-- 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