WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/linux/Escritorio/COHORTE_T2 Actual FREESURFER_HOME /usr/local/freesurfer -rw------- 1 linux linux 489180 Apr 5 23:11 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# T2/FLAIR Input Wed Apr 17 13:08:55 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019 mri_convert /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz mri_convert /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/b0_mricron_20120529_152032DTI32DirSENSEs601a1000.nii... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz... #-------------------------------------------- #@# Sphere lh Wed Apr 17 13:08:56 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.329... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization 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 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 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 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.60 pass 1: epoch 2 of 3 starting distance error %19.60 unfolding complete - removing small folds... starting distance error %19.51 removing remaining folds... final distance error %19.53 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.41 hours #-------------------------------------------- #@# Surf Reg lh Wed Apr 17 13:33:21 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 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 -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.562 curvature mean = 0.032, std = 0.932 curvature mean = 0.025, std = 0.874 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 260774.9, tmin=0.5496 d=32.00 min @ (8.00, 8.00, 8.00) sse = 208504.7, tmin=1.1038 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 180661.5, tmin=1.6655 d=8.00 min @ (0.00, 0.00, -2.00) sse = 179217.9, tmin=2.2398 d=4.00 min @ (0.00, 0.00, 1.00) sse = 178562.7, tmin=2.8213 d=2.00 min @ (0.50, 0.50, -0.50) sse = 178052.9, tmin=3.4071 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 178032.1, tmin=4.5646 tol=1.0e+00, sigma=0.5, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 4.56 min curvature mean = -0.004, std = 0.966 curvature mean = 0.009, std = 0.949 curvature mean = -0.007, std = 0.979 curvature mean = 0.003, std = 0.978 curvature mean = -0.007, std = 0.983 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.035, std = 0.293 curvature mean = 0.002, std = 0.068 curvature mean = 0.051, std = 0.381 curvature mean = 0.002, std = 0.081 curvature mean = 0.018, std = 0.576 curvature mean = 0.002, std = 0.088 curvature mean = 0.009, std = 0.707 curvature mean = 0.002, std = 0.091 curvature mean = 0.002, std = 0.801 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Apr 17 13:46:10 CEST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Wed Apr 17 13:46:12 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Apr 17 13:46:13 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1060 labels changed using aseg relabeling using gibbs priors... 000: 2712 changed, 115897 examined... 001: 583 changed, 11504 examined... 002: 137 changed, 3344 examined... 003: 43 changed, 817 examined... 004: 11 changed, 278 examined... 005: 7 changed, 72 examined... 006: 5 changed, 39 examined... 007: 1 changed, 16 examined... 008: 1 changed, 6 examined... 009: 2 changed, 8 examined... 010: 3 changed, 11 examined... 011: 0 changed, 11 examined... 200 labels changed using aseg 000: 118 total segments, 74 labels (292 vertices) changed 001: 46 total segments, 6 labels (14 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1567 vertices marked for relabeling... 1567 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 26 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Apr 17 13:46:39 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_make_surfaces -aseg aseg -white NOWRITE -mgz -T1 brain.finalsurfs ACC019 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using aseg volume aseg to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/filled.mgz... reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/brain.finalsurfs.mgz... reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... 9062 bright wm thresholded. 54 bright non-wm voxels segmented. reading original surface position from /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.orig... computing class statistics... border white: 226967 voxels (1.35%) border gray 238004 voxels (1.42%) WM (95.0): 96.0 +- 7.0 [70.0 --> 110.0] GM (85.0) : 82.4 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.3 (was 70) setting MAX_BORDER_WHITE to 109.0 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 37.8 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.8 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=73 using class modes intead of means.... mean inside = 95.0, mean outside = 79.3 smoothing surface for 5 iterations... 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 /home/linux/Escritorio/COHORTE_T2/ACC019/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->4.02) (max @ vno 75192 --> 115618) face area 0.28 +- 0.12 (0.00-->3.31) mean absolute distance = 1.33 +- 1.51 4281 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 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 348 points - only 0.00% unknown deleting segment 3 with 105 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown mean border=88.7, 103 (103) missing vertices, mean dist -0.5 [1.7 (%51.2)->0.8 (%48.8))] %35 local maxima, %53 large gradients and % 7 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=linux, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.24 (0.10-->4.37) (max @ vno 75192 --> 115618) face area 0.28 +- 0.13 (0.00-->3.13) mean absolute distance = 0.74 +- 1.04 4448 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3588104.5, rms=8.35 001: dt: 0.5000, sse=4383576.5, rms=5.326 (0.000%) 002: dt: 0.5000, sse=4581960.5, rms=3.527 (0.000%) 003: dt: 0.5000, sse=4799642.0, rms=2.787 (0.000%) 004: dt: 0.5000, sse=4940352.5, rms=2.556 (0.000%) 005: dt: 0.5000, sse=4986242.5, rms=2.490 (0.000%) rms = 2.47, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=5017637.5, rms=2.466 (0.000%) 007: dt: 0.2500, sse=3022864.5, rms=1.628 (0.000%) 008: dt: 0.2500, sse=2776013.2, rms=1.465 (0.000%) rms = 1.43, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=2698551.0, rms=1.432 (0.000%) rms = 1.41, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=2665910.5, rms=1.409 (0.000%) positioning took 0.6 minutes 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 7 points - only 0.00% unknown deleting segment 3 with 418 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 75 points - only 0.00% unknown deleting segment 6 with 12 points - only 41.67% unknown deleting segment 7 with 24 points - only 0.00% unknown deleting segment 8 with 132 points - only 9.09% unknown deleting segment 9 with 5 points - only 0.00% unknown mean border=89.0, 92 (52) missing vertices, mean dist -0.2 [1.1 (%44.9)->0.4 (%55.1))] %54 local maxima, %39 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=linux, 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 smoothing T1 volume with sigma = 0.500 vertex spacing 0.86 +- 0.24 (0.08-->4.60) (max @ vno 86725 --> 86751) face area 0.31 +- 0.15 (0.00-->3.50) mean absolute distance = 0.50 +- 0.76 4475 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3072160.2, rms=4.23 011: dt: 0.5000, sse=3453666.8, rms=2.719 (0.000%) 012: dt: 0.5000, sse=3882623.5, rms=2.255 (0.000%) rms = 2.21, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=4114549.8, rms=2.205 (0.000%) 014: dt: 0.2500, sse=3039801.8, rms=1.459 (0.000%) 015: dt: 0.2500, sse=2879566.8, rms=1.314 (0.000%) rms = 1.29, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=2808925.8, rms=1.285 (0.000%) rms = 1.26, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=2785477.8, rms=1.265 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 378 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 91 points - only 0.00% unknown deleting segment 6 with 9 points - only 22.22% unknown deleting segment 7 with 21 points - only 0.00% unknown deleting segment 8 with 102 points - only 11.76% unknown mean border=90.5, 