
013: dt: 0.5000, sse=3762432.5, rms=1.65
014: dt: 0.5000, sse=3746829.0, rms=1.49
015: dt: 0.5000, sse=3832901.5, rms=1.41
rms = 1.41, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=3843775.0, rms=1.41
017: dt: 0.2500, sse=3401710.2, rms=1.27
rms = 1.26, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=3332062.8, rms=1.26
rms = 1.26, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=3308422.0, rms=1.26
positioning took 36.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=95.9, 155 (28) missing vertices, mean dist -0.2 [0.5
(%68.6)->0.2 (%31.4))]
%78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=ALW-A, nav=1, nbrs=2, l_repulse=5.000,
l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
vertex spacing 0.89 +- 0.24 (0.06-->9.72) (max @ vno 57593 --> 140123)
face area 0.34 +- 0.16 (0.00-->5.02)
Segmentation fault
Darwin ALW-Apple-G5.local 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10
18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Sun Jan 11 11:29:52 GMT 2009