[ficus:mri] (nmr-stable5-env) nohup mris_make_surfaces -dura MEMPRAGE_4echoes.mgz 4 OB01_orig_dura lh detecting dura using 4 echos from MEMPRAGE_4echoes.mgz $Id: mris_make_surfaces.c,v 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/filled.mgz... reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/brain.mgz... smoothing contralateral hemisphere... reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/wm.mgz... 10017 bright wm thresholded. 563 bright non-wm voxels segmented. reading original surface position from /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.orig... computing class statistics... border white: 252813 voxels (1.51%) border gray 269643 voxels (1.61%) WM (94.0): 95.4 +- 7.3 [70.0 --> 110.0] GM (84.0) : 81.4 +- 12.3 [30.0 --> 110.0] using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 setting MIN_GRAY_AT_WHITE_BORDER to 57.7 (was 70) setting MAX_BORDER_WHITE to 110.3 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 45.4 (was 40) setting MAX_GRAY to 95.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.2 (was 40) mean inside = 94.7, mean outside = 77.5 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.21 (0.07-->6.06) (max @ vno 120328 --> 121851) face area 0.32 +- 0.11 (0.01-->4.45) inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 111 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown mean border=82.4, 111 (111) missing vertices, mean dist 0.2 [1.1 (%25.3)->0.7 (%74.7))] %34 local maxima, %61 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.79 +- 1.16 3384 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=ficus, 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=5914599.5, rms=8.64 001: dt: 0.5000, sse=4895093.5, rms=5.683 (0.000%) 002: dt: 0.5000, sse=5113035.5, rms=4.158 (0.000%) 003: dt: 0.5000, sse=5483725.0, rms=3.443 (0.000%) 004: dt: 0.5000, sse=5688051.5, rms=3.053 (0.000%) 005: dt: 0.5000, sse=5842555.5, rms=2.920 (0.000%) 006: dt: 0.5000, sse=5888533.0, rms=2.804 (0.000%) rms = 2.79, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=5984134.0, rms=2.795 (0.000%) 008: dt: 0.2500, sse=3712664.2, rms=1.818 (0.000%) 009: dt: 0.2500, sse=3437837.8, rms=1.622 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3342775.8, rms=1.585 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3290075.5, rms=1.546 (0.000%) positioning took 1.1 minutes smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.04-->4.70) (max @ vno 104133 --> 128923) face area 0.32 +- 0.15 (0.00-->3.03) inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 2 with 104 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 7 with 8 points - only 25.00% unknown deleting segment 8 with 12 points - only 58.33% unknown mean border=84.1, 90 (40) missing vertices, mean dist -0.3 [0.7 (%56.2)->0.2 (%43.8))] %39 local maxima, %56 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.47 +- 1.01 4268 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=1.0, host=ficus, 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=0.50 000: dt: 0.0000, sse=3603444.2, rms=3.57 012: dt: 0.5000, sse=3940048.5, rms=2.371 (0.000%) 013: dt: 0.5000, sse=4273534.0, rms=2.179 (0.000%) 014: dt: 0.5000, sse=4584672.0, rms=2.128 (0.000%) rms = 2.33, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3763632.0, rms=1.593 (0.000%) 016: dt: 0.2500, sse=3461100.2, rms=1.361 (0.000%) 017: dt: 0.2500, sse=3373298.2, rms=1.307 (0.000%) rms = 1.30, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=3331932.0, rms=1.302 (0.000%) rms = 1.28, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3302424.5, rms=1.280 (0.000%) positioning took 0.9 minutes smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.05-->4.46) (max @ vno 104133 --> 128923) face area 0.35 +- 0.16 (0.00-->3.41) inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 2 with 100 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 10 points - only 40.00% unknown deleting segment 5 with 10 points - only 0.00% unknown mean border=87.0, 72 (34) missing vertices, mean dist -0.3 [0.5 (%67.0)->0.2 (%33.0))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.42 +- 0.64 