70 (25) missing vertices, mean dist -0.2 [0.6 (%57.1)->0.3 (%42.9))] %71 local maxima, %23 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=linux, 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 smoothing T1 volume with sigma = 0.250 vertex spacing 0.86 +- 0.24 (0.10-->5.00) (max @ vno 86725 --> 86751) face area 0.31 +- 0.15 (0.00-->3.48) mean absolute distance = 0.38 +- 0.60 3486 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2971732.2, rms=3.23 018: dt: 0.5000, sse=3274002.0, rms=1.990 (0.000%) 019: dt: 0.5000, sse=3611894.8, rms=1.882 (0.000%) rms = 1.94, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3189123.2, rms=1.442 (0.000%) 021: dt: 0.2500, sse=3037544.0, rms=1.218 (0.000%) rms = 1.19, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=2971677.2, rms=1.188 (0.000%) rms = 1.17, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=2942541.8, rms=1.173 (0.000%) positioning took 0.4 minutes 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 8 points - only 0.00% unknown deleting segment 3 with 394 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 118 points - only 0.00% unknown deleting segment 6 with 74 points - only 16.22% unknown deleting segment 7 with 125 points - only 9.60% unknown mean border=91.0, 108 (23) missing vertices, mean dist -0.1 [0.5 (%52.0)->0.3 (%48.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=linux, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=2995904.2, rms=2.00 024: dt: 0.5000, sse=3715861.2, rms=1.364 (0.000%) rms = 1.63, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3444520.8, rms=1.087 (0.000%) 026: dt: 0.2500, sse=3336562.8, rms=1.013 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3360291.2, rms=0.987 (0.000%) rms = 0.98, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3358289.0, rms=0.983 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=57.6, 86 (86) missing vertices, mean dist 1.3 [2.9 (%0.0)->2.5 (%100.0))] %24 local maxima, %26 large gradients and %45 min vals, 5238 gradients ignored tol=1.0e-04, sigma=2.0, host=linux, nav=16, nbrs=2, 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 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=27050350.0, rms=33.72 001: dt: 0.5000, sse=22225238.0, rms=30.316 (0.000%) 002: dt: 0.5000, sse=18174310.0, rms=27.154 (0.000%) 003: dt: 0.5000, sse=14799678.0, rms=24.225 (0.000%) 004: dt: 0.5000, sse=12055940.0, rms=21.501 (0.000%) 005: dt: 0.5000, sse=9982814.0, rms=19.025 (0.000%) 006: dt: 0.5000, sse=8507596.0, rms=16.828 (0.000%) 007: dt: 0.5000, sse=7514199.0, rms=14.860 (0.000%) 008: dt: 0.5000, sse=6818141.0, rms=13.069 (0.000%) 009: dt: 0.5000, sse=6307253.0, rms=11.407 (0.000%) 010: dt: 0.5000, sse=5910768.0, rms=9.850 (0.000%) 011: dt: 0.5000, sse=5643465.5, rms=8.415 (0.000%) 012: dt: 0.5000, sse=5483956.5, rms=7.189 (0.000%) 013: dt: 0.5000, sse=5444668.0, rms=6.220 (0.000%) 014: dt: 0.5000, sse=5421351.5, rms=5.533 (0.000%) 015: dt: 0.5000, sse=5484780.5, rms=5.077 (0.000%) 016: dt: 0.5000, sse=5487479.0, rms=4.810 (0.000%) 017: dt: 0.5000, sse=5565425.5, rms=4.648 (0.000%) 018: dt: 0.5000, sse=5525699.5, rms=4.552 (0.000%) 019: dt: 0.5000, sse=5562978.0, rms=4.486 (0.000%) 020: dt: 0.5000, sse=5528784.0, rms=4.427 (0.000%) rms = 4.39, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=5563719.0, rms=4.389 (0.000%) 022: dt: 0.2500, sse=3445465.5, rms=3.334 (0.000%) 023: dt: 0.2500, sse=3215302.8, rms=3.022 (0.000%) 024: dt: 0.2500, sse=3073572.8, rms=2.948 (0.000%) rms = 2.91, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3040782.2, rms=2.912 (0.000%) 026: dt: 0.1250, sse=2828037.2, rms=2.763 (0.000%) rms = 2.75, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2805246.8, rms=2.746 (0.000%) positioning took 1.5 minutes mean border=53.1, 1129 (5) missing vertices, mean dist 0.1 [0.2 (%29.7)->0.4 (%70.3))] %42 local maxima, %14 large gradients and %38 min vals, 4232 gradients ignored tol=1.0e-04, sigma=1.0, host=linux, nav=8, nbrs=2, 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 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4110554.5, rms=7.67 028: dt: 0.5000, sse=4037437.2, rms=5.328 (0.000%) 029: dt: 0.5000, sse=5053246.0, rms=4.933 (0.000%) 030: dt: 0.5000, sse=4936552.5, rms=4.694 (0.000%) rms = 4.71, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3909410.8, rms=3.676 (0.000%) 032: dt: 0.2500, sse=3641822.0, rms=3.223 (0.000%) 033: dt: 0.2500, sse=3513348.0, rms=3.074 (0.000%) 034: dt: 0.2500, sse=3481149.5, rms=3.019 (0.000%) rms = 2.98, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=3460914.0, rms=2.976 (0.000%) 036: dt: 0.1250, sse=3214911.8, rms=2.732 (0.000%) rms = 2.69, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3188960.0, rms=2.691 (0.000%) positioning took 0.6 minutes mean border=51.6, 1810 (4) missing vertices, mean dist 0.0 [0.2 (%39.6)->0.2 (%60.4))] %45 local maxima, %12 large gradients and %37 min vals, 3583 gradients ignored tol=1.0e-04, sigma=0.5, host=linux, nav=4, nbrs=2, 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 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3303071.5, rms=3.45 rms = 4.21, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=3191519.5, rms=3.000 (0.000%) 039: dt: 0.2500, sse=3303034.5, rms=2.898 (0.000%) 040: dt: 0.2500, sse=3348465.2, rms=2.842 (0.000%) rms = 2.82, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=3407899.5, rms=2.822 (0.000%) 042: dt: 0.1250, sse=3253289.5, rms=2.707 (0.000%) rms = 2.68, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=3247384.0, rms=2.679 (0.000%) positioning took 0.4 minutes mean border=51.0, 3747 (3) missing vertices, mean dist 0.0 [0.2 (%49.5)->0.2 (%50.5))] %44 local maxima, %12 large gradients and %36 min vals, 3064 gradients ignored tol=1.0e-04, sigma=0.2, host=linux, nav=2, nbrs=2, 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 writing pial surface to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3275984.5, rms=2.92 rms = 3.49, time step reduction 1 of 3 to 0.250... 044: dt: 0.2500, sse=3230065.2, rms=2.778 (0.000%) rms = 2.73, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=3351999.0, rms=2.732 (0.000%) 046: dt: 0.1250, sse=3232249.0, rms=2.657 (0.000%) rms = 2.62, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=3234863.8, rms=2.622 (0.000%) positioning took 0.3 minutes writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.area.pial vertex spacing 0.96 +- 0.40 (0.06-->6.23) (max @ vno 80331 --> 80305) face area 0.37 +- 0.27 (0.00-->6.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 115897 vertices processed 25000 of 115897 vertices processed 50000 of 115897 vertices processed 75000 of 115897 vertices processed 100000 of 115897 vertices processed 0 of 115897 vertices processed 25000 of 115897 vertices processed 50000 of 115897 vertices processed 75000 of 115897 vertices processed 100000 of 115897 vertices processed thickness calculation complete, 1018:1696 truncations. 22757 vertices at 0 distance 65999 vertices at 1 distance 68537 vertices at 2 distance 37271 vertices at 3 distance 16140 vertices at 4 distance 6132 vertices at 5 distance 2229 vertices at 6 distance 854 vertices at 7 distance 335 vertices at 8 distance 159 vertices at 9 distance 115 vertices at 10 distance 82 vertices at 11 distance 43 vertices at 12 distance 30 vertices at 13 distance 38 vertices at 14 distance 48 vertices at 15 distance 39 vertices at 16 distance 33 vertices at 17 distance 29 vertices at 18 distance 23 vertices at 19 distance 13 vertices at 20 distance writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.thickness positioning took 5.8 minutes #-------------------------------------------- #@# Surf Volume lh Wed Apr 17 13:52:29 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Wed Apr 17 13:52:30 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts pctsurfcon --s ACC019 --lh-only Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/pctsurfcon.log Wed Apr 17 13:52:30 CEST 2013 setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2 cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.wm.mgh --regheader ACC019 --cortex srcvol = /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz as target reference. Loading label /home/linux/Escritorio/COHORTE_T2/ACC019/label/lh.cortex.label Reading surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 64482 Masking with /home/linux/Escritorio/COHORTE_T2/ACC019/label/lh.cortex.label Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.wm.mgh Dim: 115897 1 1 mri_vol2surf --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.gm.mgh --projfrac 0.3 --regheader ACC019 --cortex srcvol = /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz as target reference. Loading label /home/linux/Escritorio/COHORTE_T2/ACC019/label/lh.cortex.label Reading surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white Done reading source surface Reading thickness /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 75638 Masking with /home/linux/Escritorio/COHORTE_T2/ACC019/label/lh.cortex.label Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.gm.mgh Dim: 115897 1 1 mri_concat /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.wm.mgh /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5484/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.w-g.pct.mgh mri_segstats --in /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.w-g.pct.mgh --annot ACC019 lh aparc --sum /home/linux/Escritorio/COHORTE_T2/ACC019/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.w-g.pct.mgh --annot ACC019 lh aparc --sum /home/linux/Escritorio/COHORTE_T2/ACC019/stats/lh.w-g.pct.stats --snr sysname Linux hostname linux-To-be-filled-by-O-E-M machine x86_64 user linux UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.w-g.pct.mgh Vertex Area is 0.617803 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1175 755.252 2 1002 caudalanteriorcingulate 908 573.775 3 1003 caudalmiddlefrontal 2503 1600.105 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2150 1257.123 6 1006 entorhinal 380 241.805 7 1007 fusiform 3306 2135.825 8 1008 inferiorparietal 5283 3218.145 9 1009 inferiortemporal 4398 2790.892 10 1010 isthmuscingulate 1471 853.326 11 1011 lateraloccipital 7320 4395.247 12 1012 lateralorbitofrontal 3674 2207.207 13 1013 lingual 3684 2337.569 14 1014 medialorbitofrontal 2544 1544.768 15 1015 middletemporal 3966 2513.687 16 1016 parahippocampal 1051 681.589 17 1017 paracentral 1560 924.183 18 1018 parsopercularis 2030 1238.723 19 1019 parsorbitalis 866 489.763 20 1020 parstriangularis 1737 1059.301 21 1021 pericalcarine 1697 1104.045 22 1022 postcentral 5747 3369.705 23 1023 posteriorcingulate 1511 944.442 24 1024 precentral 6746 3958.060 25 1025 precuneus 4719 3020.753 26 1026 rostralanteriorcingulate 1236 653.016 27 1027 rostralmiddlefrontal 7080 4431.848 28 1028 superiorfrontal 8022 5043.707 29 1029 superiorparietal 7969 4839.345 30 1030 superiortemporal 4615 2993.418 31 1031 supramarginal 4747 2970.437 32 1032 frontalpole 221 141.004 33 1033 temporalpole 583 378.349 34 1034 transversetemporal 721 364.152 35 1035 insula 3225 2048.526 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Wed Apr 17 13:52:35 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab ACC019 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1175 755 2266 3.037 0.448 0.120 0.034 13 1.5 bankssts 908 574 2052 3.482 0.595 0.160 0.049 25 1.7 caudalanteriorcingulate 2503 1600 4995 2.884 0.498 0.129 0.043 26 4.7 caudalmiddlefrontal 2150 1257 3261 2.226 0.668 0.151 0.061 35 5.5 cuneus 380 242 1556 4.234 0.781 0.151 0.056 6 1.0 entorhinal 3306 2136 8257 3.358 0.729 0.148 0.055 56 7.5 fusiform 5283 3218 9270 2.629 0.569 0.136 0.051 81 11.4 inferiorparietal 4398 2791 10219 3.059 0.792 0.153 0.076 91 14.1 inferiortemporal 1471 853 2801 2.988 0.960 0.136 0.048 22 2.9 isthmuscingulate 7320 4395 11643 2.437 0.705 0.148 0.057 118 18.0 lateraloccipital 3674 2207 6509 2.920 0.783 0.141 0.079 133 12.6 lateralorbitofrontal 3684 2338 5677 2.240 0.664 0.138 0.056 65 8.7 lingual 2544 1545 4549 2.756 0.971 0.144 0.297 226 6.7 medialorbitofrontal 3966 2514 9750 3.180 0.578 0.152 0.066 73 11.0 middletemporal 1051 682 1857 2.414 0.522 0.090 0.020 7 0.9 parahippocampal 1560 924 2466 2.461 0.598 0.101 0.033 12 1.9 paracentral 2030 1239 3733 2.783 0.507 0.128 0.048 30 4.1 parsopercularis 866 490 1965 3.134 0.542 0.143 0.052 13 2.0 parsorbitalis 1737 1059 3315 2.750 0.544 0.125 0.048 24 3.5 parstriangularis 1697 1104 1996 1.947 0.527 0.131 0.054 22 3.7 pericalcarine 5747 3370 8040 2.125 0.703 0.122 0.042 72 10.9 postcentral 1511 944 2942 2.820 0.869 0.140 0.045 23 2.8 posteriorcingulate 6746 3958 11957 2.775 0.584 0.121 0.056 135 12.4 precentral 4719 3021 8248 2.516 0.670 0.136 0.049 63 9.6 precuneus 1236 653 2708 3.408 0.918 0.146 0.088 29 4.3 rostralanteriorcingulate 7080 4432 13055 2.602 0.520 0.147 0.057 113 15.5 rostralmiddlefrontal 8022 5044 17406 2.974 0.585 0.144 0.380 905 22.9 superiorfrontal 7969 4839 11843 2.284 0.525 0.130 0.042 95 13.6 superiorparietal 4615 2993 9298 2.843 0.685 0.113 0.030 48 5.8 superiortemporal 4747 2970 8783 2.690 0.554 0.132 0.043 65 8.6 supramarginal 221 141 590 2.920 0.573 0.183 0.083 5 0.7 frontalpole 583 378 2286 3.829 0.565 0.132 0.049 8 1.1 temporalpole 721 364 993 2.466 0.444 0.104 0.035 7 0.8 transversetemporal 3225 2049 6604 3.339 0.907 0.135 0.092 73 10.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Apr 17 13:52:42 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 62 labels changed using aseg relabeling using gibbs priors... 000: 8107 changed, 115897 examined... 001: 1961 changed, 30973 examined... 002: 656 changed, 9975 examined... 003: 261 changed, 3602 examined... 004: 120 changed, 1518 examined... 005: 48 changed, 653 examined... 006: 27 changed, 288 examined... 007: 18 changed, 165 examined... 008: 10 changed, 102 examined... 009: 6 changed, 49 examined... 010: 5 changed, 42 examined... 011: 5 changed, 25 examined... 012: 0 changed, 25 examined... 12 labels changed using aseg 000: 249 total segments, 167 labels (1927 vertices) changed 001: 94 total segments, 13 labels (39 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 104 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1054 vertices marked for relabeling... 1054 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Apr 17 13:53:12 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab ACC019 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1075 690 1800 2.443 0.512 0.154 0.080 22 2.7 G_and_S_frontomargin 1299 785 2936 3.110 0.639 0.151 0.061 23 3.3 G_and_S_occipital_inf 1160 630 1653 2.171 0.669 0.118 0.042 18 2.1 G_and_S_paracentral 1326 810 2572 2.755 0.621 0.142 0.058 21 3.6 G_and_S_subcentral 738 460 1578 2.649 0.517 0.163 0.057 16 1.8 G_and_S_transv_frontopol 2173 1273 4314 3.283 0.725 0.132 0.065 35 5.7 G_and_S_cingul-Ant 1060 716 2372 3.142 0.529 0.141 0.045 19 1.8 G_and_S_cingul-Mid-Ant 1066 700 2148 2.881 0.666 0.123 0.038 11 1.7 G_and_S_cingul-Mid-Post 399 246 1254 3.623 0.659 0.160 0.053 7 0.8 G_cingul-Post-dorsal 289 152 433 2.672 0.936 0.134 0.049 5 0.5 G_cingul-Post-ventral 1928 1116 3033 2.200 0.742 0.151 0.060 32 4.9 G_cuneus 1257 710 2817 2.954 0.415 0.143 0.059 25 3.3 G_front_inf-Opercular 202 106 546 3.577 0.439 0.167 0.092 4 0.8 G_front_inf-Orbital 1155 639 2439 2.807 0.551 0.137 0.062 20 3.0 G_front_inf-Triangul 3837 2347 8807 2.869 0.520 0.156 0.067 70 10.2 G_front_middle 5425 3277 13105 3.082 0.590 0.151 0.070 99 16.7 G_front_sup 480 265 1005 3.210 0.780 0.131 0.078 12 1.5 G_Ins_lg_and_S_cent_ins 617 349 1773 3.549 0.937 0.170 0.129 25 3.6 G_insular_short 2117 1201 4552 2.916 0.596 0.166 0.095 57 9.9 G_occipital_middle 2265 1291 2875 2.035 0.460 0.148 0.052 35 5.1 G_occipital_sup 1322 809 3718 3.397 0.675 0.153 0.067 28 3.5 G_oc-temp_lat-fusifor 2401 1416 3935 2.291 0.715 0.151 0.073 53 7.5 G_oc-temp_med-Lingual 1073 699 2879 3.133 1.078 0.136 0.050 16 2.2 G_oc-temp_med-Parahip 2422 1334 4718 2.765 0.744 0.149 0.097 125 10.1 G_orbital 1962 1117 4022 2.719 0.528 0.148 0.058 37 4.4 G_pariet_inf-Angular 2560 1525 5402 2.852 0.569 0.139 0.051 42 5.5 G_pariet_inf-Supramar 2800 1716 4825 2.306 0.540 0.137 0.046 39 5.3 G_parietal_sup 2290 1167 3176 2.144 0.548 0.122 0.046 34 4.7 G_postcentral 2753 1364 5531 3.019 0.511 0.125 0.083 92 6.1 G_precentral 2089 1287 