2929 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.5, host=ficus, 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=0.50 000: dt: 0.0000, sse=3666641.2, rms=4.13 020: dt: 0.5000, sse=3833415.0, rms=2.332 (0.000%) 021: dt: 0.5000, sse=4144833.0, rms=2.121 (0.000%) rms = 2.08, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=4491093.5, rms=2.078 (0.000%) 023: dt: 0.2500, sse=3681079.0, rms=1.339 (0.000%) 024: dt: 0.2500, sse=3526554.0, rms=1.210 (0.000%) rms = 1.20, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3464083.5, rms=1.205 (0.000%) rms = 1.17, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3434751.5, rms=1.169 (0.000%) positioning took 0.7 minutes smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.11-->4.28) (max @ vno 104133 --> 128923) face area 0.35 +- 0.15 (0.00-->3.43) inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 100 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 20 points - only 25.00% unknown deleting segment 5 with 10 points - only 40.00% unknown deleting segment 6 with 6 points - only 0.00% unknown mean border=88.4, 69 (23) missing vertices, mean dist -0.1 [0.4 (%61.2)->0.2 (%38.8))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.31 +- 0.46 2768 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.2, host=ficus, nav=0, 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=0.50 000: dt: 0.0000, sse=3504740.8, rms=2.24 027: dt: 0.5000, sse=4200485.5, rms=1.611 (0.000%) rms = 1.88, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3860981.2, rms=1.148 (0.000%) 029: dt: 0.2500, sse=3718316.8, rms=1.013 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3755688.5, rms=1.012 (0.000%) rms = 0.96, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3755391.0, rms=0.964 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 4 with 7 points - only 0.00% unknown writing white matter surface to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.white... generating cortex label... 8 non-cortical segments detected only using segment with 2016 vertices erasing segment 1 (vno[0] = 95762) erasing segment 2 (vno[0] = 98590) erasing segment 3 (vno[0] = 99417) erasing segment 4 (vno[0] = 100410) erasing segment 5 (vno[0] = 101057) erasing segment 6 (vno[0] = 101846) erasing segment 7 (vno[0] = 102656) writing cortex label to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/label/lh.cortex.label... writing smoothed curvature to lh.curv writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.area vertex spacing 0.89 +- 0.24 (0.09-->4.43) (max @ vno 97638 --> 96698) face area 0.33 +- 0.15 (0.00-->3.39) smoothing surface for 5 iterations... masking dura from pial surface locations setting dura threshold to 1.004 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 mean border=58.0, 97 (97) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.1 (%100.0))] %37 local maxima, %46 large gradients and %12 min vals, 373 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=ficus, nav=16, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=25798258.0, rms=30.85 001: dt: 0.5000, sse=20698908.0, rms=27.302 (0.000%) 002: dt: 0.5000, sse=16607715.0, rms=24.111 (0.000%) 003: dt: 0.5000, sse=13596332.0, rms=21.336 (0.000%) 004: dt: 0.5000, sse=11641072.0, rms=18.868 (0.000%) 005: dt: 0.5000, sse=10148807.0, rms=16.629 (0.000%) 006: dt: 0.5000, sse=9018499.0, rms=14.603 (0.000%) 007: dt: 0.5000, sse=8124638.5, rms=12.706 (0.000%) 008: dt: 0.5000, sse=7438765.5, rms=10.897 (0.000%) 009: dt: 0.5000, sse=6903045.5, rms=9.161 (0.000%) 010: dt: 0.5000, sse=6601680.0, rms=7.669 (0.000%) 011: dt: 0.5000, sse=6501189.0, rms=6.572 (0.000%) 012: dt: 0.5000, sse=6556919.0, rms=5.867 (0.000%) 013: dt: 0.5000, sse=6566008.5, rms=5.443 (0.000%) 014: dt: 0.5000, sse=6634854.5, rms=5.215 (0.000%) 015: dt: 0.5000, sse=6632168.0, rms=5.089 (0.000%) 016: dt: 0.5000, sse=6651123.5, rms=5.014 (0.000%) 017: dt: 0.5000, sse=6646947.0, rms=4.956 (0.000%) rms = 4.92, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6665345.5, rms=4.918 (0.000%) 019: dt: 0.2500, sse=4127284.2, rms=3.467 (0.000%) 020: dt: 