4707 2.757 0.686 0.163 0.072 43 6.2 G_precuneus 998 577 2198 2.792 0.675 0.156 0.065 21 2.7 G_rectus 528 317 706 2.387 1.149 0.192 1.263 198 2.9 G_subcallosal 552 268 868 2.547 0.412 0.100 0.036 5 0.6 G_temp_sup-G_T_transv 1760 1090 4602 3.164 0.524 0.135 0.039 25 2.8 G_temp_sup-Lateral 514 338 1159 3.220 0.867 0.092 0.029 3 0.5 G_temp_sup-Plan_polar 815 532 1677 2.760 0.443 0.114 0.031 7 1.1 G_temp_sup-Plan_tempo 2346 1453 6200 3.015 0.865 0.164 0.093 63 9.4 G_temporal_inf 2672 1642 7419 3.255 0.624 0.169 0.090 63 9.8 G_temporal_middle 315 213 491 2.577 0.474 0.111 0.021 2 0.3 Lat_Fis-ant-Horizont 278 187 397 2.486 0.462 0.104 0.036 2 0.4 Lat_Fis-ant-Vertical 1140 752 1634 2.613 0.610 0.109 0.026 8 1.2 Lat_Fis-post 2224 1298 2776 1.946 0.461 0.147 0.060 39 5.1 Pole_occipital 1408 881 5137 3.913 0.703 0.148 0.058 25 3.6 Pole_temporal 2489 1735 3255 2.101 0.595 0.129 0.040 28 4.5 S_calcarine 2709 1832 3313 2.006 0.749 0.112 0.029 18 3.4 S_central 842 561 1328 2.565 0.572 0.102 0.027 6 1.0 S_cingul-Marginalis 484 323 881 3.347 0.491 0.116 0.106 5 1.0 S_circular_insula_ant 1347 926 2146 2.690 1.020 0.085 0.023 7 1.1 S_circular_insula_inf 1508 1034 2512 3.221 0.611 0.129 0.077 27 4.2 S_circular_insula_sup 685 459 1412 3.442 0.616 0.128 0.048 6 1.2 S_collat_transv_ant 271 178 341 2.296 0.334 0.125 0.031 2 0.4 S_collat_transv_post 2051 1312 3114 2.565 0.507 0.122 0.033 19 3.0 S_front_inf 1152 763 1608 2.313 0.426 0.121 0.032 10 1.5 S_front_middle 1787 1179 2907 2.622 0.462 0.129 1.476 799 4.8 S_front_sup 360 250 465 2.416 0.470 0.115 0.020 2 0.3 S_interm_prim-Jensen 2829 1766 3700 2.281 0.470 0.109 0.029 24 3.2 S_intrapariet_and_P_trans 936 626 1264 2.375 0.465 0.130 0.035 8 1.3 S_oc_middle_and_Lunatus 1145 719 1628 2.298 0.505 0.130 0.035 12 1.7 S_oc_sup_and_transversal 924 595 1265 2.634 0.568 0.131 0.039 9 1.5 S_occipital_ant 893 592 1645 2.920 0.574 0.147 0.049 13 1.8 S_oc-temp_lat 1811 1256 2856 2.569 0.665 0.113 0.027 15 2.0 S_oc-temp_med_and_Lingual 287 185 478 2.718 0.320 0.152 0.053 4 0.7 S_orbital_lateral 709 462 958 2.345 0.816 0.125 0.042 8 1.3 S_orbital_med-olfact 1237 800 2448 3.314 0.595 0.132 0.048 13 2.4 S_orbital-H_Shaped 2122 1319 2811 2.318 0.546 0.116 0.037 19 3.1 S_parieto_occipital 1310 737 1606 2.823 1.153 0.144 0.045 26 2.4 S_pericallosal 2450 1599 3300 2.232 0.465 0.121 0.032 22 3.2 S_postcentral 1515 1001 2493 2.774 0.438 0.120 0.033 14 2.1 S_precentral-inf-part 874 598 1293 2.513 0.384 0.105 0.027 4 1.0 S_precentral-sup-part 495 300 915 3.233 1.122 0.133 0.050 7 1.0 S_suborbital 910 583 1442 2.631 0.631 0.122 0.031 8 1.3 S_subparietal 1295 841 2126 2.967 0.560 0.134 0.039 15 2.3 S_temporal_inf 4091 2656 6892 2.892 0.554 0.117 0.031 36 5.1 S_temporal_sup 237 147 295 2.549 0.481 0.125 0.032 9 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Apr 17 13:53:20 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1010 labels changed using aseg relabeling using gibbs priors... 000: 2355 changed, 115897 examined... 001: 515 changed, 10199 examined... 002: 124 changed, 2852 examined... 003: 36 changed, 708 examined... 004: 15 changed, 223 examined... 005: 8 changed, 91 examined... 006: 5 changed, 46 examined... 007: 6 changed, 32 examined... 008: 5 changed, 26 examined... 009: 4 changed, 25 examined... 010: 4 changed, 25 examined... 011: 3 changed, 25 examined... 012: 1 changed, 21 examined... 013: 2 changed, 7 examined... 014: 1 changed, 8 examined... 015: 1 changed, 7 examined... 016: 1 changed, 7 examined... 017: 0 changed, 7 examined... 165 labels changed using aseg 000: 54 total segments, 21 labels (144 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 885 vertices marked for relabeling... 885 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 26 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Apr 17 13:53:47 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab ACC019 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1415 910 2988 3.330 0.580 0.146 0.046 29 2.5 caudalanteriorcingulate 2682 1701 5381 2.892 0.490 0.128 0.043 28 5.0 caudalmiddlefrontal 3138 1852 4638 2.218 0.657 0.143 0.055 45 7.2 cuneus 355 227 1451 4.237 0.801 0.155 0.057 5 0.9 entorhinal 2988 1954 6905 3.234 0.646 0.147 0.054 48 6.3 fusiform 5164 3129 8974 2.609 0.567 0.136 0.051 80 11.4 inferiorparietal 4558 2860 11364 3.155 0.867 0.154 0.077 97 15.1 inferiortemporal 1484 864 2844 2.990 0.967 0.134 0.048 22 2.9 isthmuscingulate 7485 4486 11830 2.412 0.698 0.149 0.057 122 18.5 lateraloccipital 4067 2488 7272 2.782 0.838 0.149 0.232 270 13.8 lateralorbitofrontal 3701 2357 5709 2.244 0.664 0.140 0.057 65 8.9 lingual 2068 1242 3806 2.710 0.886 0.143 0.062 42 5.4 medialorbitofrontal 5121 3254 11676 3.128 0.575 0.145 0.059 84 12.4 middletemporal 1038 672 1843 2.415 0.530 0.090 0.020 7 0.9 parahippocampal 1719 1026 2839 2.525 0.613 0.101 0.032 13 2.1 paracentral 1837 1116 3412 2.873 0.507 0.132 0.051 29 3.9 parsopercularis 890 543 1846 3.095 0.517 0.131 0.047 10 1.8 parsorbitalis 2228 1352 4012 2.649 0.542 0.122 0.045 28 4.3 parstriangularis 1668 1084 1967 1.956 0.527 0.131 0.054 22 3.6 pericalcarine 6399 3811 9028 2.155 0.709 0.123 0.043 79 12.0 postcentral 1623 1020 3104 2.811 0.846 0.141 0.045 24 3.0 posteriorcingulate 6644 3900 11711 2.780 0.590 0.121 0.057 135 12.4 precentral 4624 2927 8119 2.516 0.667 0.137 0.050 64 9.6 precuneus 1514 835 3240 3.474 0.920 0.149 0.083 33 4.8 rostralanteriorcingulate 4738 2899 8747 2.684 0.543 0.150 0.068 133 12.2 rostralmiddlefrontal 9359 5883 20115 2.874 0.612 0.145 0.333 932 25.7 superiorfrontal 6163 3760 9377 2.310 0.512 0.128 0.040 72 10.1 superiorparietal 6228 4018 13696 3.004 0.727 0.120 0.036 74 9.0 superiortemporal 4558 2867 8297 2.670 0.568 0.131 0.041 60 8.0 supramarginal 721 364 993 2.470 0.443 0.105 0.036 7 0.8 transversetemporal 2668 1680 5703 3.403 0.788 0.128 0.082 61 8.5 insula #-------------------------------------------- #@# Sphere rh Wed Apr 17 13:53:54 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.335... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization 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 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 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 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.72 pass 1: epoch 2 of 3 starting distance error %19.70 unfolding complete - removing small folds... starting distance error %19.61 removing remaining folds... final distance error %19.63 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.38 hours #-------------------------------------------- #@# Surf Reg rh Wed Apr 17 14:16:30 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 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 -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 0.566 curvature mean = 0.024, std = 0.946 curvature mean = 0.024, std = 0.872 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 237953.6, tmin=0.5511 d=16.00 min @ (0.00, 4.00, -4.00) sse = 182295.3, tmin=1.6585 d=8.00 min @ (2.00, 0.00, 0.00) sse = 176644.6, tmin=2.2423 d=1.00 min @ (-0.25, -0.25, -0.25) sse = 176448.9, tmin=4.0012 d=0.50 min @ (0.00, 0.12, 0.00) sse = 176414.1, tmin=4.5708 tol=1.0e+00, sigma=0.5, host=linux, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 4.57 min curvature mean = -0.002, std = 0.963 curvature mean = 0.008, std = 0.950 curvature mean = -0.005, std = 0.975 curvature mean = 0.003, std = 0.978 curvature mean = -0.006, std = 0.976 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.034, std = 0.309 curvature mean = 0.004, std = 0.071 curvature mean = 0.038, std = 0.363 curvature mean = 0.004, std = 0.085 curvature mean = 0.010, std = 0.543 curvature mean = 0.003, std = 0.093 curvature mean = 0.005, std = 0.669 curvature mean = 0.004, std = 0.097 curvature mean = 0.000, std = 0.754 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Apr 17 14:29:55 CEST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Wed Apr 17 14:29:56 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Apr 17 14:29:57 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1084 labels changed using aseg relabeling using gibbs priors... 000: 2666 changed, 115847 examined... 001: 625 changed, 11350 examined... 002: 145 changed, 3462 examined... 003: 58 changed, 870 examined... 004: 21 changed, 304 examined... 005: 8 changed, 127 examined... 006: 3 changed, 42 examined... 007: 1 changed, 18 examined... 008: 1 changed, 5 examined... 009: 0 changed, 6 examined... 188 labels changed using aseg 000: 87 total segments, 48 labels (252 vertices) changed 001: 38 total segments, 1 labels (17 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1551 vertices marked for relabeling... 1551 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 26 seconds. #-------------------------------------------- #@# Make Pial Surf rh Wed Apr 17 14:30:24 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_make_surfaces -aseg aseg -white NOWRITE -mgz -T1 brain.finalsurfs ACC019 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... using aseg volume aseg to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/filled.mgz... reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/brain.finalsurfs.mgz... reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... 10333 bright wm thresholded. 54 bright non-wm voxels segmented. reading original surface position from /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.orig... computing class statistics... border white: 226967 voxels (1.35%) border gray 238004 voxels (1.42%) WM (95.0): 96.0 +- 7.1 [70.0 --> 110.0] GM (85.0) : 82.5 +- 11.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.6 (was 70) setting MAX_BORDER_WHITE to 110.1 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 41.7 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=76 using class modes intead of means.... mean inside = 95.1, mean outside = 79.8 smoothing surface for 5 iterations... 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 /home/linux/Escritorio/COHORTE_T2/ACC019/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.89) (max @ vno 77723 --> 115485) face area 0.28 +- 0.12 (0.00-->2.91) mean absolute distance = 1.90 +- 1.88 3832 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 3 with 215 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 6 with 17 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 6 points - only 0.00% unknown mean border=93.7, 134 (134) missing vertices, mean dist -0.9 [2.4 (%59.0)->0.8 (%41.0))] %25 local maxima, %55 large gradients and %15 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=linux, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.88 +- 0.27 (0.03-->5.77) (max @ vno 77723 --> 115485) face area 0.28 +- 0.14 (0.00-->3.98) mean absolute distance = 0.93 +- 1.08 3406 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4842740.5, rms=11.22 001: dt: 0.5000, sse=4719566.0, rms=7.855 (0.000%) 002: dt: 0.5000, sse=4493961.0, rms=5.242 (0.000%) 003: dt: 0.5000, sse=4674777.5, rms=3.618 (0.000%) 004: dt: 0.5000, sse=4870366.0, rms=2.902 (0.000%) 005: dt: 0.5000, sse=4955935.0, rms=2.632 (0.000%) 006: dt: 0.5000, sse=5042572.5, rms=2.523 (0.000%) 007: dt: 0.5000, sse=5055736.5, rms=2.464 (0.000%) rms = 2.44, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5109173.0, rms=2.436 (0.000%) 009: dt: 0.2500, sse=3164726.5, rms=1.744 (0.000%) 010: dt: 0.2500, sse=2956637.2, rms=1.620 (0.000%) rms = 1.60, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=2875769.0, rms=1.597 (0.000%) rms = 1.58, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2836969.2, rms=1.579 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 387 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 43 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 65 points - only 20.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 15 with 37 points - only 0.00% unknown mean border=91.5, 184 (68) missing vertices, mean dist -0.1 [1.5 (%33.3)->0.6 (%66.7))] %51 local maxima, %40 large gradients and % 4 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=linux, 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 smoothing T1 volume with sigma = 0.500 vertex spacing 0.86 +- 0.25 (0.06-->4.43) (max @ vno 115194 --> 115197) face area 0.32 +- 0.16 (0.00-->4.23) mean absolute distance = 0.55 +- 0.85 4619 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3418121.5, rms=5.13 013: dt: 0.5000, sse=3693884.2, rms=3.120 (0.000%) 014: dt: 0.5000, sse=4073576.0, rms=2.357 (0.000%) 015: dt: 0.5000, sse=4324936.5, rms=2.231 (0.000%) rms = 2.23, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4544739.5, rms=2.226 (0.000%) 017: dt: 0.2500, sse=3206791.5, rms=1.486 (0.000%) 018: dt: 0.2500, sse=3032667.8, rms=1.371 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=2967907.8, rms=1.356 (0.000%) rms = 1.34, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=2937474.5, rms=1.342 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 336 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 36 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 65 points - only 20.00% unknown deleting segment 10 with 12 points - only 58.33% unknown deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 35 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown mean border=92.2, 195 (57) missing vertices, mean dist -0.2 [0.8 (%47.8)->0.3 (%52.2))] %71 local maxima, %22 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=linux, 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 smoothing T1 volume with sigma = 0.250 vertex spacing 0.86 +- 0.25 (0.09-->4.74) (max @ vno 115194 --> 115197) face area 0.31 +- 0.15 (0.00-->4.14) mean absolute distance = 0.41 +- 0.67 3971 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3077186.2, rms=2.94 021: dt: 0.5000, sse=3425613.0, rms=1.944 (0.000%) 022: dt: 0.5000, sse=3738328.2, rms=1.844 (0.000%) rms = 1.97, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3292519.5, rms=1.452 (0.000%) 024: dt: 0.2500, sse=3130153.5, rms=1.284 (0.000%) rms = 1.26, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3079957.0, rms=1.259 (0.000%) rms = 1.25, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3053868.8, rms=1.245 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 359 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 31 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 22 points - only 22.73% unknown deleting segment 8 with 12 points - only 58.33% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 35 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=92.6, 225 (53) missing vertices, mean dist -0.1 [0.6 (%47.6)->0.3 (%52.4))] %79 local maxima, %15 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=linux, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3100597.8, rms=1.98 027: dt: 0.5000, sse=3861674.2, rms=1.395 (0.000%) rms = 1.60, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3588400.8, rms=1.137 (0.000%) 029: dt: 0.2500, sse=3477409.5, rms=1.060 (0.000%) rms = 1.04, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3487422.2, rms=1.039 (0.000%) rms = 1.03, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3482646.8, rms=1.035 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=60.6, 128 (128) missing vertices, mean dist 1.4 [1.0 (%0.0)->2.4 (%100.0))] %27 local maxima, %27 large gradients and %41 min vals, 5377 gradients ignored tol=1.0e-04, sigma=2.0, host=linux, nav=16, nbrs=2, 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 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=24842670.0, rms=32.19 001: dt: 0.5000, sse=20320308.0, rms=28.830 (0.000%) 002: dt: 0.5000, sse=16571449.0, rms=25.743 (0.000%) 003: dt: 0.5000, sse=13483090.0, rms=22.922 (0.000%) 004: dt: 0.5000, sse=10999791.0, rms=20.308 (0.000%) 005: dt: 0.5000, sse=9118177.0, rms=17.937 (0.000%) 006: dt: 0.5000, sse=7809257.5, rms=15.866 (0.000%) 007: dt: 0.5000, sse=6973519.5, rms=14.026 (0.000%) 008: dt: 0.5000, sse=6402408.0, rms=12.372 (0.000%) 009: dt: 0.5000, sse=6016715.0, rms=10.830 (0.000%) 010: dt: 0.5000, sse=5673039.5, rms=9.369 (0.000%) 011: dt: 0.5000, sse=5443668.5, rms=8.013 (0.000%) 012: dt: 0.5000, sse=5321283.5, rms=6.861 (0.000%) 013: dt: 0.5000, sse=5307655.5, rms=5.954 (0.000%) 014: dt: 0.5000, sse=5304185.5, rms=5.309 (0.000%) 015: dt: 0.5000, sse=5343397.0, rms=4.863 (0.000%) 016: dt: 0.5000, sse=5368893.0, rms=4.607 (0.000%) 017: dt: 0.5000, sse=5388899.0, rms=4.436 (0.000%) 018: dt: 0.5000, sse=5412267.0, rms=4.348 (0.000%) 019: dt: 0.5000, sse=5424610.0, rms=4.270 (0.000%) rms = 4.23, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=5456515.0, rms=4.235 (0.000%) 021: dt: 0.2500, sse=3324230.2, rms=3.172 (0.000%) 022: dt: 0.2500, sse=3104074.5, rms=2.850 (0.000%) 023: dt: 0.2500, sse=2953415.2, rms=2.759 (0.000%) rms = 2.71, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=2914418.2, rms=2.714 (0.000%) 025: dt: 0.1250, sse=2733377.8, rms=2.583 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=2711773.2, rms=2.569 (0.000%) positioning took 1.4 minutes mean border=55.7, 1028 (7) missing vertices, mean dist 0.2 [0.3 (%25.6)->0.4 (%74.4))] %46 local maxima, %14 large gradients and %34 min vals, 3808 gradients ignored tol=1.0e-04, sigma=1.0, host=linux, nav=8, nbrs=2, 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 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4097373.2, rms=7.84 027: dt: 0.5000, sse=3873849.0, rms=5.204 (0.000%) 028: dt: 0.5000, sse=4926759.5, rms=4.714 (0.000%) 029: dt: 0.5000, sse=4792968.5, rms=4.497 (0.000%) rms = 4.52, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3755094.0, rms=3.404 (0.000%) 031: dt: 0.2500, sse=3481276.2, rms=2.921 (0.000%) 032: dt: 0.2500, sse=3352762.2, rms=2.790 (0.000%) rms = 2.74, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3338779.5, rms=2.743 (0.000%) 034: dt: 0.1250, sse=3075859.5, rms=2.461 (0.000%) rms = 2.42, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3048603.0, rms=2.421 (0.000%) positioning took 0.6 minutes mean border=54.2, 1578 (3) missing vertices, mean dist 0.0 [0.2 (%35.6)->0.2 (%64.4))] %49 local maxima, %12 large gradients and %33 min vals, 3052 gradients ignored tol=1.0e-04, sigma=0.5, host=linux, nav=4, nbrs=2, 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 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3166360.5, rms=3.28 rms = 4.09, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3045402.5, rms=2.729 (0.000%) 037: dt: 0.2500, sse=3138657.0, rms=2.612 (0.000%) rms = 2.57, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=3174919.8, rms=2.574 (0.000%) 039: dt: 0.1250, sse=3065568.5, rms=2.461 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=3063072.5, rms=2.441 (0.000%) positioning took 0.3 minutes mean border=53.7, 3151 (3) missing vertices, mean dist 0.0 [0.2 (%46.2)->0.2 (%53.8))] %49 local maxima, %11 large gradients and %32 min vals, 2590 gradients ignored tol=1.0e-04, sigma=0.2, host=linux, nav=2, nbrs=2, 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 writing pial surface to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3083927.5, rms=2.64 rms = 3.24, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=3048624.8, rms=2.479 (0.000%) 042: dt: 0.2500, sse=3177045.8, rms=2.427 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=3184564.0, rms=2.400 (0.000%) 044: dt: 0.1250, sse=3101152.8, rms=2.310 (0.000%) rms = 2.29, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=3100480.0, rms=2.289 (0.000%) positioning took 0.3 minutes writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.area.pial vertex spacing 0.96 +- 0.40 (0.07-->8.07) (max @ vno 115466 --> 115469) face area 0.37 +- 0.28 (0.00-->12.19) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 115847 vertices processed 25000 of 115847 vertices processed 50000 of 115847 vertices processed 75000 of 115847 vertices processed 100000 of 115847 vertices processed 0 of 115847 vertices processed 25000 of 115847 vertices processed 50000 of 115847 vertices processed 75000 of 115847 vertices processed 100000 of 115847 vertices processed thickness calculation complete, 828:1950 truncations. 22786 vertices at 0 distance 66821 vertices at 1 distance 68176 vertices at 2 distance 37304 vertices at 3 distance 15893 vertices at 4 distance 6158 vertices at 5 distance 2361 vertices at 6 distance 838 vertices at 7 distance 302 vertices at 8 distance 137 vertices at 9 distance 84 vertices at 10 distance 69 vertices at 11 distance 75 vertices at 12 distance 61 vertices at 13 distance 62 vertices at 14 distance 36 vertices at 15 distance 30 vertices at 16 distance 26 vertices at 17 distance 22 vertices at 18 distance 13 vertices at 19 distance 14 vertices at 20 distance writing curvature file /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.thickness positioning took 5.9 minutes #-------------------------------------------- #@# Surf Volume rh Wed Apr 17 14:36:17 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Wed Apr 17 14:36:17 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts pctsurfcon --s ACC019 --rh-only Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/pctsurfcon.log Wed Apr 17 14:36:17 CEST 2013 setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2 cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.wm.mgh --regheader ACC019 --cortex srcvol = /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz as target reference. Loading label /home/linux/Escritorio/COHORTE_T2/ACC019/label/rh.cortex.label Reading surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 63968 Masking with /home/linux/Escritorio/COHORTE_T2/ACC019/label/rh.cortex.label Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.wm.mgh Dim: 115847 1 1 mri_vol2surf --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.gm.mgh --projfrac 0.3 --regheader ACC019 --cortex srcvol = /home/linux/Escritorio/COHORTE_T2/ACC019/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz as target reference. Loading label /home/linux/Escritorio/COHORTE_T2/ACC019/label/rh.cortex.label Reading surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white Done reading source surface Reading thickness /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 75193 Masking with /home/linux/Escritorio/COHORTE_T2/ACC019/label/rh.cortex.label Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.gm.mgh Dim: 115847 1 1 mri_concat /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.wm.mgh /home/linux/Escritorio/COHORTE_T2/ACC019/surf/tmp.pctsurfcon.5820/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.w-g.pct.mgh mri_segstats --in /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.w-g.pct.mgh --annot ACC019 rh aparc --sum /home/linux/Escritorio/COHORTE_T2/ACC019/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.w-g.pct.mgh --annot ACC019 rh aparc --sum /home/linux/Escritorio/COHORTE_T2/ACC019/stats/rh.w-g.pct.stats --snr sysname Linux hostname linux-To-be-filled-by-O-E-M machine x86_64 user linux UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.w-g.pct.mgh Vertex Area is 0.617795 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1160 774.151 2 2002 caudalanteriorcingulate 1046 633.260 3 2003 caudalmiddlefrontal 2530 1620.015 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2470 1448.072 6 2006 entorhinal 405 275.973 7 2007 fusiform 3281 2055.856 8 2008 inferiorparietal 6180 3945.882 9 2009 inferiortemporal 4119 2491.713 10 2010 isthmuscingulate 1466 886.387 11 2011 lateraloccipital 6127 3622.850 12 2012 lateralorbitofrontal 3403 2052.469 13 2013 lingual 3826 2338.361 14 2014 medialorbitofrontal 2459 1444.124 15 2015 middletemporal 4406 2740.747 16 2016 parahippocampal 844 536.644 17 2017 paracentral 1993 1171.506 18 2018 parsopercularis 1548 982.481 19 2019 parsorbitalis 1007 553.437 20 2020 parstriangularis 1713 1044.293 21 2021 pericalcarine 2397 1534.887 22 2022 postcentral 5581 3200.357 23 2023 posteriorcingulate 1689 1062.154 24 2024 precentral 6689 4031.958 25 2025 precuneus 4437 2734.792 26 2026 rostralanteriorcingulate 644 380.533 27 2027 rostralmiddlefrontal 7764 4868.657 28 2028 superiorfrontal 8121 5079.772 29 2029 superiorparietal 6924 4297.333 30 2030 superiortemporal 4589 2890.455 31 2031 supramarginal 5002 3179.324 32 2032 frontalpole 378 217.746 33 2033 temporalpole 563 383.329 34 2034 transversetemporal 591 268.940 35 2035 insula 3533 2309.881 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Wed Apr 17 14:36:22 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab ACC019 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1160 