0.2500, sse=3812944.2, rms=3.031 (0.000%) 021: dt: 0.2500, sse=3644851.5, rms=2.937 (0.000%) rms = 2.90, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3611454.5, rms=2.899 (0.000%) 023: dt: 0.1250, sse=3234973.5, rms=2.435 (0.000%) 024: dt: 0.1250, sse=3192133.0, rms=2.375 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3169082.2, rms=2.367 (0.000%) positioning took 2.4 minutes smoothing T1 volume with sigma = 1.000 mean border=54.3, 388 (18) missing vertices, mean dist 0.2 [0.2 (%36.1)->0.4 (%63.9))] %53 local maxima, %34 large gradients and % 7 min vals, 121 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=1.0, host=ficus, nav=8, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=4045927.2, rms=5.81 026: dt: 0.5000, sse=4282624.5, rms=4.775 (0.000%) rms = 4.98, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3772825.8, rms=3.479 (0.000%) 028: dt: 0.2500, sse=3759278.5, rms=3.024 (0.000%) 029: dt: 0.2500, sse=3742178.5, rms=2.850 (0.000%) rms = 2.84, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3768118.8, rms=2.843 (0.000%) 031: dt: 0.1250, sse=3504319.2, rms=2.417 (0.000%) 032: dt: 0.1250, sse=3477935.2, rms=2.338 (0.000%) rms = 2.34, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3465753.5, rms=2.335 (0.000%) positioning took 0.8 minutes smoothing T1 volume with sigma = 0.500 mean border=52.2, 491 (12) missing vertices, mean dist 0.1 [0.1 (%36.6)->0.3 (%63.4))] %63 local maxima, %25 large gradients and % 7 min vals, 115 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=0.5, host=ficus, nav=4, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=3680106.8, rms=3.70 rms = 4.60, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=3501743.0, rms=2.824 (0.000%) 035: dt: 0.2500, sse=3532152.0, rms=2.547 (0.000%) 036: dt: 0.2500, sse=3619908.8, rms=2.491 (0.000%) rms = 2.50, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=3561697.5, rms=2.383 (0.000%) 038: dt: 0.1250, sse=3507276.8, rms=2.224 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=3484271.8, rms=2.188 (0.000%) positioning took 0.7 minutes smoothing T1 volume with sigma = 0.250 mean border=51.1, 1121 (10) missing vertices, mean dist 0.0 [0.2 (%44.5)->0.2 (%55.5))] %66 local maxima, %22 large gradients and % 7 min vals, 102 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=0.2, host=ficus, nav=2, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=3528229.5, rms=2.60 rms = 3.89, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=3448306.8, rms=2.217 (0.000%) rms = 2.18, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=3551610.5, rms=2.182 (0.000%) 042: dt: 0.1250, sse=3480980.5, rms=2.078 (0.000%) 043: dt: 0.1250, sse=3479683.0, rms=2.025 (0.000%) rms = 2.01, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=3486761.5, rms=2.007 (0.000%) positioning took 0.5 minutes writing pial surface to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.pial... writing smoothed curvature to lh.curv.pial writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.area.pial vertex spacing 0.98 +- 0.38 (0.10-->5.84) (max @ vno 93987 --> 94918) face area 0.39 +- 0.26 (0.00-->5.57) measuring cortical thickness... 0 of 129015 vertices processed 25000 of 129015 vertices processed 50000 of 129015 vertices processed 75000 of 129015 vertices processed 100000 of 129015 vertices processed 125000 of 129015 vertices processed 0 of 129015 vertices processed 25000 of 129015 vertices processed 50000 of 129015 vertices processed 75000 of 129015 vertices processed 100000 of 129015 vertices processed 125000 of 129015 vertices processed thickness calculation complete, 194:524 truncations. 45402 vertices at 0 distance 99876 vertices at 1 distance 69062 vertices at 2 distance 22900 vertices at 3 distance 6412 vertices at 4 distance 1796 vertices at 5 distance 634 vertices at 6 distance 240 vertices at 7 distance 71 vertices at 8 distance 31 vertices at 9 distance 18 vertices at 10 distance 9 vertices at 11 distance 14 vertices at 12 distance 6 vertices at 13 distance 3 vertices at 14 distance 2 vertices at 15 distance 2 vertices at 16 distance 0 vertices at 17 distance 2 vertices at 18 distance 0 vertices at 19 distance 2 vertices at 20 distance writing cortical thickness estimate to 'thickness' file. writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/lh.thickness positioning took 11.0 minutes [ficus:mri] (nmr-stable5-env) nohup mris_make_surfaces -dura MEMPRAGE_4echoes.mgz 4 OB01_orig_dura rh detecting dura using 4 echos from MEMPRAGE_4echoes.mgz $Id: mris_make_surfaces.c,v 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/filled.mgz... reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/brain.mgz... smoothing contralateral hemisphere... reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/wm.mgz... 10202 bright wm thresholded. 563 bright non-wm voxels segmented. reading original surface position from /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.orig... computing class statistics... border white: 252813 voxels (1.51%) border gray 269643 voxels (1.61%) WM (94.0): 95.3 +- 7.3 [70.0 --> 110.0] GM (84.0) : 81.5 +- 11.9 [30.0 --> 110.0] using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=73 setting MIN_GRAY_AT_WHITE_BORDER to 61.1 (was 70) setting MAX_BORDER_WHITE to 109.3 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 49.2 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40) mean inside = 94.5, mean outside = 78.3 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.21 (0.04-->7.00) (max @ vno 127976 --> 129954) face area 0.32 +- 0.12 (0.01-->4.13) inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 3 with 20 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=84.1, 142 (142) missing vertices, mean dist 0.2 [0.9 (%30.1)->0.6 (%69.9))] %34 local maxima, %62 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.71 +- 1.07 3394 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=ficus, 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 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=5607260.5, rms=7.56 001: dt: 0.5000, sse=4791862.5, rms=4.833 (0.000%) 002: dt: 0.5000, sse=5062168.0, rms=3.517 (0.000%) 003: dt: 0.5000, sse=5373449.0, rms=2.961 (0.000%) 004: dt: 0.5000, sse=5557377.5, rms=2.701 (0.000%) 005: dt: 0.5000, sse=5640355.5, rms=2.610 (0.000%) 006: dt: 0.5000, sse=5705436.5, rms=2.548 (0.000%) rms = 2.54, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=5736608.0, rms=2.538 (0.000%) 008: dt: 0.2500, sse=3608507.2, rms=1.679 (0.000%) 009: dt: 0.2500, sse=3362703.2, rms=1.530 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3281658.8, rms=1.504 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3233350.5, rms=1.480 (0.000%) positioning took 1.2 minutes smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.11-->4.76) (max @ vno 130506 --> 130456) face area 0.32 +- 0.15 (0.00-->3.41) inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.5, 113 (78) missing vertices, mean dist -0.2 [0.6 (%56.5)->0.2 (%43.5))] %38 local maxima, %57 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.43 +- 0.91 4055 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=1.0, host=ficus, 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=0.50 000: dt: 0.0000, sse=3480866.8, rms=3.18 012: dt: 0.5000, sse=3820107.5, rms=2.123 (0.000%) 013: dt: 0.5000, sse=4108179.8, rms=1.912 (0.000%) 014: dt: 0.5000, sse=4304494.5, rms=1.857 (0.000%) rms = 2.01, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=3658117.0, rms=1.474 (0.000%) 016: dt: 0.2500, sse=3417037.5, rms=1.313 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3345704.5, rms=1.285 (0.000%) rms = 1.27, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3310094.5, rms=1.268 (0.000%) positioning took 0.8 minutes smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.12-->5.10) (max @ vno 130506 --> 130456) face area 0.35 +- 0.16 (0.00-->4.20) inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 25 points - only 44.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=88.1, 48 (18) missing vertices, mean dist -0.2 [0.5 (%68.1)->0.2 (%31.9))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.39 +- 0.57 3682 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.5, host=ficus, 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=0.50 000: dt: 0.0000, sse=3614157.2, rms=3.80 019: dt: 0.5000, sse=3763139.0, rms=2.097 (0.000%) 020: dt: 0.5000, sse=4019293.0, rms=1.868 (0.000%) 021: dt: 0.5000, sse=4290499.0, rms=1.780 (0.000%) rms = 2.06, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3700056.0, rms=1.325 (0.000%) 023: dt: 0.2500, sse=3512163.0, rms=1.169 (0.000%) rms = 1.15, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3446395.0, rms=1.151 (0.000%) rms = 1.14, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3418304.0, rms=1.135 (0.000%) positioning took 0.8 minutes smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.10-->5.30) (max @ vno 130506 --> 130456) face area 0.34 +- 0.16 (0.00-->4.64) inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 25 points - only 44.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=89.6, 36 (14) missing vertices, mean dist -0.1 [0.3 (%61.9)->0.2 (%38.1))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored mean absolute distance = 0.29 +- 0.41 3424 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=0.2, host=ficus, nav=0, 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=0.50 000: dt: 0.0000, sse=3474603.2, rms=2.08 026: dt: 0.5000, sse=4091914.2, rms=1.358 (0.000%) rms = 1.63, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3791872.0, rms=1.034 (0.000%) 028: dt: 0.2500, sse=3660507.8, rms=0.947 (0.000%) rms = 0.92, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3695270.5, rms=0.924 (0.000%) rms = 0.92, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3693350.2, rms=0.919 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 5 with 5 points - only 20.00% unknown writing white matter surface to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.white... generating cortex label... 7 non-cortical segments detected only using segment with 1900 vertices erasing segment 1 (vno[0] = 95741) erasing segment 2 (vno[0] = 98451) erasing segment 3 (vno[0] = 99263) erasing segment 4 (vno[0] = 101110) erasing segment 5 (vno[0] = 102002) erasing segment 6 (vno[0] = 102876) writing cortex label to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/label/rh.cortex.label... writing smoothed curvature to rh.curv writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.area vertex spacing 0.88 +- 0.24 (0.07-->5.69) (max @ vno 130494 --> 130356) face area 0.33 +- 0.15 (0.00-->4.57) smoothing surface for 5 iterations... masking dura from pial surface locations setting dura threshold to 1.003 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 mean border=60.7, 45 (45) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.1 (%100.0))] %39 local maxima, %44 large gradients and %12 min vals, 486 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=ficus, nav=16, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=24080666.0, rms=29.40 001: dt: 0.5000, sse=19493332.0, rms=26.117 (0.000%) 002: dt: 0.5000, sse=15801399.0, rms=23.168 (0.000%) 003: dt: 0.5000, sse=13107579.0, rms=20.589 (0.000%) 004: dt: 0.5000, sse=11312712.0, rms=18.265 (0.000%) 005: dt: 0.5000, sse=9901415.0, rms=16.123 (0.000%) 006: dt: 0.5000, sse=8786927.0, rms=14.159 (0.000%) 007: dt: 0.5000, sse=7925665.5, rms=12.309 (0.000%) 008: dt: 0.5000, sse=7294936.0, rms=10.529 (0.000%) 009: dt: 0.5000, sse=6750358.5, rms=8.797 (0.000%) 010: dt: 0.5000, sse=6477374.0, rms=7.291 (0.000%) 011: dt: 0.5000, sse=6338928.5, rms=6.158 (0.000%) 012: dt: 0.5000, sse=6384000.5, rms=5.474 (0.000%) 013: dt: 0.5000, sse=6416477.0, rms=5.110 (0.000%) 014: dt: 0.5000, sse=6484987.5, rms=4.944 (0.000%) 015: dt: 0.5000, sse=6456108.0, rms=4.822 (0.000%) 016: dt: 0.5000, sse=6515969.5, rms=4.761 (0.000%) 017: dt: 0.5000, sse=6481574.0, rms=4.693 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6532372.0, rms=4.662 (0.000%) 019: dt: 0.2500, sse=4002183.0, rms=3.250 (0.000%) 020: dt: 0.2500, sse=3690594.2, rms=2.806 (0.000%) 021: dt: 0.2500, sse=3543033.0, rms=2.717 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3498530.8, rms=2.674 (0.000%) 023: dt: 0.1250, sse=3158340.0, rms=2.239 (0.000%) 024: dt: 0.1250, sse=3120391.8, rms=2.183 (0.000%) rms = 2.18, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3101862.5, rms=2.180 (0.000%) positioning took 2.4 minutes smoothing T1 volume with sigma = 1.000 mean border=56.8, 316 (2) missing vertices, mean dist 0.2 [0.2 (%34.8)->0.4 (%65.2))] %57 local maxima, %32 large gradients and % 7 min vals, 112 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=1.0, host=ficus, nav=8, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=4069703.8, rms=5.99 026: dt: 0.5000, sse=4102239.2, rms=4.462 (0.000%) rms = 4.72, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3660923.8, rms=3.240 (0.000%) 028: dt: 0.2500, sse=3680566.2, rms=2.776 (0.000%) 029: dt: 0.2500, sse=3656430.0, rms=2.587 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3690968.2, rms=2.576 (0.000%) 031: dt: 0.1250, sse=3451356.8, rms=2.160 (0.000%) 032: dt: 0.1250, sse=3427188.5, rms=2.088 (0.000%) rms = 2.08, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3413666.0, rms=2.077 (0.000%) positioning took 0.8 minutes smoothing T1 volume with sigma = 0.500 mean border=54.5, 416 (1) missing vertices, mean dist 0.1 [0.2 (%35.0)->0.3 (%65.0))] %67 local maxima, %22 large gradients and % 6 min vals, 111 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=0.5, host=ficus, nav=4, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=3636353.0, rms=3.56 rms = 4.44, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=3453620.5, rms=2.626 (0.000%) 035: dt: 0.2500, sse=3475338.8, rms=2.289 (0.000%) 036: dt: 0.2500, sse=3562840.0, rms=2.196 (0.000%) rms = 2.22, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=3510918.2, rms=2.101 (0.000%) 038: dt: 0.1250, sse=3461697.0, rms=1.966 (0.000%) rms = 1.94, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=3443585.8, rms=1.942 (0.000%) positioning took 0.7 minutes smoothing T1 volume with sigma = 0.250 mean border=53.5, 943 (1) missing vertices, mean dist 0.0 [0.2 (%43.5)->0.2 (%56.5))] %71 local maxima, %18 large gradients and % 6 min vals, 101 gradients ignored averaging target values for 5 iterations... tol=1.0e-04, sigma=0.2, host=ficus, nav=2, nbrs=2, l_dura=10.000, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=3483979.8, rms=2.35 rms = 3.60, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=3406125.0, rms=1.984 (0.000%) 041: dt: 0.2500, sse=3501273.5, rms=1.927 (0.000%) rms = 1.93, time step reduction 2 of 3 to 0.125... rms = 1.89, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=3472249.0, rms=1.887 (0.000%) positioning took 0.4 minutes writing pial surface to /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.pial... writing smoothed curvature to rh.curv.pial writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.area.pial vertex spacing 0.97 +- 0.38 (0.06-->9.08) (max @ vno 130494 --> 130356) face area 0.38 +- 0.26 (0.00-->6.97) measuring cortical thickness... 0 of 130719 vertices processed 25000 of 130719 vertices processed 50000 of 130719 vertices processed 75000 of 130719 vertices processed 100000 of 130719 vertices processed 125000 of 130719 vertices processed 0 of 130719 vertices processed 25000 of 130719 vertices processed 50000 of 130719 vertices processed 75000 of 130719 vertices processed 100000 of 130719 vertices processed 125000 of 130719 vertices processed thickness calculation complete, 266:660 truncations. 46143 vertices at 0 distance 101469 vertices at 1 distance 70127 vertices at 2 distance 23823 vertices at 3 distance 6412 vertices at 4 distance 1837 vertices at 5 distance 637 vertices at 6 distance 245 vertices at 7 distance 91 vertices at 8 distance 56 vertices at 9 distance 36 vertices at 10 distance 33 vertices at 11 distance 24 vertices at 12 distance 15 vertices at 13 distance 20 vertices at 14 distance 8 vertices at 15 distance 5 vertices at 16 distance 5 vertices at 17 distance 4 vertices at 18 distance 1 vertices at 19 distance 7 vertices at 20 distance writing cortical thickness estimate to 'thickness' file. writing curvature file /autofs/space/ficus_006/users/SNEF_edits/OB01_orig_dura/surf/rh.thickness positioning took 10.8 minutes [ficus:mri] (nmr-stable5-env)