774 2181 3.026 0.562 0.129 0.041 23 2.0 bankssts 1046 633 2176 3.244 0.829 0.150 0.074 31 2.7 caudalanteriorcingulate 2530 1620 4654 2.689 0.441 0.127 0.041 26 4.5 caudalmiddlefrontal 2470 1448 3876 2.387 0.550 0.149 0.054 39 5.6 cuneus 405 276 1693 3.927 0.769 0.131 0.045 6 0.6 entorhinal 3281 2056 8104 3.513 0.735 0.153 0.067 99 9.8 fusiform 6180 3946 11607 2.693 0.575 0.147 0.060 108 15.1 inferiorparietal 4119 2492 9336 3.153 0.730 0.164 0.122 244 23.9 inferiortemporal 1466 886 2706 2.759 1.002 0.149 0.062 28 3.7 isthmuscingulate 6127 3623 10020 2.530 0.713 0.148 0.067 122 18.8 lateraloccipital 3403 2052 6048 2.860 0.735 0.150 0.129 161 10.5 lateralorbitofrontal 3826 2338 6055 2.337 0.633 0.146 0.056 66 9.1 lingual 2459 1444 4501 2.827 0.686 0.142 0.128 64 7.4 medialorbitofrontal 4406 2741 10358 3.187 0.632 0.148 0.225 229 13.0 middletemporal 844 537 1910 3.086 0.816 0.104 0.031 7 0.9 parahippocampal 1993 1172 3228 2.628 0.656 0.114 0.122 490 3.5 paracentral 1548 982 2807 2.702 0.443 0.132 0.043 20 2.7 parsopercularis 1007 553 2091 3.160 0.529 0.140 0.052 14 2.3 parsorbitalis 1713 1044 3098 2.642 0.505 0.125 0.038 21 2.9 parstriangularis 2397 1535 3048 2.099 0.617 0.150 0.064 60 6.3 pericalcarine 5581 3200 7721 2.140 0.633 0.110 0.035 58 8.4 postcentral 1689 1062 3205 2.621 0.845 0.140 0.049 52 3.6 posteriorcingulate 6689 4032 11610 2.707 0.531 0.123 0.047 78 14.7 precentral 4437 2735 7933 2.706 0.677 0.131 0.049 64 8.2 precuneus 644 381 1235 3.137 0.707 0.107 0.045 6 1.1 rostralanteriorcingulate 7764 4869 13764 2.537 0.524 0.141 0.056 118 18.4 rostralmiddlefrontal 8121 5080 17842 2.993 0.684 0.147 0.081 233 23.7 superiorfrontal 6924 4297 10536 2.256 0.510 0.139 0.141 523 25.4 superiorparietal 4589 2890 9427 2.943 0.658 0.108 0.030 43 5.6 superiortemporal 5002 3179 9177 2.679 0.511 0.134 0.046 71 9.5 supramarginal 378 218 881 2.908 0.582 0.165 0.083 8 1.2 frontalpole 563 383 2402 3.864 0.625 0.146 0.047 9 1.2 temporalpole 591 269 820 2.585 0.425 0.099 0.028 5 0.7 transversetemporal 3533 2310 6975 3.159 0.942 0.164 7.310 3538 15.7 insula #----------------------------------------- #@# Cortical Parc 2 rh Wed Apr 17 14:36:30 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 23 labels changed using aseg relabeling using gibbs priors... 000: 8326 changed, 115847 examined... 001: 2040 changed, 32160 examined... 002: 603 changed, 10331 examined... 003: 262 changed, 3385 examined... 004: 108 changed, 1463 examined... 005: 64 changed, 624 examined... 006: 40 changed, 360 examined... 007: 14 changed, 225 examined... 008: 15 changed, 91 examined... 009: 12 changed, 82 examined... 010: 12 changed, 61 examined... 011: 5 changed, 53 examined... 012: 2 changed, 33 examined... 013: 0 changed, 11 examined... 16 labels changed using aseg 000: 255 total segments, 174 labels (2059 vertices) changed 001: 97 total segments, 16 labels (89 vertices) changed 002: 82 total segments, 1 labels (4 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 118 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1134 vertices marked for relabeling... 1134 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Wed Apr 17 14:37:00 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab ACC019 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 899 560 1573 2.595 0.475 0.159 0.060 15 2.2 G_and_S_frontomargin 1054 677 2240 2.938 0.599 0.155 0.110 39 6.9 G_and_S_occipital_inf 1311 688 2023 2.390 0.629 0.116 0.064 19 4.8 G_and_S_paracentral 1459 854 2684 2.806 0.507 0.122 0.033 17 2.0 G_and_S_subcentral 1795 1059 3262 2.516 0.620 0.141 0.054 29 4.1 G_and_S_transv_frontopol 1929 1217 3703 3.186 0.525 0.126 0.054 25 3.8 G_and_S_cingul-Ant 1071 689 2254 3.135 0.633 0.133 0.061 26 2.4 G_and_S_cingul-Mid-Ant 1169 776 2303 2.755 0.506 0.127 0.042 12 2.0 G_and_S_cingul-Mid-Post 524 303 1446 3.432 0.709 0.163 0.072 33 1.4 G_cingul-Post-dorsal 328 192 837 3.124 0.759 0.168 0.075 7 0.8 G_cingul-Post-ventral 2455 1432 3828 2.306 0.540 0.154 0.062 46 6.2 G_cuneus 1015 599 2242 2.883 0.378 0.159 0.069 23 2.9 G_front_inf-Opercular 235 134 588 3.242 0.334 0.141 0.054 3 0.5 G_front_inf-Orbital 906 495 1794 2.687 0.471 0.139 0.049 15 1.9 G_front_inf-Triangul 3579 2157 7810 2.708 0.514 0.159 0.069 68 11.3 G_front_middle 5790 3399 14300 3.174 0.654 0.165 0.133 697 21.8 G_front_sup 495 288 937 3.126 0.568 0.224 51.511 3444 1.6 G_Ins_lg_and_S_cent_ins 464 261 1406 4.071 0.650 0.176 0.185 26 4.3 G_insular_short 2137 1240 4805 2.931 0.594 0.177 0.093 57 8.5 G_occipital_middle 1489 872 2233 2.151 0.451 0.142 0.054 25 3.1 G_occipital_sup 1413 834 3923 3.539 0.664 0.175 0.104 73 6.9 G_oc-temp_lat-fusifor 2445 1380 3918 2.324 0.620 0.148 0.062 46 6.4 G_oc-temp_med-Lingual 1430 926 4105 3.509 1.064 0.146 0.055 26 3.3 G_oc-temp_med-Parahip 2339 1309 4840 2.820 0.761 0.152 0.155 73 9.9 G_orbital 2052 1256 4343 2.703 0.574 0.161 0.068 44 5.4 G_pariet_inf-Angular 2414 1465 5341 2.851 0.516 0.146 0.055 41 5.8 G_pariet_inf-Supramar 2172 1325 3937 2.386 0.546 0.152 0.130 224 16.9 G_parietal_sup 2043 987 2961 2.254 0.524 0.115 0.039 28 3.4 G_postcentral 2607 1323 5039 2.876 0.431 0.121 0.049 31 5.6 G_precentral 1938 1137 4093 2.679 0.674 0.154 0.069 42 4.7 G_precuneus 743 391 1414 2.614 0.823 0.165 0.271 36 3.9 G_rectus 369 214 455 2.297 0.991 0.122 0.097 6 1.1 G_subcallosal 481 203 760 2.820 0.586 0.110 0.033 5 0.7 G_temp_sup-G_T_transv 1587 911 4124 3.183 0.487 0.131 0.043 24 2.7 G_temp_sup-Lateral 532 354 1275 3.174 0.677 0.085 0.022 3 0.5 G_temp_sup-Plan_polar 550 358 1041 2.570 0.454 0.095 0.022 3 0.4 G_temp_sup-Plan_tempo 2257 1265 5959 3.276 0.811 0.184 0.162 212 18.8 G_temporal_inf 2652 1564 7017 3.276 0.642 0.159 0.114 77 9.6 G_temporal_middle 347 236 561 2.522 0.458 0.089 0.020 2 0.3 Lat_Fis-ant-Horizont 168 120 296 2.442 0.419 0.127 0.035 2 0.2 Lat_Fis-ant-Vertical 1415 979 2079 2.559 0.554 0.117 0.039 13 2.1 Lat_Fis-post 3860 2196 5312 2.146 0.657 0.146 0.056 64 9.2 Pole_occipital 1340 848 5095 3.925 0.581 0.150 0.051 24 2.9 Pole_temporal 2219 1509 2970 2.211 0.683 0.139 0.049 49 4.7 S_calcarine 2499 1763 2995 1.926 0.620 0.106 0.025 13 2.7 S_central 1047 727 1560 2.320 0.516 0.089 0.017 4 0.7 S_cingul-Marginalis 570 360 1019 3.319 0.530 0.123 0.042 5 1.1 S_circular_insula_ant 1323 879 1991 2.614 0.858 0.111 0.076 31 3.0 S_circular_insula_inf 1255 865 2099 2.992 0.516 0.126 0.044 11 2.3 S_circular_insula_sup 764 534 1493 3.209 0.559 0.116 0.022 6 0.7 S_collat_transv_ant 371 236 615 3.009 0.517 0.128 0.032 3 0.5 S_collat_transv_post 1351 904 1915 2.440 0.468 0.120 0.051 16 2.3 S_front_inf 1974 1326 2808 2.421 0.502 0.119 0.035 17 2.7 S_front_middle 1758 1162 2770 2.485 0.411 0.111 0.033 12 2.3 S_front_sup 734 474 973 2.430 0.372 0.121 0.038 9 1.3 S_interm_prim-Jensen 2590 1675 3436 2.253 0.502 0.131 0.234 270 4.8 S_intrapariet_and_P_trans 613 394 801 2.677 0.544 0.147 0.046 7 1.1 S_oc_middle_and_Lunatus 1386 877 1929 2.517 0.536 0.131 0.036 16 1.9 S_oc_sup_and_transversal 693 464 1154 2.730 0.506 0.134 0.050 11 1.4 S_occipital_ant 770 478 1265 3.123 0.773 0.151 0.073 14 1.9 S_oc-temp_lat 1275 917 2295 3.003 0.599 0.110 0.026 8 1.3 S_oc-temp_med_and_Lingual 282 179 410 2.682 0.407 0.135 0.045 3 0.5 S_orbital_lateral 658 442 914 2.317 0.670 0.142 0.124 91 1.0 S_orbital_med-olfact 1381 867 2542 3.169 0.555 0.139 0.051 19 3.2 S_orbital-H_Shaped 1865 1184 2632 2.564 0.576 0.121 0.038 19 3.0 S_parieto_occipital 1532 924 1810 2.364 1.092 0.139 0.052 30 3.4 S_pericallosal 2369 1558 3046 2.155 0.463 0.112 0.027 18 2.6 S_postcentral 1524 1002 2393 2.689 0.423 0.122 0.039 14 2.5 S_precentral-inf-part 1182 800 1870 2.596 0.438 0.116 0.033 10 1.7 S_precentral-sup-part 432 276 635 2.830 0.497 0.119 0.037 3 0.6 S_suborbital 934 600 1703 3.078 0.652 0.128 0.038 10 1.5 S_subparietal 1252 817 2031 2.900 0.556 0.159 0.584 159 4.8 S_temporal_inf 4710 3199 8315 2.922 0.593 0.122 0.037 59 7.2 S_temporal_sup 314 194 479 2.723 0.417 0.097 0.019 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Wed Apr 17 14:37:09 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ACC019 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1091 labels changed using aseg relabeling using gibbs priors... 000: 2402 changed, 115847 examined... 001: 491 changed, 10185 examined... 002: 110 changed, 2765 examined... 003: 37 changed, 650 examined... 004: 15 changed, 227 examined... 005: 11 changed, 85 examined... 006: 5 changed, 67 examined... 007: 0 changed, 22 examined... 121 labels changed using aseg 000: 54 total segments, 21 labels (538 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 705 vertices marked for relabeling... 705 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 26 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Wed Apr 17 14:37:35 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab ACC019 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/wm.mgz... reading input surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... reading input pial surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.pial... reading input white surface /home/linux/Escritorio/COHORTE_T2/ACC019/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1002 605 2124 3.285 0.825 0.153 0.077 31 2.7 caudalanteriorcingulate 2525 1633 4642 2.690 0.443 0.130 0.042 27 4.6 caudalmiddlefrontal 2950 1741 4485 2.384 0.518 0.146 0.052 46 6.5 cuneus 443 300 1791 3.974 0.755 0.127 0.042 6 0.6 entorhinal 2817 1783 6716 3.456 0.695 0.155 0.070 89 8.8 fusiform 5467 3501 10174 2.681 0.578 0.152 0.063 102 13.8 inferiorparietal 4636 2784 10927 3.225 0.782 0.165 0.248 386 25.7 inferiortemporal 1523 919 2778 2.766 1.013 0.148 0.061 29 3.7 isthmuscingulate 6381 3803 10523 2.525 0.715 0.147 0.066 126 19.1 lateraloccipital 4090 2493 7375 2.810 0.748 0.157 0.125 186 14.5 lateralorbitofrontal 3827 2339 6076 2.340 0.634 0.146 0.056 68 8.8 lingual 2054 1196 3565 2.634 0.779 0.150 0.149 61 7.6 medialorbitofrontal 5324 3345 12060 3.139 0.624 0.141 0.075 107 13.8 middletemporal 857 541 1904 3.062 0.815 0.107 0.036 8 1.2 parahippocampal 2087 1237 3501 2.663 0.671 0.117 0.120 491 3.8 paracentral 1716 1091 3100 2.710 0.440 0.135 0.045 23 3.3 parsopercularis 1086 609 2102 3.021 0.481 0.128 0.046 13 2.1 parsorbitalis 1781 1068 3111 2.600 0.518 0.125 0.053 26 3.3 parstriangularis 2353 1507 2975 2.099 0.621 0.149 0.062 55 6.1 pericalcarine 5968 3453 8393 2.171 0.637 0.112 0.035 63 9.1 postcentral 1676 1056 3172 2.625 0.841 0.140 0.049 52 3.6 posteriorcingulate 6579 3926 11364 2.696 0.533 0.122 0.047 76 14.3 precentral 4524 2787 8096 2.660 0.689 0.130 0.049 65 8.3 precuneus 741 445 1392 3.196 0.638 0.112 0.054 9 1.3 rostralanteriorcingulate 4062 2603 7164 2.486 0.473 0.139 0.050 54 9.0 rostralmiddlefrontal 12045 7483 25102 2.890 0.670 0.144 0.073 295 32.9 superiorfrontal 5928 3681 9109 2.258 0.508 0.142 0.158 512 23.8 superiorparietal 6241 3985 14053 3.089 0.712 0.117 0.036 77 9.4 superiortemporal 4835 3082 8772 2.644 0.513 0.133 0.045 65 9.0 supramarginal 569 260 793 2.577 0.425 0.099 0.028 5 0.7 transversetemporal 2798 1802 5689 3.293 0.787 0.161 9.200 3514 11.1 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Apr 17 14:37:42 CEST 2013 bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2 Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.log Wed Apr 17 14:37:42 CEST 2013 setenv SUBJECTS_DIR /home/linux/Escritorio/COHORTE_T2 cd /home/linux/Escritorio/COHORTE_T2/ACC019/scripts /usr/local/freesurfer/bin/bbregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --lta /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii... fslregister --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask Log file is /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fslregister.log Wed Apr 17 14:37:42 CEST 2013 --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister --dof 6 --fsvol brainmask $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ linux-To-be-filled-by-O-E-M Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /home/linux/Escritorio/COHORTE_T2/ACC019/mri/ERROR: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii mri_convert: extra arguments ("not" and following) type mri_convert -u for usage -------------------------------------- /home/linux/Escritorio/COHORTE_T2/ACC019/scripts mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) keeping frame 0 writing to /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii... Mov determinant is -5.12001 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat --regheader --fslregout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0 --s ACC019 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii reg file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/reg0.6003.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.600 0.000 0.000 128.000; 0.000 0.000 2.000 -80.000; 0.000 -1.600 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; Determinant 1 subject = ACC019 RegMat --------------------------- 0.997 -0.073 0.034 0.214; -0.046 -0.182 0.982 -30.911; -0.065 -0.981 -0.185 1.512; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -5.12001, ref det = -1 Wed Apr 17 14:37:44 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat0 ** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) Wed Apr 17 14:37:44 CEST 2013 /home/linux/Escritorio/COHORTE_T2/ACC019/scripts flirt.fsl -ref /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii -in /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat -init /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch ** ERROR (nifti_image_read): failed to find header file for '/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister ERROR: Could not open image /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister Image Exception : #22 :: Failed to read volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/fslregister/refvol.fslregister.nii terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) tkregister2_cmdl --s ACC019 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --fslreg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ERROR: cannot open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat.fsl.mat cat: /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat: No such file or directory tmp: Subscript out of range. Started at Wed Apr 17 14:37:42 CEST 2013 Ended at Wed Apr 17 14:37:44 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --surf orig mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.init.dat mri_segreg --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/template.nii --init-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat --out-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/tmp.bbregister.5969/bbr.pass1.dat tkregister2_cmdl --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --noedit --ltaout /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta regio_read_register(): No such file or directory Could not open /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz reg file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ERROR: reading /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat Cleaning up Started at Wed Apr 17 14:37:42 CEST 2013 Ended at Wed Apr 17 14:37:45 CEST 2013 BBR-Run-Time-Sec 3 bbregister Done To check results, run: tkregister2 --mov /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz --reg /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.dat --surf mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz mri_convert -at /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta -rl /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz /home/linux/Escritorio/COHORTE_T2/ACC019/mri/T2.mgz ltaReadFile(/home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/linux/Escritorio/COHORTE_T2/ACC019/mri/orig/T2raw.mgz... TR=10800.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996796, 0.0725774, -0.0336276) j_ras = (0.065149, 0.980551, 0.185135) k_ras = (-0.0464102, -0.182351, 0.982138) INFO: Reading transformation from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /home/linux/Escritorio/COHORTE_T2/ACC019/mri/transforms/T2raw.lta Linux linux-To-be-filled-by-O-E-M 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ACC019 exited with ERRORS at Wed Apr 17 14:37:45 CEST 2013 For more details, see the log file /home/linux/Escritorio/COHORTE_T2/ACC019/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting