New invocation of recon-all Sat Jul 21 02:14:21 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -inflate2 #-------------------------------------------- #@# Inflation2 lh Sat Jul 21 02:14:21 BST 2012 /home/clare/subjects/subject_20/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 50.5 mm, total surface area = 98576 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.068 (target=0.015) step 015: RMS=0.056 (target=0.015) step 020: RMS=0.048 (target=0.015) step 025: RMS=0.040 (target=0.015) step 030: RMS=0.035 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.019 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 400 vertices thresholded to be in k1 ~ [-0.29 0.55], k2 ~ [-0.15 0.11] total integrated curvature = 0.298*4pi (3.747) --> 1 handles ICI = 1.6, FI = 11.3, variation=193.364 282 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 225 vertices thresholded to be in [-0.15 0.20] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023 done. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 02:16:26 BST 2012 New invocation of recon-all Sat Jul 21 02:16:26 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -inflate2 #-------------------------------------------- #@# Inflation2 rh Sat Jul 21 02:16:26 BST 2012 /home/clare/subjects/subject_20/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 100215 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.086 (target=0.015) step 010: RMS=0.066 (target=0.015) step 015: RMS=0.054 (target=0.015) step 020: RMS=0.046 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.018 (target=0.015) step 060: RMS=0.017 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 448 vertices thresholded to be in k1 ~ [-0.18 0.34], k2 ~ [-0.08 0.05] total integrated curvature = 0.469*4pi (5.889) --> 1 handles ICI = 1.5, FI = 10.9, variation=181.257 196 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 196 vertices thresholded to be in [-0.12 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.014, std = 0.022 done. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 02:18:34 BST 2012 New invocation of recon-all Sat Jul 21 02:18:34 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -sphere #-------------------------------------------- #@# Sphere lh Sat Jul 21 02:18:34 BST 2012 /home/clare/subjects/subject_20/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 0.96 hours scaling brain by 0.269... pass 1: epoch 1 of 3 starting distance error %21.02 pass 1: epoch 2 of 3 starting distance error %21.02 unfolding complete - removing small folds... starting distance error %20.94 removing remaining folds... final distance error %20.96 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 03:16:16 BST 2012 New invocation of recon-all Sat Jul 21 03:16:16 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -sphere #-------------------------------------------- #@# Sphere rh Sat Jul 21 03:16:16 BST 2012 /home/clare/subjects/subject_20/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.03 hours scaling brain by 0.268... pass 1: epoch 1 of 3 starting distance error %20.12 pass 1: epoch 2 of 3 starting distance error %20.09 unfolding complete - removing small folds... starting distance error %19.98 removing remaining folds... final distance error %20.01 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 04:18:01 BST 2012 New invocation of recon-all Sat Jul 21 04:18:01 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -surfreg #-------------------------------------------- #@# Surf Reg lh Sat Jul 21 04:18:01 BST 2012 /home/clare/subjects/subject_20/scripts mris_register -curv ../surf/lh.sphere /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /home/clare/freesurfer/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.593 curvature mean = 0.025, std = 0.925 curvature mean = 0.023, std = 0.843 curvature mean = -0.012, std = 0.938 curvature mean = 0.009, std = 0.932 curvature mean = -0.019, std = 0.947 curvature mean = 0.004, std = 0.968 curvature mean = -0.022, std = 0.947 curvature mean = 0.001, std = 0.985 curvature mean = -0.035, std = 0.359 curvature mean = 0.002, std = 0.066 curvature mean = 0.067, std = 0.260 curvature mean = 0.001, std = 0.079 curvature mean = 0.044, std = 0.406 curvature mean = 0.001, std = 0.084 curvature mean = 0.027, std = 0.532 curvature mean = 0.001, std = 0.087 curvature mean = 0.011, std = 0.644 expanding nbhd size to 1 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 04:47:54 BST 2012 New invocation of recon-all Sat Jul 21 04:47:54 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -surfreg #-------------------------------------------- #@# Surf Reg rh Sat Jul 21 04:47:54 BST 2012 /home/clare/subjects/subject_20/scripts mris_register -curv ../surf/rh.sphere /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /home/clare/freesurfer/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.594 curvature mean = 0.038, std = 0.928 curvature mean = 0.021, std = 0.839 curvature mean = 0.004, std = 0.930 curvature mean = 0.007, std = 0.927 curvature mean = -0.002, std = 0.936 curvature mean = 0.004, std = 0.965 curvature mean = -0.005, std = 0.936 curvature mean = 0.001, std = 0.984 curvature mean = -0.029, std = 0.347 curvature mean = 0.006, std = 0.069 curvature mean = 0.063, std = 0.263 curvature mean = 0.005, std = 0.082 curvature mean = 0.041, std = 0.414 curvature mean = 0.005, std = 0.087 curvature mean = 0.027, std = 0.541 curvature mean = 0.006, std = 0.089 curvature mean = 0.012, std = 0.650 expanding nbhd size to 1 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:16:44 BST 2012 New invocation of recon-all Sat Jul 21 05:16:44 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -jacobian_white #-------------------------------------------- #@# Jacobian white lh Sat Jul 21 05:16:44 BST 2012 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 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:16:46 BST 2012 New invocation of recon-all Sat Jul 21 05:16:46 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -jacobian_white #-------------------------------------------- #@# Jacobian white rh Sat Jul 21 05:16:46 BST 2012 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 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:16:49 BST 2012 New invocation of recon-all Sat Jul 21 05:16:49 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -avgcurv #-------------------------------------------- #@# AvgCurv lh Sat Jul 21 05:16:49 BST 2012 /home/clare/subjects/subject_20/scripts mrisp_paint -a 5 /home/clare/freesurfer/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 /home/clare/freesurfer/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:16:50 BST 2012 New invocation of recon-all Sat Jul 21 05:16:50 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -avgcurv #-------------------------------------------- #@# AvgCurv rh Sat Jul 21 05:16:50 BST 2012 /home/clare/subjects/subject_20/scripts mrisp_paint -a 5 /home/clare/freesurfer/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 /home/clare/freesurfer/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:16:52 BST 2012 New invocation of recon-all Sat Jul 21 05:16:52 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortparc #----------------------------------------- #@# Cortical Parc lh Sat Jul 21 05:16:52 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 lh ../surf/lh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 1805 labels changed using aseg relabeling using gibbs priors... 000: 3528 changed, 171341 examined... 001: 882 changed, 15049 examined... 002: 257 changed, 4774 examined... 003: 88 changed, 1550 examined... 004: 36 changed, 520 examined... 005: 15 changed, 211 examined... 006: 6 changed, 85 examined... 007: 7 changed, 37 examined... 008: 1 changed, 26 examined... 009: 2 changed, 6 examined... 010: 1 changed, 10 examined... 011: 3 changed, 8 examined... 012: 1 changed, 11 examined... 013: 0 changed, 7 examined... 307 labels changed using aseg 000: 156 total segments, 103 labels (494 vertices) changed 001: 54 total segments, 1 labels (10 vertices) changed 002: 53 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2039 vertices marked for relabeling... 2039 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 43 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:17:36 BST 2012 New invocation of recon-all Sat Jul 21 05:17:36 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -cortparc #----------------------------------------- #@# Cortical Parc rh Sat Jul 21 05:17:36 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 rh ../surf/rh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 1305 labels changed using aseg relabeling using gibbs priors... 000: 3410 changed, 171608 examined... 001: 820 changed, 14651 examined... 002: 199 changed, 4579 examined... 003: 79 changed, 1159 examined... 004: 28 changed, 487 examined... 005: 15 changed, 184 examined... 006: 2 changed, 81 examined... 007: 3 changed, 16 examined... 008: 0 changed, 9 examined... 178 labels changed using aseg 000: 120 total segments, 78 labels (530 vertices) changed 001: 43 total segments, 1 labels (11 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2086 vertices marked for relabeling... 2086 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 43 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:18:19 BST 2012 New invocation of recon-all Sat Jul 21 05:18:19 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -parcstats #----------------------------------------- #@# Parcellation Stats lh Sat Jul 21 05:18:19 BST 2012 /home/clare/subjects/subject_20/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 subject_20 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/lh.white... reading input pial surface /home/clare/subjects/subject_20/surf/lh.pial... reading input white surface /home/clare/subjects/subject_20/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 2208 1491 3835 2.726 0.544 0.108 0.028 15 2.6 bankssts 1804 1106 3946 3.120 0.914 0.159 0.090 37 7.3 caudalanteriorcingulate 4149 2437 6802 2.607 0.530 0.157 0.194 377 22.0 caudalmiddlefrontal 2409 1493 2584 1.676 0.450 0.174 0.102 119 10.8 cuneus 666 419 1980 3.242 1.030 0.185 0.111 15 3.1 entorhinal 5100 3390 10957 2.719 0.834 0.191 0.137 189 29.7 fusiform 8381 5186 15791 2.687 0.593 0.147 0.203 572 96.9 inferiorparietal 6062 3955 14603 2.992 0.745 0.156 0.090 171 23.0 inferiortemporal 2052 1239 3424 2.532 0.857 0.185 0.298 395 11.9 isthmuscingulate 9882 6057 14919 2.231 0.695 0.174 0.119 1372 51.9 lateraloccipital 4842 3094 9539 2.784 0.812 0.188 0.160 359 33.0 lateralorbitofrontal 5617 3517 7821 2.053 0.564 0.199 0.171 245 37.3 lingual 3566 2354 7299 2.724 0.916 0.165 0.135 226 17.2 medialorbitofrontal 5960 3934 15703 3.087 0.724 0.154 0.079 183 17.1 middletemporal 1202 768 3022 3.225 0.795 0.180 0.113 46 5.9 parahippocampal 2901 1711 4052 2.275 0.656 0.158 0.146 186 19.2 paracentral 2995 1992 6321 2.772 0.561 0.134 0.056 61 7.1 parsopercularis 1077 738 2952 3.136 0.644 0.158 0.095 46 3.1 parsorbitalis 2187 1453 5023 2.932 0.608 0.143 0.084 44 5.2 parstriangularis 1922 1335 2107 1.637 0.390 0.194 0.150 76 9.2 pericalcarine 8983 5474 11178 1.943 0.706 0.155 0.092 353 37.5 postcentral 2570 1615 5241 2.856 0.896 0.168 0.089 70 9.5 posteriorcingulate 11586 7035 16430 2.268 0.708 0.158 0.150 1291 89.9 precentral 6698 4306 11790 2.516 0.620 0.176 0.124 206 34.2 precuneus 1594 1000 3717 3.334 0.857 0.167 0.080 51 5.6 rostralanteriorcingulate 11574 7493 23381 2.670 0.621 0.157 0.152 554 46.1 rostralmiddlefrontal 13000 8190 26908 2.935 0.652 0.154 0.119 629 68.1 superiorfrontal 9690 5969 16170 2.409 0.613 0.159 0.110 253 42.4 superiorparietal 6805 4456 16465 3.103 0.696 0.151 0.075 136 21.8 superiortemporal 8338 5481 16023 2.629 0.552 0.149 0.456 470 39.7 supramarginal 339 208 970 3.248 0.526 0.185 0.071 10 1.0 frontalpole 912 588 2501 3.061 0.801 0.222 0.205 39 8.4 temporalpole 765 437 1071 2.310 0.641 0.157 0.124 21 3.4 transversetemporal 3891 2472 8193 3.245 0.919 0.162 0.581 170 20.5 insula #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:18:35 BST 2012 New invocation of recon-all Sat Jul 21 05:18:35 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -parcstats #----------------------------------------- #@# Parcellation Stats rh Sat Jul 21 05:18:35 BST 2012 /home/clare/subjects/subject_20/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 subject_20 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/rh.white... reading input pial surface /home/clare/subjects/subject_20/surf/rh.pial... reading input white surface /home/clare/subjects/subject_20/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 1523 1084 2798 2.646 0.357 0.109 0.028 10 1.7 bankssts 1579 994 3254 2.767 0.783 0.153 0.064 28 4.4 caudalanteriorcingulate 4323 2636 7389 2.544 0.564 0.159 0.130 143 21.6 caudalmiddlefrontal 2735 1737 3133 1.704 0.515 0.171 0.087 61 10.4 cuneus 596 399 2006 3.950 0.733 0.206 0.208 17 3.8 entorhinal 5026 3435 11881 2.958 0.815 0.192 0.135 202 27.0 fusiform 10732 7185 21973 2.733 0.607 0.143 0.438 903 27.5 inferiorparietal 6154 4069 15190 3.087 0.788 0.159 0.100 205 28.3 inferiortemporal 1623 951 2489 2.600 0.805 0.154 0.116 39 7.0 isthmuscingulate 10173 6216 15477 2.242 0.701 0.184 0.166 593 60.5 lateraloccipital 4674 2956 9237 2.791 0.807 0.186 0.201 270 48.9 lateralorbitofrontal 5555 3758 8751 2.170 0.665 0.214 0.151 478 37.7 lingual 2997 2006 6613 2.865 0.763 0.164 0.074 75 9.7 medialorbitofrontal 6692 4486 17328 3.088 0.650 0.158 0.700 2664 20.0 middletemporal 1350 832 2860 2.914 0.917 0.185 0.440 301 16.5 parahippocampal 3952 2272 5010 2.232 0.562 0.150 0.129 142 23.4 paracentral 2199 1458 4762 2.931 0.450 0.139 0.053 34 4.9 parsopercularis 1542 959 3338 2.794 0.694 0.172 0.138 59 9.6 parsorbitalis 2819 1880 6568 3.016 0.649 0.150 0.064 57 8.0 parstriangularis 2097 1322 2178 1.680 0.643 0.182 0.133 86 9.7 pericalcarine 8717 5343 11759 2.036 0.693 0.148 0.085 268 30.5 postcentral 2187 1434 4570 2.877 0.687 0.172 0.089 48 8.4 posteriorcingulate 10024 6368 14817 2.239 0.748 0.158 0.108 366 46.3 precentral 7312 4705 12435 2.415 0.627 0.160 0.091 147 25.5 precuneus 1208 775 2946 3.125 0.695 0.165 0.084 31 4.3 rostralanteriorcingulate 12372 8117 25066 2.725 0.652 0.161 0.113 430 59.8 rostralmiddlefrontal 13931 8534 28380 2.952 0.661 0.158 0.167 1361 89.5 superiorfrontal 10055 6257 16744 2.370 0.625 0.165 0.169 501 58.7 superiorparietal 6553 4444 16278 3.079 0.775 0.144 0.070 117 20.8 superiortemporal 5847 3918 11493 2.720 0.569 0.148 0.058 96 13.9 supramarginal 592 389 1825 3.454 0.535 0.207 0.122 21 3.0 frontalpole 727 490 2656 3.988 0.850 0.199 0.191 74 5.6 temporalpole 665 409 816 1.992 0.604 0.156 0.076 12 2.1 transversetemporal 4424 2904 9167 3.193 0.807 0.176 0.166 162 22.3 insula #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:18:51 BST 2012 New invocation of recon-all Sat Jul 21 05:18:51 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortparc2 #----------------------------------------- #@# Cortical Parc 2 lh Sat Jul 21 05:18:51 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 lh ../surf/lh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 38 labels changed using aseg relabeling using gibbs priors... 000: 10994 changed, 171341 examined... 001: 2781 changed, 42368 examined... 002: 838 changed, 14147 examined... 003: 390 changed, 4678 examined... 004: 186 changed, 2171 examined... 005: 86 changed, 1038 examined... 006: 41 changed, 480 examined... 007: 31 changed, 236 examined... 008: 23 changed, 166 examined... 009: 9 changed, 124 examined... 010: 5 changed, 60 examined... 011: 4 changed, 26 examined... 012: 4 changed, 19 examined... 013: 3 changed, 20 examined... 014: 1 changed, 18 examined... 015: 0 changed, 5 examined... 2 labels changed using aseg 000: 339 total segments, 259 labels (3565 vertices) changed 001: 110 total segments, 31 labels (298 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 135 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1050 vertices marked for relabeling... 1050 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 49 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:19:40 BST 2012 New invocation of recon-all Sat Jul 21 05:19:40 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -cortparc2 #----------------------------------------- #@# Cortical Parc 2 rh Sat Jul 21 05:19:40 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 rh ../surf/rh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 37 labels changed using aseg relabeling using gibbs priors... 000: 11545 changed, 171608 examined... 001: 2852 changed, 44293 examined... 002: 980 changed, 14587 examined... 003: 432 changed, 5467 examined... 004: 219 changed, 2370 examined... 005: 129 changed, 1231 examined... 006: 73 changed, 718 examined... 007: 33 changed, 409 examined... 008: 21 changed, 191 examined... 009: 10 changed, 132 examined... 010: 9 changed, 66 examined... 011: 3 changed, 40 examined... 012: 2 changed, 19 examined... 013: 3 changed, 12 examined... 014: 0 changed, 14 examined... 19 labels changed using aseg 000: 335 total segments, 246 labels (3281 vertices) changed 001: 100 total segments, 11 labels (35 vertices) changed 002: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1330 vertices marked for relabeling... 1330 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 49 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:20:29 BST 2012 New invocation of recon-all Sat Jul 21 05:20:29 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -parcstats2 #----------------------------------------- #@# Parcellation Stats 2 lh Sat Jul 21 05:20:29 BST 2012 /home/clare/subjects/subject_20/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 subject_20 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/lh.white... reading input pial surface /home/clare/subjects/subject_20/surf/lh.pial... reading input white surface /home/clare/subjects/subject_20/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 1530 1013 2957 2.664 0.619 0.171 0.143 102 11.7 G_and_S_frontomargin 2454 1532 4564 2.624 0.705 0.173 0.096 77 9.0 G_and_S_occipital_inf 2422 1380 3020 1.968 0.634 0.161 0.099 64 10.1 G_and_S_paracentral 2293 1417 3775 2.581 0.686 0.172 0.133 211 16.4 G_and_S_subcentral 908 574 2025 2.783 0.504 0.167 0.063 22 2.5 G_and_S_transv_frontopol 2972 1937 6123 2.964 0.759 0.144 0.060 63 7.6 G_and_S_cingul-Ant 2293 1476 4915 3.143 0.704 0.153 0.080 40 8.5 G_and_S_cingul-Mid-Ant 1921 1206 3803 2.827 0.721 0.161 0.128 108 12.7 G_and_S_cingul-Mid-Post 810 503 1821 3.061 0.864 0.193 0.125 27 4.5 G_cingul-Post-dorsal 398 227 685 2.687 0.962 0.180 0.120 12 1.9 G_cingul-Post-ventral 2167 1345 2532 1.721 0.495 0.187 0.115 127 11.0 G_cuneus 1728 1123 4524 2.908 0.626 0.169 0.100 82 7.3 G_front_inf-Opercular 296 188 873 3.199 0.419 0.186 0.097 10 1.1 G_front_inf-Orbital 1161 777 3533 3.237 0.590 0.175 0.129 37 3.9 G_front_inf-Triangul 6381 3834 13710 2.774 0.630 0.168 0.266 627 30.4 G_front_middle 9139 5581 20754 3.048 0.692 0.171 0.160 657 63.9 G_front_sup 815 515 2002 3.577 0.996 0.178 0.122 24 4.5 G_Ins_lg_and_S_cent_ins 919 562 2724 3.773 0.701 0.191 0.136 30 5.3 G_insular_short 3370 1957 7109 2.807 0.636 0.173 0.189 145 22.2 G_occipital_middle 1951 1115 2874 2.142 0.720 0.149 0.134 50 6.6 G_occipital_sup 1805 1189 4480 2.888 0.771 0.226 0.181 89 14.6 G_oc-temp_lat-fusifor 3716 2308 5495 2.033 0.552 0.211 0.165 180 25.1 G_oc-temp_med-Lingual 1601 1011 4678 3.388 0.855 0.198 0.155 71 10.0 G_oc-temp_med-Parahip 3291 2065 7611 2.877 0.761 0.212 0.234 420 29.0 G_orbital 3430 1963 7890 2.888 0.616 0.167 0.293 481 62.2 G_pariet_inf-Angular 4279 2802 8937 2.676 0.574 0.152 0.772 158 29.0 G_pariet_inf-Supramar 3208 1954 6738 2.711 0.569 0.173 0.117 100 15.0 G_parietal_sup 3489 1937 4620 1.997 0.665 0.154 0.096 99 12.3 G_postcentral 4543 2482 6486 2.212 0.769 0.167 0.253 1152 64.2 G_precentral 3473 2180 7178 2.663 0.630 0.205 0.181 173 25.1 G_precuneus 1363 875 3296 2.795 0.798 0.197 0.114 45 7.1 G_rectus 460 297 1032 3.467 0.775 0.147 0.106 13 1.8 G_subcallosal 575 324 932 2.346 0.622 0.157 0.134 18 2.9 G_temp_sup-G_T_transv 2536 1671 8621 3.421 0.704 0.181 0.108 78 12.0 G_temp_sup-Lateral 802 521 2153 3.458 0.694 0.202 0.168 24 6.2 G_temp_sup-Plan_polar 1297 844 2550 2.777 0.523 0.120 0.033 13 1.7 G_temp_sup-Plan_tempo 3320 2146 9600 3.215 0.730 0.176 0.123 141 17.1 G_temporal_inf 3835 2530 12044 3.263 0.731 0.168 0.096 159 13.0 G_temporal_middle 413 274 680 2.566 0.473 0.101 0.029 2 0.5 Lat_Fis-ant-Horizont 422 283 735 2.816 0.513 0.119 0.039 3 0.6 Lat_Fis-ant-Vertical 1455 958 1990 2.528 0.472 0.143 0.053 16 3.0 Lat_Fis-post 2782 1712 3128 1.724 0.527 0.203 0.188 1177 27.8 Pole_occipital 2179 1457 6651 3.136 0.954 0.194 0.137 88 12.4 Pole_temporal 2621 1745 3095 1.925 0.699 0.185 0.221 342 12.6 S_calcarine 4061 2769 3888 1.642 0.552 0.156 0.080 64 16.4 S_central 1122 757 1931 2.605 0.698 0.164 0.083 22 4.1 S_cingul-Marginalis 611 394 1040 2.898 0.513 0.132 0.067 7 1.6 S_circular_insula_ant 1632 1053 2820 3.049 0.837 0.119 0.062 18 4.1 S_circular_insula_inf 1983 1295 3029 2.805 0.521 0.121 0.049 18 4.7 S_circular_insula_sup 1208 804 2109 2.596 0.740 0.125 0.059 13 3.2 S_collat_transv_ant 592 355 602 1.867 0.421 0.197 0.208 28 6.0 S_collat_transv_post 2621 1714 4362 2.540 0.443 0.116 0.039 23 4.3 S_front_inf 2596 1722 4381 2.495 0.580 0.140 0.070 45 5.5 S_front_middle 3372 2188 6107 2.658 0.612 0.153 0.084 91 13.1 S_front_sup 507 339 733 2.688 0.462 0.119 0.035 3 0.8 S_interm_prim-Jensen 3744 2455 5255 2.328 0.404 0.141 0.065 54 10.8 S_intrapariet_and_P_trans 1400 914 1938 2.207 0.512 0.142 0.052 17 3.0 S_oc_middle_and_Lunatus 1612 1020 2037 2.096 0.483 0.128 0.075 28 6.1 S_oc_sup_and_transversal 750 497 981 2.187 0.466 0.137 0.046 9 1.4 S_occipital_ant 1098 722 1742 2.761 0.494 0.146 0.060 13 2.7 S_oc-temp_lat 2453 1620 3504 2.276 0.548 0.164 0.100 53 10.5 S_oc-temp_med_and_Lingual 604 415 750 2.190 0.377 0.105 0.023 4 0.6 S_orbital_lateral 1284 860 2150 2.580 0.967 0.170 1.621 226 11.5 S_orbital_med-olfact 1658 1074 3303 3.005 0.923 0.154 0.105 39 7.9 S_orbital-H_Shaped 2328 1473 2973 2.191 0.549 0.142 0.081 32 9.2 S_parieto_occipital 1653 977 1753 2.215 0.951 0.153 0.198 110 4.4 S_pericallosal 4661 3004 6355 2.190 0.583 0.147 0.126 335 14.0 S_postcentral 2276 1481 3672 2.559 0.399 0.127 0.046 22 4.4 S_precentral-inf-part 1792 1163 2308 2.349 0.486 0.143 0.102 30 6.5 S_precentral-sup-part 570 394 784 2.049 0.558 0.125 0.039 5 1.0 S_suborbital 1551 1030 2709 2.425 0.694 0.161 0.069 26 4.6 S_subparietal 1815 1196 2593 2.528 0.460 0.118 0.040 15 2.9 S_temporal_inf 6891 4623 11266 2.672 0.513 0.128 0.075 77 29.0 S_temporal_sup 459 291 700 2.795 0.476 0.119 0.031 4 0.7 S_temporal_transverse #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:20:46 BST 2012 New invocation of recon-all Sat Jul 21 05:20:46 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -parcstats2 #----------------------------------------- #@# Parcellation Stats 2 rh Sat Jul 21 05:20:46 BST 2012 /home/clare/subjects/subject_20/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 subject_20 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/rh.white... reading input pial surface /home/clare/subjects/subject_20/surf/rh.pial... reading input white surface /home/clare/subjects/subject_20/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 1565 1024 3573 2.772 0.818 0.186 0.141 66 7.9 G_and_S_frontomargin 1459 929 3218 2.819 0.685 0.187 0.119 57 7.7 G_and_S_occipital_inf 2162 1273 2479 1.883 0.549 0.159 0.126 78 14.0 G_and_S_paracentral 1716 1143 3537 2.762 0.552 0.156 0.070 30 5.1 G_and_S_subcentral 1454 952 3272 2.838 0.657 0.187 0.177 90 11.3 G_and_S_transv_frontopol 3281 2198 6999 2.997 0.534 0.139 0.050 43 6.9 G_and_S_cingul-Ant 1903 1235 4390 3.141 0.603 0.154 0.075 32 6.4 G_and_S_cingul-Mid-Ant 2170 1425 4027 2.695 0.594 0.162 0.099 40 8.8 G_and_S_cingul-Mid-Post 618 371 1392 2.991 0.656 0.175 0.184 23 3.2 G_cingul-Post-dorsal 372 209 636 2.722 0.805 0.163 0.118 9 1.8 G_cingul-Post-ventral 2390 1517 2818 1.702 0.560 0.173 0.097 62 9.9 G_cuneus 1566 1029 4190 3.068 0.520 0.153 0.072 36 4.6 G_front_inf-Opercular 362 243 1190 3.378 0.418 0.207 0.119 16 1.7 G_front_inf-Orbital 1379 913 3964 3.316 0.609 0.174 0.090 39 5.5 G_front_inf-Triangul 6231 3849 14244 2.907 0.640 0.184 0.174 313 46.1 G_front_middle 9617 5545 20576 2.977 0.718 0.172 0.223 1355 81.9 G_front_sup 761 488 1904 3.784 0.601 0.203 0.287 54 5.2 G_Ins_lg_and_S_cent_ins 706 480 2239 3.496 0.779 0.212 0.229 32 6.0 G_insular_short 3564 2079 7459 2.825 0.688 0.179 1.274 1122 26.4 G_occipital_middle 2208 1352 4117 2.467 0.685 0.174 0.197 70 25.9 G_occipital_sup 1851 1257 4856 3.095 0.689 0.226 0.175 102 13.6 G_oc-temp_lat-fusifor 3649 2513 6210 2.119 0.759 0.223 0.168 426 26.7 G_oc-temp_med-Lingual 1903 1206 5174 3.447 0.902 0.207 0.373 331 19.4 G_oc-temp_med-Parahip 3262 2055 7780 2.918 0.867 0.207 0.264 214 45.9 G_orbital 4359 2855 10783 3.009 0.546 0.171 0.095 118 15.8 G_pariet_inf-Angular 3213 2167 7346 2.906 0.528 0.168 0.087 79 13.1 G_pariet_inf-Supramar 3060 1857 5964 2.561 0.627 0.168 0.282 336 16.0 G_parietal_sup 3516 1901 4881 2.120 0.624 0.167 0.135 210 18.7 G_postcentral 3837 2219 6059 2.284 0.834 0.171 0.163 225 25.6 G_precentral 3277 2079 6913 2.578 0.663 0.185 0.120 95 14.9 G_precuneus 840 555 2254 2.937 0.729 0.190 0.110 25 4.0 G_rectus 463 272 996 3.322 1.022 0.160 0.184 20 3.0 G_subcallosal 499 320 785 2.281 1.025 0.166 0.079 10 1.6 G_temp_sup-G_T_transv 2159 1508 7520 3.471 0.802 0.171 0.082 50 8.0 G_temp_sup-Lateral 1055 704 2992 3.567 0.751 0.173 0.158 83 7.5 G_temp_sup-Plan_polar 896 586 1621 2.557 0.581 0.113 0.032 8 1.3 G_temp_sup-Plan_tempo 3313 2218 10231 3.348 0.856 0.180 0.107 129 14.4 G_temporal_inf 3895 2640 12096 3.284 0.566 0.179 1.165 2630 14.2 G_temporal_middle 532 346 799 2.571 0.436 0.094 0.021 2 0.5 Lat_Fis-ant-Horizont 219 146 405 2.665 0.459 0.112 0.040 2 0.4 Lat_Fis-ant-Vertical 1469 990 2083 2.519 0.521 0.129 0.042 12 2.8 Lat_Fis-post 4339 2604 4940 1.763 0.551 0.201 0.227 163 26.1 Pole_occipital 2279 1502 7465 3.591 0.907 0.190 0.151 96 12.2 Pole_temporal 2423 1588 2996 2.090 0.771 0.181 0.096 57 10.1 S_calcarine 3981 2742 3794 1.555 0.440 0.151 0.072 82 13.1 S_central 1700 1120 2696 2.497 0.434 0.122 0.043 13 3.1 S_cingul-Marginalis 618 395 1057 2.923 0.489 0.135 0.089 9 2.4 S_circular_insula_ant 1498 1002 2475 3.022 0.669 0.130 0.099 23 3.0 S_circular_insula_inf 1746 1179 2713 2.747 0.481 0.124 0.040 13 2.9 S_circular_insula_sup 1138 782 2191 2.704 0.674 0.135 0.060 14 2.8 S_collat_transv_ant 780 531 1043 2.104 0.527 0.198 0.128 18 3.9 S_collat_transv_post 2678 1811 4722 2.503 0.516 0.137 0.051 36 5.5 S_front_inf 3269 2194 5215 2.574 0.520 0.131 0.043 35 5.6 S_front_middle 3949 2439 6405 2.542 0.574 0.142 0.089 98 14.7 S_front_sup 313 200 423 2.369 0.420 0.123 0.041 2 0.6 S_interm_prim-Jensen 4052 2561 5493 2.216 0.495 0.153 0.086 79 14.9 S_intrapariet_and_P_trans 1894 1237 2744 2.333 0.467 0.145 0.059 26 4.9 S_oc_middle_and_Lunatus 1852 1272 2916 2.222 0.627 0.141 0.051 22 3.8 S_oc_sup_and_transversal 1092 719 1955 2.606 0.538 0.150 0.071 17 2.8 S_occipital_ant 1306 854 1992 2.595 0.552 0.141 0.139 60 10.8 S_oc-temp_lat 2167 1473 3433 2.556 0.677 0.168 0.101 40 11.0 S_oc-temp_med_and_Lingual 698 452 1140 2.756 0.585 0.140 0.046 9 1.4 S_orbital_lateral 921 649 1747 2.450 0.905 0.145 0.058 13 2.4 S_orbital_med-olfact 2013 1279 3430 2.720 0.680 0.164 0.107 101 9.8 S_orbital-H_Shaped 2542 1605 3174 2.170 0.558 0.151 0.072 38 7.7 S_parieto_occipital 2041 1203 2300 2.327 0.814 0.153 0.077 45 5.8 S_pericallosal 3199 2084 3711 2.034 0.525 0.128 0.046 31 6.5 S_postcentral 2060 1396 3279 2.571 0.425 0.127 0.047 21 4.1 S_precentral-inf-part 1913 1266 2550 2.369 0.549 0.148 0.071 43 6.2 S_precentral-sup-part 207 131 325 2.955 0.508 0.150 0.045 3 0.4 S_suborbital 1443 962 2341 2.367 0.584 0.135 0.055 16 3.6 S_subparietal 1968 1296 2940 2.673 0.462 0.124 0.043 18 3.4 S_temporal_inf 7723 5305 13183 2.582 0.448 0.116 0.040 82 11.5 S_temporal_sup 402 241 426 2.093 0.475 0.132 0.049 4 0.9 S_temporal_transverse #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:21:03 BST 2012 New invocation of recon-all Sat Jul 21 05:21:03 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortribbon #-------------------------------------------- #@# Cortical ribbon mask Sat Jul 21 05:21:03 BST 2012 /home/clare/subjects/subject_20/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon subject_20 SUBJECTS_DIR is /home/clare/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 14 writing volume /home/clare/subjects/subject_20/mri/ribbon.mgz writing ribbon files #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:37:10 BST 2012 New invocation of recon-all Sat Jul 21 05:37:10 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -segstats #-------------------------------------------- #@# ASeg Stats Sat Jul 21 05:37:10 BST 2012 /home/clare/subjects/subject_20 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /home/clare/freesurfer/freesurfer/ASegStatsLUT.txt --subject subject_20 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /home/clare/freesurfer/freesurfer/ASegStatsLUT.txt --subject subject_20 sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare atlas_icv (eTIV) = 1896950 mm^3 (det: 1.026967 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 322822 rh white matter volume 331711 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 339442.438861, pTot = 636266.573971 c = 296824.135111 rh surface-based volumes (mm3): wTot = 353631.046563, pTot = 656601.589520 c = 302970.542957 Computing SupraTentVolCor SupraTentVolCor = 72328.000 SupraTentVol = 1365196.163 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 3513 3513 4 5 Left-Inf-Lat-Vent 293 293 5 7 Left-Cerebellum-White-Matter 16337 16337 6 8 Left-Cerebellum-Cortex 56869 56869 7 10 Left-Thalamus-Proper 9899 9899 8 11 Left-Caudate 4012 4012 9 12 Left-Putamen 5644 5644 10 13 Left-Pallidum 1959 1959 11 14 3rd-Ventricle 1250 1250 12 15 4th-Ventricle 2684 2684 13 16 Brain-Stem 25436 25436 14 17 Left-Hippocampus 4292 4292 15 18 Left-Amygdala 1585 1585 16 24 CSF 1273 1273 17 26 Left-Accumbens-area 692 692 18 28 Left-VentralDC 4498 4498 19 30 Left-vessel 46 46 20 31 Left-choroid-plexus 1638 1638 23 43 Right-Lateral-Ventricle 8609 8609 24 44 Right-Inf-Lat-Vent 277 277 25 46 Right-Cerebellum-White-Matter 15719 15719 26 47 Right-Cerebellum-Cortex 58103 58103 27 49 Right-Thalamus-Proper 9115 9115 28 50 Right-Caudate 3981 3981 29 51 Right-Putamen 5823 5823 30 52 Right-Pallidum 2052 2052 31 53 Right-Hippocampus 4631 4631 32 54 Right-Amygdala 1972 1972 33 58 Right-Accumbens-area 572 572 34 60 Right-VentralDC 5344 5344 35 62 Right-vessel 43 43 36 63 Right-choroid-plexus 2084 2084 37 72 5th-Ventricle 1 1 38 77 WM-hypointensities 2905 2905 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 33 33 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 279 279 45 251 CC_Posterior 1294 1294 46 252 CC_Mid_Posterior 837 837 47 253 CC_Central 683 683 48 254 CC_Mid_Anterior 797 797 49 255 CC_Anterior 1093 1093 Reporting on 45 segmentations SubCortGrayVol = 206479 #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:43:46 BST 2012 New invocation of recon-all Sat Jul 21 05:43:46 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -aparc2aseg #----------------------------------------- #@# AParc-to-ASeg Sat Jul 21 05:43:46 BST 2012 /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --volmask SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol /home/clare/subjects/subject_20/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 591591 Used brute-force search on 0 voxels Writing output aseg to /home/clare/subjects/subject_20/mri/aparc+aseg.mgz /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --volmask --a2009s SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol /home/clare/subjects/subject_20/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.a2009s.annot 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) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.a2009s.annot 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) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 591591 Used brute-force search on 0 voxels Writing output aseg to /home/clare/subjects/subject_20/mri/aparc.a2009s+aseg.mgz #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:46:34 BST 2012 New invocation of recon-all Sat Jul 21 05:46:34 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -wmparc #----------------------------------------- #@# WMParc Sat Jul 21 05:46:34 BST 2012 /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/clare/subjects/subject_20/mri/aparc+aseg.mgz Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Loading filled from /home/clare/subjects/subject_20/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9614 vertices from left hemi Ripped 8653 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz Loading Ctx Seg File /home/clare/subjects/subject_20/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1209552 Used brute-force search on 179 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 7.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 10.000000 6 k 1.000000 7 k 1793.000000 8 k 5.000000 Fixing Parahip RH WM Found 9 clusters 0 k 2.000000 1 k 4.000000 2 k 2.000000 3 k 2.000000 4 k 2.000000 5 k 1.000000 6 k 1.000000 7 k 1974.000000 8 k 2.000000 Writing output aseg to mri/wmparc.mgz /home/clare/subjects/subject_20 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject_20 --surf-wm-vol --ctab /home/clare/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject_20 --surf-wm-vol --ctab /home/clare/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare atlas_icv (eTIV) = 1896950 mm^3 (det: 1.026967 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 322822 rh white matter volume 331711 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1918546 # brainmaskvolume 1918546.0 # nbrainsegvoxels 261617 # brainsegvolume 261617.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 4134 4134 2 3002 wm-lh-caudalanteriorcingulate 4008 4008 3 3003 wm-lh-caudalmiddlefrontal 7072 7072 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2968 2968 6 3006 wm-lh-entorhinal 855 855 7 3007 wm-lh-fusiform 8247 8247 8 3008 wm-lh-inferiorparietal 11788 11788 9 3009 wm-lh-inferiortemporal 7926 7926 10 3010 wm-lh-isthmuscingulate 4846 4846 11 3011 wm-lh-lateraloccipital 12976 12976 12 3012 wm-lh-lateralorbitofrontal 7827 7827 13 3013 wm-lh-lingual 6726 6726 14 3014 wm-lh-medialorbitofrontal 4471 4471 15 3015 wm-lh-middletemporal 6980 6980 16 3016 wm-lh-parahippocampal 1955 1955 17 3017 wm-lh-paracentral 5348 5348 18 3018 wm-lh-parsopercularis 5041 5041 19 3019 wm-lh-parsorbitalis 1154 1154 20 3020 wm-lh-parstriangularis 3565 3565 21 3021 wm-lh-pericalcarine 4012 4012 22 3022 wm-lh-postcentral 11291 11291 23 3023 wm-lh-posteriorcingulate 5726 5726 24 3024 wm-lh-precentral 20728 20728 25 3025 wm-lh-precuneus 11762 11762 26 3026 wm-lh-rostralanteriorcingulate 3149 3149 27 3027 wm-lh-rostralmiddlefrontal 17316 17316 28 3028 wm-lh-superiorfrontal 21824 21824 29 3029 wm-lh-superiorparietal 15444 15444 30 3030 wm-lh-superiortemporal 10062 10062 31 3031 wm-lh-supramarginal 12248 12248 32 3032 wm-lh-frontalpole 229 229 33 3033 wm-lh-temporalpole 1000 1000 34 3034 wm-lh-transversetemporal 865 865 35 3035 wm-lh-insula 10319 10319 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 3371 3371 120 4002 wm-rh-caudalanteriorcingulate 4059 4059 121 4003 wm-rh-caudalmiddlefrontal 6903 6903 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 2992 2992 124 4006 wm-rh-entorhinal 797 797 125 4007 wm-rh-fusiform 8124 8124 126 4008 wm-rh-inferiorparietal 17047 17047 127 4009 wm-rh-inferiortemporal 8004 8004 128 4010 wm-rh-isthmuscingulate 3844 3844 129 4011 wm-rh-lateraloccipital 13278 13278 130 4012 wm-rh-lateralorbitofrontal 7877 7877 131 4013 wm-rh-lingual 7385 7385 132 4014 wm-rh-medialorbitofrontal 4500 4500 133 4015 wm-rh-middletemporal 8354 8354 134 4016 wm-rh-parahippocampal 2144 2144 135 4017 wm-rh-paracentral 7983 7983 136 4018 wm-rh-parsopercularis 4040 4040 137 4019 wm-rh-parsorbitalis 1574 1574 138 4020 wm-rh-parstriangularis 4104 4104 139 4021 wm-rh-pericalcarine 3336 3336 140 4022 wm-rh-postcentral 11614 11614 141 4023 wm-rh-posteriorcingulate 5421 5421 142 4024 wm-rh-precentral 20047 20047 143 4025 wm-rh-precuneus 13136 13136 144 4026 wm-rh-rostralanteriorcingulate 2541 2541 145 4027 wm-rh-rostralmiddlefrontal 19681 19681 146 4028 wm-rh-superiorfrontal 22719 22719 147 4029 wm-rh-superiorparietal 15321 15321 148 4030 wm-rh-superiortemporal 9188 9188 149 4031 wm-rh-supramarginal 9679 9679 150 4032 wm-rh-frontalpole 525 525 151 4033 wm-rh-temporalpole 1014 1014 152 4034 wm-rh-transversetemporal 912 912 153 4035 wm-rh-insula 11400 11400 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 53925 53925 237 5002 Right-UnsegmentedWhiteMatter 52484 52484 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations #------------------------------------------ recon-all -s subject_20 finished without error at Sat Jul 21 05:59:54 BST 2012 New invocation of recon-all Mon Jul 23 12:31:50 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -normalization #-------------------------------------------- #@# Intensity Normalization Mon Jul 23 12:31:50 BST 2012 /home/clare/subjects/subject_20/mri mri_normalize -g 1 -f /home/clare/subjects/subject_20/tmp/control.dat -b 18 -n 7 nu.mgz T1.mgz using max gradient = 1.000 using control points from file /home/clare/subjects/subject_20/tmp/control.dat... using control point with intensity 18.0 below target. performing 3d normalization 7 times reading from nu.mgz... normalizing image... Reading 4 control points... only using 4 control points from file, mean 106.5, scaling by 1.03... building Voronoi diagram... performing soap bubble smoothing... talairach transform 1.001 -0.025 0.012 -0.535; 0.010 0.976 0.061 -30.315; 0.005 -0.011 1.051 -12.512; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 3 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 4 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 5 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 6 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 7 of 7 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 5 minutes and 18 seconds. MRIsplineNormalize(): npeaks = 22 Starting OpenSpline(): npoints = 22 white matter peak found at 111 white matter peak found at 110 gm peak at 87 (87), valley at 58 (58) csf peak at 44, setting threshold to 72 white matter peak found at 111 white matter peak found at 110 gm peak at 87 (87), valley at 46 (46) csf peak at 44, setting threshold to 72 white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 47 (47) csf peak at 44, setting threshold to 73 white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 47 (47) csf peak at 44, setting threshold to 73 white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 45 (45) csf peak at 44, setting threshold to 73 white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 46 (46) csf peak at 44, setting threshold to 73 white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 46 (46) csf peak at 44, setting threshold to 73 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 12:37:09 BST 2012 New invocation of recon-all Mon Jul 23 12:37:09 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -skullstrip #-------------------------------------------- #@# Skull Stripping Mon Jul 23 12:37:09 BST 2012 /home/clare/subjects/subject_20/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /home/clare/freesurfer/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading extra input line fscale 0.150000 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=103 z=106 r=93 first estimation of the main basin volume: 3424296 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=101, y=94, z=66, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=30662287732 voxels, voxel volume =1.000 = 30662287732 mmm3 = 30662287.360 cm3 done. PostAnalyze...Basin Prior 216 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=106, z=102, r=9957 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=65 , nb = 42786 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=44 , nb = 2448 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1872 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=71 , nb = 19962 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 18306 OTHER CSF_MIN=0, CSF_intensity=2, CSF_MAX=3 , nb = 198 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 65, 57, 54, 82 after analyzing : 30, 57, 57, 63 RIGHT_CER before analyzing : 44, 42, 41, 90 after analyzing : 22, 42, 42, 54 LEFT_CER before analyzing : 5, 8, 52, 90 after analyzing : 5, 37, 52, 50 RIGHT_BRAIN before analyzing : 71, 59, 55, 79 after analyzing : 32, 59, 59, 64 LEFT_BRAIN before analyzing : 18, 33, 56, 79 after analyzing : 18, 48, 56, 55 OTHER before analyzing : 3, 3, 8, 67 after analyzing : 3, 17, 25, 29 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.009 curvature mean = 75.214, std = 6.816 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.41, sigma = 4.81 after rotation: sse = 3.41, sigma = 4.81 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.44, its var is 3.78 before Erosion-Dilatation 0.10% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1949397 voxels, voxel volume = 1.000 mm3 = 1949397 mmm3 = 1949.397 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 12:37:35 BST 2012 New invocation of recon-all Mon Jul 23 12:37:35 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -gcareg #------------------------------------- #@# EM Registration Mon Jul 23 12:37:35 BST 2012 /home/clare/subjects/subject_20/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=23.0 skull bounding box = (57, 37, 22) --> (200, 167, 197) using (105, 80, 110) as brain centroid... mean wm in atlas = 107, using box (87,64,88) --> (122, 95,131) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -7397.4 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-3.1, 10.5, -0.3): log p = -6972.583 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6972.6, old_max_log_p =-6972.6 (thresh=-6965.6) 1.000 0.000 0.000 -3.125; 0.000 1.000 0.000 10.511; 0.000 0.000 1.000 -0.284; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6931.7, old_max_log_p =-6972.6 (thresh=-6965.6) 0.998 -0.004 0.065 -7.401; 0.000 0.998 0.065 3.836; -0.064 -0.064 0.977 21.097; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6931.7, old_max_log_p =-6931.7 (thresh=-6924.7) 0.998 -0.004 0.065 -7.401; 0.000 0.998 0.065 3.836; -0.064 -0.064 0.977 21.097; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6909.6, old_max_log_p =-6931.7 (thresh=-6924.7) 0.999 -0.018 0.032 -3.651; 0.015 0.997 0.082 0.338; -0.031 -0.080 0.977 17.705; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6909.6, old_max_log_p =-6909.6 (thresh=-6902.7) 0.999 -0.018 0.032 -3.651; 0.015 0.997 0.082 0.338; -0.031 -0.080 0.977 17.705; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99931 -0.01795 0.03196 -3.65051; 0.01530 0.99652 0.08191 0.33830; -0.03148 -0.08045 0.97746 17.70532; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.99931 -0.01795 0.03196 -3.65051; 0.01530 0.99652 0.08191 0.33830; -0.03148 -0.08045 0.97746 17.70532; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 6909.6 tol 0.000010 Resulting transform: 0.999 -0.018 0.032 -3.651; 0.015 0.997 0.082 0.338; -0.031 -0.080 0.977 17.705; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6909.6 (old=-7397.4) transform before final EM align: 0.999 -0.018 0.032 -3.651; 0.015 0.997 0.082 0.338; -0.031 -0.080 0.977 17.705; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99931 -0.01795 0.03196 -3.65051; 0.01530 0.99652 0.08191 0.33830; -0.03148 -0.08045 0.97746 17.70532; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.99931 -0.01795 0.03196 -3.65051; 0.01530 0.99652 0.08191 0.33830; -0.03148 -0.08045 0.97746 17.70532; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 828584.0 after pass:transform: ( 1.00, -0.01, 0.04, -3.65) ( 0.02, 1.00, 0.09, 0.34) ( -0.03, -0.08, 0.98, 17.71) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 828584.0 tol 0.000000 final transform: 1.004 -0.013 0.037 -3.651; 0.023 1.003 0.088 0.338; -0.027 -0.077 0.979 17.705; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 15 minutes and 20 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 12:52:55 BST 2012 New invocation of recon-all Mon Jul 23 12:52:55 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -canorm #-------------------------------------- #@# CA Normalize Mon Jul 23 12:52:55 BST 2012 /home/clare/subjects/subject_20/mri mri_ca_normalize -f /home/clare/subjects/subject_20/tmp/control.dat -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz reading manually defined control points from /home/clare/subjects/subject_20/tmp/control.dat writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=23.0 skull bounding box = (57, 37, 22) --> (200, 167, 196) using (105, 80, 109) as brain centroid... mean wm in atlas = 107, using box (87,64,88) --> (122, 95,130) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.004 -0.013 0.037 -3.651; 0.023 1.003 0.088 0.338; -0.027 -0.077 0.979 17.705; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 39, 22) --> (193, 154, 192) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 120.0 1 of 216 (0.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 41, 21) --> (127, 157, 192) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 255.0 0 of 240 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 47) --> (178, 168, 102) Left_Cerebellum_White_Matter: limiting intensities to 119.0 --> 255.0 6 of 7 (85.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 44) --> (129, 169, 101) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 255.0 2 of 7 (28.6%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 81) --> (143, 186, 113) Reading 4 control points... Brain_Stem: limiting intensities to 78.0 --> 255.0 0 of 1 (0.0%) samples deleted using 471 total control points for intensity normalization... bias field = 1.011 +- 0.048 3 of 466 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 39, 22) --> (193, 154, 192) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 123.0 1 of 199 (0.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 41, 21) --> (127, 157, 192) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 245.0 0 of 230 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 47) --> (178, 168, 102) Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 245.0 6 of 22 (27.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 44) --> (129, 169, 101) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 245.0 9 of 31 (29.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 81) --> (143, 186, 113) Reading 4 control points... Brain_Stem: limiting intensities to 77.0 --> 245.0 6 of 55 (10.9%) samples deleted using 537 total control points for intensity normalization... bias field = 0.996 +- 0.049 7 of 519 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 39, 22) --> (193, 154, 192) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 124.0 1 of 338 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (62, 41, 21) --> (127, 157, 192) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 253.0 0 of 377 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 47) --> (178, 168, 102) Left_Cerebellum_White_Matter: limiting intensities to 73.0 --> 253.0 0 of 41 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 44) --> (129, 169, 101) Right_Cerebellum_White_Matter: limiting intensities to 69.0 --> 253.0 0 of 39 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 117, 81) --> (143, 186, 113) Reading 4 control points... Brain_Stem: limiting intensities to 88.0 --> 253.0 26 of 55 (47.3%) samples deleted using 850 total control points for intensity normalization... bias field = 0.996 +- 0.039 6 of 827 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 42 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 12:54:38 BST 2012 New invocation of recon-all Mon Jul 23 12:54:38 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -careg -careginv #-------------------------------------- #@# CA Reg Mon Jul 23 12:54:38 BST 2012 /home/clare/subjects/subject_20/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 0.99 (predicted orig area = 8.0) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.811, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21213.188 ms 0001: dt=129.472000, rms=0.764 (5.766%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21463.133 ms 0002: dt=369.920000, rms=0.729 (4.538%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21562.176 ms 0003: dt=221.952000, rms=0.714 (2.164%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21431.430 ms 0004: dt=92.480000, rms=0.712 (0.223%), neg=0, invalid=766 0005: dt=92.480000, rms=0.711 (0.105%), neg=0, invalid=766 0006: dt=92.480000, rms=0.710 (0.200%), neg=0, invalid=766 0007: dt=92.480000, rms=0.708 (0.326%), neg=0, invalid=766 0008: dt=92.480000, rms=0.704 (0.446%), neg=0, invalid=766 0009: dt=92.480000, rms=0.702 (0.289%), neg=0, invalid=766 0010: dt=92.480000, rms=0.701 (0.123%), neg=0, invalid=766 0011: dt=92.480000, rms=0.701 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23975.967 ms 0012: dt=369.920000, rms=0.698 (0.371%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23230.113 ms 0013: dt=73.984000, rms=0.698 (0.076%), neg=0, invalid=766 0014: dt=73.984000, rms=0.697 (0.086%), neg=0, invalid=766 0015: dt=73.984000, rms=0.696 (0.129%), neg=0, invalid=766 0016: dt=73.984000, rms=0.696 (0.094%), neg=0, invalid=766 0017: dt=73.984000, rms=0.695 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27865.449 ms 0018: dt=221.952000, rms=0.695 (0.048%), neg=0, invalid=766 0019: dt=221.952000, rms=0.695 (0.005%), neg=0, invalid=766 0020: dt=221.952000, rms=0.694 (0.187%), neg=0, invalid=766 0021: dt=221.952000, rms=0.692 (0.166%), neg=0, invalid=766 0022: dt=221.952000, rms=0.691 (0.231%), neg=0, invalid=766 0023: dt=221.952000, rms=0.690 (0.085%), neg=0, invalid=766 0024: dt=221.952000, rms=0.688 (0.258%), neg=0, invalid=766 0025: dt=221.952000, rms=0.686 (0.277%), neg=0, invalid=766 0026: dt=221.952000, rms=0.685 (0.192%), neg=0, invalid=766 0027: dt=221.952000, rms=0.685 (0.022%), neg=0, invalid=766 0028: dt=221.952000, rms=0.684 (0.200%), neg=0, invalid=766 0029: dt=221.952000, rms=0.682 (0.231%), neg=0, invalid=766 0030: dt=221.952000, rms=0.681 (0.094%), neg=0, invalid=766 0031: dt=221.952000, rms=0.681 (-0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23264.865 ms 0032: dt=129.472000, rms=0.681 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23351.730 ms 0033: dt=0.000000, rms=0.681 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.681, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24069.850 ms 0034: dt=221.952000, rms=0.676 (0.754%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26844.180 ms 0035: dt=73.984000, rms=0.676 (0.050%), neg=0, invalid=766 0036: dt=73.984000, rms=0.676 (0.001%), neg=0, invalid=766 0037: dt=73.984000, rms=0.675 (0.032%), neg=0, invalid=766 0038: dt=73.984000, rms=0.675 (0.060%), neg=0, invalid=766 0039: dt=73.984000, rms=0.674 (0.112%), neg=0, invalid=766 0040: dt=73.984000, rms=0.673 (0.154%), neg=0, invalid=766 0041: dt=73.984000, rms=0.672 (0.164%), neg=0, invalid=766 0042: dt=73.984000, rms=0.671 (0.123%), neg=0, invalid=766 0043: dt=73.984000, rms=0.671 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28084.195 ms 0044: dt=129.472000, rms=0.671 (0.014%), neg=0, invalid=766 0045: dt=129.472000, rms=0.671 (0.008%), neg=0, invalid=766 0046: dt=129.472000, rms=0.671 (0.012%), neg=0, invalid=766 0047: dt=129.472000, rms=0.670 (0.059%), neg=0, invalid=766 0048: dt=129.472000, rms=0.670 (0.081%), neg=0, invalid=766 0049: dt=129.472000, rms=0.669 (0.099%), neg=0, invalid=766 0050: dt=129.472000, rms=0.668 (0.074%), neg=0, invalid=766 0051: dt=129.472000, rms=0.668 (0.083%), neg=0, invalid=766 0052: dt=129.472000, rms=0.667 (0.142%), neg=0, invalid=766 0053: dt=129.472000, rms=0.666 (0.135%), neg=0, invalid=766 0054: dt=129.472000, rms=0.666 (0.069%), neg=0, invalid=766 0055: dt=129.472000, rms=0.665 (0.073%), neg=0, invalid=766 0056: dt=129.472000, rms=0.664 (0.094%), neg=0, invalid=766 0057: dt=129.472000, rms=0.664 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26049.471 ms 0058: dt=0.000000, rms=0.664 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.672, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22851.902 ms 0059: dt=9.072000, rms=0.672 (0.030%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23172.854 ms 0060: dt=9.072000, rms=0.672 (0.021%), neg=0, invalid=766 0061: dt=9.072000, rms=0.672 (0.025%), neg=0, invalid=766 0062: dt=9.072000, rms=0.672 (0.014%), neg=0, invalid=766 0063: dt=9.072000, rms=0.672 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.672, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24677.414 ms 0064: dt=145.152000, rms=0.662 (1.501%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25706.943 ms 0065: dt=36.288000, rms=0.659 (0.358%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25941.674 ms 0066: dt=145.152000, rms=0.656 (0.412%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26471.805 ms 0067: dt=82.944000, rms=0.652 (0.695%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25771.773 ms 0068: dt=25.920000, rms=0.651 (0.165%), neg=0, invalid=766 0069: dt=25.920000, rms=0.650 (0.076%), neg=0, invalid=766 0070: dt=25.920000, rms=0.649 (0.137%), neg=0, invalid=766 0071: dt=25.920000, rms=0.648 (0.226%), neg=0, invalid=766 0072: dt=25.920000, rms=0.646 (0.335%), neg=0, invalid=766 0073: dt=25.920000, rms=0.643 (0.376%), neg=0, invalid=766 0074: dt=25.920000, rms=0.641 (0.367%), neg=0, invalid=766 0075: dt=25.920000, rms=0.639 (0.354%), neg=0, invalid=766 0076: dt=25.920000, rms=0.637 (0.355%), neg=0, invalid=766 0077: dt=25.920000, rms=0.634 (0.346%), neg=0, invalid=766 0078: dt=25.920000, rms=0.632 (0.344%), neg=0, invalid=766 0079: dt=25.920000, rms=0.630 (0.308%), neg=0, invalid=766 0080: dt=25.920000, rms=0.628 (0.275%), neg=0, invalid=766 0081: dt=25.920000, rms=0.627 (0.265%), neg=0, invalid=766 0082: dt=25.920000, rms=0.625 (0.266%), neg=0, invalid=766 0083: dt=25.920000, rms=0.624 (0.241%), neg=0, invalid=766 0084: dt=25.920000, rms=0.622 (0.228%), neg=0, invalid=766 0085: dt=25.920000, rms=0.621 (0.213%), neg=0, invalid=766 0086: dt=25.920000, rms=0.620 (0.188%), neg=0, invalid=766 0087: dt=25.920000, rms=0.619 (0.166%), neg=0, invalid=766 0088: dt=25.920000, rms=0.618 (0.150%), neg=0, invalid=766 0089: dt=25.920000, rms=0.617 (0.144%), neg=0, invalid=766 0090: dt=25.920000, rms=0.616 (0.142%), neg=0, invalid=766 0091: dt=25.920000, rms=0.615 (0.149%), neg=0, invalid=766 0092: dt=25.920000, rms=0.614 (0.117%), neg=0, invalid=766 0093: dt=25.920000, rms=0.614 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27371.502 ms 0094: dt=36.288000, rms=0.614 (0.019%), neg=0, invalid=766 0095: dt=36.288000, rms=0.614 (-0.004%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24536.260 ms 0096: dt=4.800000, rms=0.639 (0.047%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25552.436 ms 0097: dt=2.400000, rms=0.639 (0.008%), neg=0, invalid=766 0098: dt=2.400000, rms=0.639 (0.001%), neg=0, invalid=766 0099: dt=2.400000, rms=0.639 (-0.029%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25865.932 ms 0100: dt=6.400000, rms=0.639 (0.040%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26043.641 ms 0101: dt=2.800000, rms=0.639 (0.010%), neg=0, invalid=766 0102: dt=2.800000, rms=0.639 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.702, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25677.322 ms 0103: dt=5.836364, rms=0.688 (2.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27167.629 ms 0104: dt=4.941176, rms=0.686 (0.261%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26068.932 ms 0105: dt=2.880000, rms=0.686 (0.036%), neg=0, invalid=766 0106: dt=2.880000, rms=0.686 (-0.006%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.686, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24553.824 ms 0107: dt=0.000000, rms=0.686 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.743, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24718.877 ms 0108: dt=0.281250, rms=0.743 (0.036%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25948.650 ms 0109: dt=0.384000, rms=0.742 (0.040%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28137.020 ms 0110: dt=0.787402, rms=0.742 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26112.562 ms 0111: dt=2.057143, rms=0.739 (0.314%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24293.809 ms 0112: dt=1.800000, rms=0.738 (0.260%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25194.059 ms 0113: dt=0.952663, rms=0.736 (0.164%), neg=0, invalid=766 0114: dt=0.952663, rms=0.736 (0.088%), neg=0, invalid=766 0115: dt=0.952663, rms=0.735 (0.088%), neg=0, invalid=766 0116: dt=0.952663, rms=0.734 (0.110%), neg=0, invalid=766 0117: dt=0.952663, rms=0.734 (-0.021%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.734, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23057.076 ms 0118: dt=1.536000, rms=0.733 (0.190%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21322.096 ms 0119: dt=0.000000, rms=0.733 (0.001%), neg=0, invalid=766 0120: dt=0.100000, rms=0.733 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.696, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21315.793 ms 0121: dt=0.448000, rms=0.682 (1.919%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18882.838 ms 0122: dt=0.000000, rms=0.682 (0.003%), neg=0, invalid=766 0123: dt=0.050000, rms=0.682 (-0.209%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.682, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18926.523 ms 0124: dt=0.005000, rms=0.682 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18007.039 ms 0125: dt=0.000438, rms=0.682 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24964.059 ms 0126: dt=0.000027, rms=0.682 (-0.002%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09359 (24) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1055 voxels, overlap=0.699) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (1055 voxels, peak = 22), gca=21.6 gca peak = 0.14022 (22) mri peak = 0.09761 (26) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2506 voxels, overlap=0.845) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2506 voxels, peak = 22), gca=22.0 gca peak = 0.24234 (100) mri peak = 0.08535 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (616 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (616 voxels, peak = 100), gca=100.0 gca peak = 0.19192 (97) mri peak = 0.06412 (106) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (481 voxels, overlap=0.975) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (481 voxels, peak = 99), gca=99.4 gca peak = 0.24007 (63) mri peak = 0.05285 (74) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1013 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1013 voxels, peak = 76), gca=75.6 gca peak = 0.29892 (64) mri peak = 0.06563 (78) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1039 voxels, overlap=0.010) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1039 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.07629 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (113923 voxels, overlap=0.633) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (113923 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.06961 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (119357 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (119357 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.04578 (84) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (57773 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (57773 voxels, peak = 83), gca=83.5 gca peak = 0.13270 (63) mri peak = 0.04856 (83) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (57568 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (57568 voxels, peak = 82), gca=81.9 gca peak = 0.15182 (70) mri peak = 0.07773 (85) Right_Caudate (50): linear fit = 1.17 x + 0.0 (860 voxels, overlap=0.059) Right_Caudate (50): linear fit = 1.17 x + 0.0 (860 voxels, peak = 82), gca=82.2 gca peak = 0.14251 (76) mri peak = 0.08354 (85) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1193 voxels, overlap=0.675) Left_Caudate (11): linear fit = 1.08 x + 0.0 (1193 voxels, peak = 82), gca=81.7 gca peak = 0.12116 (60) mri peak = 0.03870 (79) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (18810 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (18810 voxels, peak = 78), gca=78.0 gca peak = 0.12723 (61) mri peak = 0.04048 (75) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (24626 voxels, overlap=0.002) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (24626 voxels, peak = 76), gca=76.2 gca peak = 0.22684 (88) mri peak = 0.04678 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (11899 voxels, overlap=0.969) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (11899 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.03895 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (9622 voxels, overlap=0.994) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (9622 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.07362 (73) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (398 voxels, overlap=0.419) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (398 voxels, peak = 68), gca=68.2 gca peak = 0.39668 (62) mri peak = 0.08056 (83) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (377 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (377 voxels, peak = 81), gca=80.6 gca peak = 0.10129 (93) mri peak = 0.06518 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6986 voxels, overlap=0.962) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6986 voxels, peak = 93), gca=93.0 gca peak = 0.12071 (89) mri peak = 0.07313 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5997 voxels, overlap=0.911) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5997 voxels, peak = 89), gca=89.0 gca peak = 0.13716 (82) mri peak = 0.06529 (101) Left_Putamen (12): linear fit = 1.23 x + 0.0 (3360 voxels, overlap=0.009) Left_Putamen (12): linear fit = 1.23 x + 0.0 (3360 voxels, peak = 100), gca=100.5 gca peak = 0.15214 (84) mri peak = 0.08205 (99) Right_Putamen (51): linear fit = 1.17 x + 0.0 (3274 voxels, overlap=0.009) Right_Putamen (51): linear fit = 1.17 x + 0.0 (3274 voxels, peak = 99), gca=98.7 gca peak = 0.08983 (85) mri peak = 0.06422 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13121 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13121 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.08392 (95) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (942 voxels, overlap=0.782) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (942 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.06647 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1218 voxels, overlap=0.863) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1218 voxels, peak = 94), gca=94.0 gca peak = 0.21100 (36) mri peak = 0.25018 (24) gca peak = 0.13542 (27) mri peak = 0.07661 (25) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (705 voxels, overlap=0.691) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (705 voxels, peak = 24), gca=24.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.93 x + 0.0 Left_Putamen too bright - rescaling by 0.978 (from 1.225) to 98.3 (was 100.5) Right_Putamen too bright - rescaling by 0.996 (from 1.175) to 98.3 (was 98.7) saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25271.346 ms 0127: dt=129.472000, rms=0.640 (4.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24879.812 ms 0128: dt=295.936000, rms=0.626 (2.232%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26402.316 ms 0129: dt=129.472000, rms=0.624 (0.343%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28578.189 ms 0130: dt=129.472000, rms=0.622 (0.282%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30956.719 ms 0131: dt=295.936000, rms=0.619 (0.452%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27800.566 ms 0132: dt=73.984000, rms=0.618 (0.208%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28258.080 ms 0133: dt=1183.744000, rms=0.614 (0.700%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26539.758 ms 0134: dt=129.472000, rms=0.612 (0.306%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24203.795 ms 0135: dt=73.984000, rms=0.612 (0.043%), neg=0, invalid=766 0136: dt=73.984000, rms=0.611 (0.058%), neg=0, invalid=766 0137: dt=73.984000, rms=0.611 (0.093%), neg=0, invalid=766 0138: dt=73.984000, rms=0.610 (0.106%), neg=0, invalid=766 0139: dt=73.984000, rms=0.609 (0.110%), neg=0, invalid=766 0140: dt=73.984000, rms=0.609 (0.122%), neg=0, invalid=766 0141: dt=73.984000, rms=0.608 (0.125%), neg=0, invalid=766 0142: dt=73.984000, rms=0.607 (0.116%), neg=0, invalid=766 0143: dt=73.984000, rms=0.607 (0.097%), neg=0, invalid=766 0144: dt=73.984000, rms=0.606 (0.076%), neg=0, invalid=766 0145: dt=73.984000, rms=0.606 (0.074%), neg=0, invalid=766 0146: dt=73.984000, rms=0.605 (0.060%), neg=0, invalid=766 0147: dt=73.984000, rms=0.605 (0.068%), neg=0, invalid=766 0148: dt=73.984000, rms=0.605 (0.066%), neg=0, invalid=766 0149: dt=73.984000, rms=0.604 (0.069%), neg=0, invalid=766 0150: dt=73.984000, rms=0.604 (0.087%), neg=0, invalid=766 0151: dt=73.984000, rms=0.603 (0.074%), neg=0, invalid=766 0152: dt=73.984000, rms=0.603 (0.062%), neg=0, invalid=766 0153: dt=73.984000, rms=0.603 (0.039%), neg=0, invalid=766 0154: dt=73.984000, rms=0.602 (0.032%), neg=0, invalid=766 0155: dt=73.984000, rms=0.602 (0.058%), neg=0, invalid=766 0156: dt=73.984000, rms=0.602 (0.073%), neg=0, invalid=766 0157: dt=73.984000, rms=0.601 (0.067%), neg=0, invalid=766 0158: dt=73.984000, rms=0.601 (0.069%), neg=0, invalid=766 0159: dt=73.984000, rms=0.600 (0.082%), neg=0, invalid=766 0160: dt=73.984000, rms=0.600 (0.086%), neg=0, invalid=766 0161: dt=73.984000, rms=0.599 (0.090%), neg=0, invalid=766 0162: dt=73.984000, rms=0.599 (0.094%), neg=0, invalid=766 0163: dt=73.984000, rms=0.598 (0.083%), neg=0, invalid=766 0164: dt=73.984000, rms=0.598 (0.069%), neg=0, invalid=766 0165: dt=73.984000, rms=0.597 (0.056%), neg=0, invalid=766 0166: dt=73.984000, rms=0.597 (0.049%), neg=0, invalid=766 0167: dt=73.984000, rms=0.597 (0.049%), neg=0, invalid=766 0168: dt=73.984000, rms=0.596 (0.050%), neg=0, invalid=766 0169: dt=73.984000, rms=0.596 (0.057%), neg=0, invalid=766 0170: dt=73.984000, rms=0.596 (0.063%), neg=0, invalid=766 0171: dt=73.984000, rms=0.595 (0.072%), neg=0, invalid=766 0172: dt=73.984000, rms=0.595 (0.060%), neg=0, invalid=766 0173: dt=73.984000, rms=0.595 (0.058%), neg=0, invalid=766 0174: dt=73.984000, rms=0.594 (0.066%), neg=0, invalid=766 0175: dt=73.984000, rms=0.594 (0.071%), neg=0, invalid=766 0176: dt=73.984000, rms=0.594 (0.049%), neg=0, invalid=766 0177: dt=73.984000, rms=0.593 (0.032%), neg=0, invalid=766 0178: dt=73.984000, rms=0.593 (0.032%), neg=0, invalid=766 0179: dt=73.984000, rms=0.593 (0.038%), neg=0, invalid=766 0180: dt=73.984000, rms=0.593 (0.046%), neg=0, invalid=766 0181: dt=73.984000, rms=0.592 (0.036%), neg=0, invalid=766 0182: dt=73.984000, rms=0.592 (0.036%), neg=0, invalid=766 0183: dt=73.984000, rms=0.592 (0.040%), neg=0, invalid=766 0184: dt=73.984000, rms=0.592 (0.051%), neg=0, invalid=766 0185: dt=73.984000, rms=0.591 (0.052%), neg=0, invalid=766 0186: dt=73.984000, rms=0.591 (0.032%), neg=0, invalid=766 0187: dt=73.984000, rms=0.591 (0.024%), neg=0, invalid=766 0188: dt=73.984000, rms=0.591 (0.027%), neg=0, invalid=766 0189: dt=73.984000, rms=0.591 (0.038%), neg=0, invalid=766 0190: dt=73.984000, rms=0.590 (0.039%), neg=0, invalid=766 0191: dt=73.984000, rms=0.590 (0.031%), neg=0, invalid=766 0192: dt=73.984000, rms=0.590 (0.025%), neg=0, invalid=766 0193: dt=73.984000, rms=0.590 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25208.211 ms 0194: dt=129.472000, rms=0.590 (0.011%), neg=0, invalid=766 0195: dt=129.472000, rms=0.590 (0.009%), neg=0, invalid=766 0196: dt=129.472000, rms=0.590 (0.006%), neg=0, invalid=766 0197: dt=129.472000, rms=0.590 (0.006%), neg=0, invalid=766 0198: dt=129.472000, rms=0.590 (0.026%), neg=0, invalid=766 0199: dt=129.472000, rms=0.589 (0.024%), neg=0, invalid=766 0200: dt=129.472000, rms=0.589 (0.026%), neg=0, invalid=766 0201: dt=129.472000, rms=0.589 (0.012%), neg=0, invalid=766 0202: dt=129.472000, rms=0.589 (0.027%), neg=0, invalid=766 0203: dt=129.472000, rms=0.589 (0.025%), neg=0, invalid=766 0204: dt=129.472000, rms=0.589 (0.024%), neg=0, invalid=766 0205: dt=129.472000, rms=0.589 (0.037%), neg=0, invalid=766 0206: dt=129.472000, rms=0.589 (0.016%), neg=0, invalid=766 0207: dt=129.472000, rms=0.588 (0.040%), neg=0, invalid=766 0208: dt=129.472000, rms=0.588 (0.022%), neg=0, invalid=766 0209: dt=129.472000, rms=0.588 (-0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26405.369 ms 0210: dt=18.496000, rms=0.588 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26418.082 ms 0211: dt=32.368000, rms=0.588 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25005.121 ms 0212: dt=8.092000, rms=0.588 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.588, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25888.004 ms 0213: dt=295.936000, rms=0.587 (0.163%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25122.207 ms 0214: dt=92.480000, rms=0.587 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26166.617 ms 0215: dt=295.936000, rms=0.586 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29159.377 ms 0216: dt=129.472000, rms=0.586 (0.050%), neg=0, invalid=766 0217: dt=129.472000, rms=0.586 (0.018%), neg=0, invalid=766 0218: dt=129.472000, rms=0.586 (0.035%), neg=0, invalid=766 0219: dt=129.472000, rms=0.585 (0.067%), neg=0, invalid=766 0220: dt=129.472000, rms=0.585 (0.054%), neg=0, invalid=766 0221: dt=129.472000, rms=0.585 (0.056%), neg=0, invalid=766 0222: dt=129.472000, rms=0.584 (0.066%), neg=0, invalid=766 0223: dt=129.472000, rms=0.584 (0.058%), neg=0, invalid=766 0224: dt=129.472000, rms=0.584 (0.043%), neg=0, invalid=766 0225: dt=129.472000, rms=0.583 (0.049%), neg=0, invalid=766 0226: dt=129.472000, rms=0.583 (0.014%), neg=0, invalid=766 0227: dt=129.472000, rms=0.583 (0.038%), neg=0, invalid=766 0228: dt=129.472000, rms=0.583 (0.028%), neg=0, invalid=766 0229: dt=129.472000, rms=0.583 (0.031%), neg=0, invalid=766 0230: dt=129.472000, rms=0.583 (0.020%), neg=0, invalid=766 0231: dt=129.472000, rms=0.582 (0.038%), neg=0, invalid=766 0232: dt=129.472000, rms=0.582 (0.029%), neg=0, invalid=766 0233: dt=129.472000, rms=0.582 (0.021%), neg=0, invalid=766 0234: dt=129.472000, rms=0.582 (0.021%), neg=0, invalid=766 0235: dt=129.472000, rms=0.582 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26156.449 ms 0236: dt=129.472000, rms=0.582 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27334.537 ms 0237: dt=92.480000, rms=0.582 (0.003%), neg=0, invalid=766 0238: dt=92.480000, rms=0.582 (0.005%), neg=0, invalid=766 0239: dt=92.480000, rms=0.582 (0.006%), neg=0, invalid=766 0240: dt=92.480000, rms=0.582 (0.008%), neg=0, invalid=766 0241: dt=92.480000, rms=0.582 (0.011%), neg=0, invalid=766 0242: dt=92.480000, rms=0.582 (0.011%), neg=0, invalid=766 0243: dt=92.480000, rms=0.581 (0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.583, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25912.266 ms 0244: dt=103.680000, rms=0.581 (0.364%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25163.912 ms 0245: dt=145.152000, rms=0.576 (0.765%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23226.912 ms 0246: dt=36.288000, rms=0.575 (0.270%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24869.113 ms 0247: dt=145.152000, rms=0.573 (0.372%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25012.385 ms 0248: dt=62.208000, rms=0.571 (0.352%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24032.236 ms 0249: dt=36.288000, rms=0.570 (0.144%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27494.193 ms 0250: dt=145.152000, rms=0.568 (0.397%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24332.477 ms 0251: dt=36.288000, rms=0.567 (0.132%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25403.264 ms 0252: dt=145.152000, rms=0.565 (0.334%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23556.164 ms 0253: dt=25.920000, rms=0.564 (0.116%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25129.355 ms 0254: dt=580.608000, rms=0.559 (0.873%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25886.512 ms 0255: dt=31.104000, rms=0.558 (0.287%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26062.723 ms 0256: dt=36.288000, rms=0.557 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24717.600 ms 0257: dt=414.720000, rms=0.555 (0.341%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22959.559 ms 0258: dt=25.920000, rms=0.555 (0.152%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25536.840 ms 0259: dt=36.288000, rms=0.554 (0.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23521.988 ms 0260: dt=103.680000, rms=0.553 (0.116%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27774.160 ms 0261: dt=36.288000, rms=0.553 (0.036%), neg=0, invalid=766 0262: dt=36.288000, rms=0.553 (0.052%), neg=0, invalid=766 0263: dt=36.288000, rms=0.553 (0.079%), neg=0, invalid=766 0264: dt=36.288000, rms=0.552 (0.103%), neg=0, invalid=766 0265: dt=36.288000, rms=0.551 (0.127%), neg=0, invalid=766 0266: dt=36.288000, rms=0.551 (0.135%), neg=0, invalid=766 0267: dt=36.288000, rms=0.550 (0.157%), neg=0, invalid=766 0268: dt=36.288000, rms=0.549 (0.182%), neg=0, invalid=766 0269: dt=36.288000, rms=0.548 (0.191%), neg=0, invalid=766 0270: dt=36.288000, rms=0.547 (0.183%), neg=0, invalid=766 0271: dt=36.288000, rms=0.546 (0.176%), neg=0, invalid=766 0272: dt=36.288000, rms=0.545 (0.167%), neg=0, invalid=766 0273: dt=36.288000, rms=0.544 (0.162%), neg=0, invalid=766 0274: dt=36.288000, rms=0.543 (0.164%), neg=0, invalid=766 0275: dt=36.288000, rms=0.542 (0.156%), neg=0, invalid=766 0276: dt=36.288000, rms=0.541 (0.166%), neg=0, invalid=766 0277: dt=36.288000, rms=0.540 (0.145%), neg=0, invalid=766 0278: dt=36.288000, rms=0.540 (0.138%), neg=0, invalid=766 0279: dt=36.288000, rms=0.539 (0.109%), neg=0, invalid=766 0280: dt=36.288000, rms=0.539 (0.078%), neg=0, invalid=766 0281: dt=36.288000, rms=0.538 (0.079%), neg=0, invalid=766 0282: dt=36.288000, rms=0.538 (0.132%), neg=0, invalid=766 0283: dt=36.288000, rms=0.537 (0.131%), neg=0, invalid=766 0284: dt=36.288000, rms=0.536 (0.119%), neg=0, invalid=766 0285: dt=36.288000, rms=0.536 (0.090%), neg=0, invalid=766 0286: dt=36.288000, rms=0.535 (0.057%), neg=0, invalid=766 0287: dt=36.288000, rms=0.535 (0.059%), neg=0, invalid=766 0288: dt=36.288000, rms=0.535 (0.097%), neg=0, invalid=766 0289: dt=36.288000, rms=0.534 (0.107%), neg=0, invalid=766 0290: dt=36.288000, rms=0.534 (0.089%), neg=0, invalid=766 0291: dt=36.288000, rms=0.533 (0.061%), neg=0, invalid=766 0292: dt=36.288000, rms=0.533 (0.051%), neg=0, invalid=766 0293: dt=36.288000, rms=0.533 (0.039%), neg=0, invalid=766 0294: dt=36.288000, rms=0.532 (0.054%), neg=0, invalid=766 0295: dt=36.288000, rms=0.532 (0.057%), neg=0, invalid=766 0296: dt=36.288000, rms=0.532 (0.005%), neg=0, invalid=766 0297: dt=36.288000, rms=0.532 (0.028%), neg=0, invalid=766 0298: dt=36.288000, rms=0.532 (0.038%), neg=0, invalid=766 0299: dt=36.288000, rms=0.532 (0.015%), neg=0, invalid=766 0300: dt=36.288000, rms=0.532 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24362.559 ms 0301: dt=82.944000, rms=0.531 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26466.486 ms 0302: dt=6.480000, rms=0.531 (0.000%), neg=0, invalid=766 0303: dt=6.480000, rms=0.531 (0.003%), neg=0, invalid=766 0304: dt=6.480000, rms=0.531 (0.002%), neg=0, invalid=766 0305: dt=6.480000, rms=0.531 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27350.863 ms 0306: dt=145.152000, rms=0.529 (0.409%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24780.488 ms 0307: dt=36.288000, rms=0.528 (0.122%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23428.205 ms 0308: dt=36.288000, rms=0.528 (0.029%), neg=0, invalid=766 0309: dt=36.288000, rms=0.528 (0.054%), neg=0, invalid=766 0310: dt=36.288000, rms=0.528 (0.068%), neg=0, invalid=766 0311: dt=9.072000, rms=0.528 (0.002%), neg=0, invalid=766 0312: dt=9.072000, rms=0.528 (0.008%), neg=0, invalid=766 0313: dt=0.035437, rms=0.528 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 15079.430 ms 0314: dt=0.007594, rms=0.528 (0.000%), neg=0, invalid=766 0315: dt=0.000475, rms=0.528 (0.000%), neg=0, invalid=766 0316: dt=0.000030, rms=0.528 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.539, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 12062.190 ms 0317: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 12083.500 ms 0318: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24433.451 ms 0319: dt=16.128000, rms=0.547 (4.852%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23615.125 ms 0320: dt=13.824000, rms=0.537 (1.839%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21865.334 ms 0321: dt=4.032000, rms=0.536 (0.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23352.156 ms 0322: dt=13.824000, rms=0.532 (0.610%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22912.578 ms 0323: dt=4.032000, rms=0.532 (0.151%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23542.006 ms 0324: dt=11.520000, rms=0.530 (0.355%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23359.197 ms 0325: dt=4.032000, rms=0.529 (0.046%), neg=0, invalid=766 0326: dt=4.032000, rms=0.529 (0.122%), neg=0, invalid=766 0327: dt=4.032000, rms=0.528 (0.139%), neg=0, invalid=766 0328: dt=4.032000, rms=0.527 (0.149%), neg=0, invalid=766 0329: dt=4.032000, rms=0.526 (0.184%), neg=0, invalid=766 0330: dt=4.032000, rms=0.525 (0.183%), neg=0, invalid=766 0331: dt=4.032000, rms=0.524 (0.165%), neg=0, invalid=766 0332: dt=4.032000, rms=0.524 (0.106%), neg=0, invalid=766 0333: dt=4.032000, rms=0.524 (0.075%), neg=0, invalid=766 0334: dt=4.032000, rms=0.523 (0.048%), neg=0, invalid=766 0335: dt=4.032000, rms=0.523 (0.050%), neg=0, invalid=766 0336: dt=4.032000, rms=0.523 (0.059%), neg=0, invalid=766 0337: dt=4.032000, rms=0.522 (0.067%), neg=0, invalid=766 0338: dt=4.032000, rms=0.522 (0.053%), neg=0, invalid=766 0339: dt=4.032000, rms=0.522 (0.069%), neg=0, invalid=766 0340: dt=4.032000, rms=0.521 (0.074%), neg=0, invalid=766 0341: dt=4.032000, rms=0.521 (0.074%), neg=0, invalid=766 0342: dt=4.032000, rms=0.521 (0.080%), neg=0, invalid=766 0343: dt=4.032000, rms=0.520 (0.066%), neg=0, invalid=766 0344: dt=4.032000, rms=0.520 (0.067%), neg=0, invalid=766 0345: dt=4.032000, rms=0.520 (0.066%), neg=0, invalid=766 0346: dt=4.032000, rms=0.519 (0.031%), neg=0, invalid=766 0347: dt=4.032000, rms=0.519 (0.026%), neg=0, invalid=766 0348: dt=4.032000, rms=0.519 (0.020%), neg=0, invalid=766 0349: dt=4.032000, rms=0.519 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22459.756 ms 0350: dt=4.032000, rms=0.519 (0.009%), neg=0, invalid=766 0351: dt=4.032000, rms=0.519 (0.004%), neg=0, invalid=766 0352: dt=4.032000, rms=0.519 (0.010%), neg=0, invalid=766 0353: dt=4.032000, rms=0.519 (0.010%), neg=0, invalid=766 0354: dt=4.032000, rms=0.519 (0.008%), neg=0, invalid=766 0355: dt=4.032000, rms=0.519 (0.012%), neg=0, invalid=766 0356: dt=4.032000, rms=0.519 (0.017%), neg=0, invalid=766 0357: dt=4.032000, rms=0.519 (0.014%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26125.791 ms 0358: dt=8.000000, rms=0.518 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25082.018 ms 0359: dt=4.032000, rms=0.518 (0.019%), neg=0, invalid=766 0360: dt=4.032000, rms=0.518 (0.006%), neg=0, invalid=766 0361: dt=4.032000, rms=0.518 (0.007%), neg=0, invalid=766 0362: dt=4.032000, rms=0.518 (0.005%), neg=0, invalid=766 0363: dt=4.032000, rms=0.518 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.535, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22311.158 ms 0364: dt=0.000000, rms=0.535 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21913.314 ms 0365: dt=0.000000, rms=0.535 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.506, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24040.121 ms 0366: dt=0.148936, rms=0.501 (0.934%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23038.801 ms 0367: dt=0.130507, rms=0.498 (0.582%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23019.842 ms 0368: dt=0.118392, rms=0.496 (0.399%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21937.615 ms 0369: dt=0.096000, rms=0.495 (0.256%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22058.543 ms 0370: dt=0.112000, rms=0.494 (0.253%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23349.340 ms 0371: dt=0.320000, rms=0.491 (0.593%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20155.617 ms 0372: dt=0.028000, rms=0.491 (0.028%), neg=0, invalid=766 0373: dt=0.028000, rms=0.491 (0.028%), neg=0, invalid=766 0374: dt=0.028000, rms=0.490 (0.049%), neg=0, invalid=766 0375: dt=0.028000, rms=0.490 (0.069%), neg=0, invalid=766 0376: dt=0.028000, rms=0.490 (0.085%), neg=0, invalid=766 0377: dt=0.028000, rms=0.489 (0.094%), neg=0, invalid=766 0378: dt=0.028000, rms=0.489 (0.102%), neg=0, invalid=766 0379: dt=0.028000, rms=0.488 (0.106%), neg=0, invalid=766 0380: dt=0.028000, rms=0.488 (0.106%), neg=0, invalid=766 0381: dt=0.028000, rms=0.487 (0.100%), neg=0, invalid=766 0382: dt=0.028000, rms=0.487 (0.098%), neg=0, invalid=766 0383: dt=0.028000, rms=0.486 (0.093%), neg=0, invalid=766 0384: dt=0.028000, rms=0.486 (0.083%), neg=0, invalid=766 0385: dt=0.028000, rms=0.485 (0.074%), neg=0, invalid=766 0386: dt=0.028000, rms=0.485 (0.064%), neg=0, invalid=766 0387: dt=0.028000, rms=0.485 (0.058%), neg=0, invalid=766 0388: dt=0.028000, rms=0.485 (0.048%), neg=0, invalid=766 0389: dt=0.028000, rms=0.484 (0.042%), neg=0, invalid=766 0390: dt=0.028000, rms=0.484 (0.036%), neg=0, invalid=766 0391: dt=0.028000, rms=0.484 (0.029%), neg=0, invalid=766 0392: dt=0.028000, rms=0.484 (0.026%), neg=0, invalid=766 0393: dt=0.028000, rms=0.484 (0.019%), neg=0, invalid=766 0394: dt=0.028000, rms=0.484 (0.020%), neg=0, invalid=766 0395: dt=0.028000, rms=0.484 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23470.457 ms 0396: dt=0.112000, rms=0.484 (0.002%), neg=0, invalid=766 0397: dt=0.112000, rms=0.484 (0.000%), neg=0, invalid=766 0398: dt=0.112000, rms=0.484 (0.001%), neg=0, invalid=766 0399: dt=0.112000, rms=0.484 (0.003%), neg=0, invalid=766 0400: dt=0.112000, rms=0.484 (0.000%), neg=0, invalid=766 0401: dt=0.056000, rms=0.484 (0.000%), neg=0, invalid=766 0402: dt=0.056000, rms=0.484 (0.001%), neg=0, invalid=766 0403: dt=0.056000, rms=0.484 (0.002%), neg=0, invalid=766 0404: dt=0.056000, rms=0.484 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22396.119 ms 0405: dt=0.112000, rms=0.482 (0.283%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21245.646 ms 0406: dt=0.112000, rms=0.481 (0.212%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21807.176 ms 0407: dt=0.112000, rms=0.481 (0.154%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21510.051 ms 0408: dt=0.112000, rms=0.480 (0.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22872.379 ms 0409: dt=0.320000, rms=0.479 (0.243%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21204.432 ms 0410: dt=0.112000, rms=0.479 (0.027%), neg=0, invalid=766 0411: dt=0.028000, rms=0.479 (0.008%), neg=0, invalid=766 0412: dt=0.028000, rms=0.479 (0.009%), neg=0, invalid=766 0413: dt=0.028000, rms=0.479 (0.014%), neg=0, invalid=766 0414: dt=0.028000, rms=0.478 (0.015%), neg=0, invalid=766 0415: dt=0.028000, rms=0.478 (0.002%), neg=0, invalid=766 0416: dt=0.028000, rms=0.478 (0.005%), neg=0, invalid=766 0417: dt=0.028000, rms=0.478 (0.006%), neg=0, invalid=766 0418: dt=0.028000, rms=0.478 (0.009%), neg=0, invalid=766 0419: dt=0.028000, rms=0.478 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21289.074 ms 0420: dt=0.112000, rms=0.478 (0.006%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26913.363 ms 0421: dt=32.000000, rms=0.470 (1.253%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27085.314 ms iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0422: dt=44.800000, rms=0.466 (0.827%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26284.703 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0423: dt=11.200000, rms=0.466 (0.102%), neg=0, invalid=766 0424: dt=11.200000, rms=0.465 (0.136%), neg=0, invalid=766 0425: dt=11.200000, rms=0.464 (0.190%), neg=0, invalid=766 0426: dt=11.200000, rms=0.464 (0.162%), neg=0, invalid=766 0427: dt=11.200000, rms=0.463 (0.179%), neg=0, invalid=766 0428: dt=11.200000, rms=0.462 (0.212%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0429: dt=11.200000, rms=0.461 (0.148%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0430: dt=11.200000, rms=0.461 (0.088%), neg=0, invalid=766 0431: dt=11.200000, rms=0.460 (0.093%), neg=0, invalid=766 0432: dt=11.200000, rms=0.460 (0.112%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0433: dt=11.200000, rms=0.459 (0.137%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0434: dt=11.200000, rms=0.459 (0.114%), neg=0, invalid=766 0435: dt=11.200000, rms=0.458 (0.144%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=11.200000, rms=0.457 (0.172%), neg=0, invalid=766 0437: dt=11.200000, rms=0.456 (0.172%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0438: dt=11.200000, rms=0.456 (0.085%), neg=0, invalid=766 0439: dt=11.200000, rms=0.456 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28113.191 ms 0440: dt=11.200000, rms=0.456 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27409.957 ms 0441: dt=25.600000, rms=0.455 (0.144%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27272.398 ms 0442: dt=8.000000, rms=0.455 (0.022%), neg=0, invalid=766 0443: dt=8.000000, rms=0.455 (0.023%), neg=0, invalid=766 0444: dt=8.000000, rms=0.455 (0.027%), neg=0, invalid=766 0445: dt=8.000000, rms=0.455 (0.036%), neg=0, invalid=766 0446: dt=8.000000, rms=0.454 (0.028%), neg=0, invalid=766 0447: dt=8.000000, rms=0.454 (0.019%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28479.094 ms 0448: dt=44.800000, rms=0.450 (0.960%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28930.938 ms 0449: dt=25.600000, rms=0.449 (0.218%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 12 iterations, nbhd size=2, neg = 0 0450: dt=25.600000, rms=0.449 (-0.061%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29975.613 ms iter 0, gcam->neg = 12 after 0 iterations, nbhd size=0, neg = 0 0451: dt=5.680000, rms=0.460 (0.343%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31114.805 ms 0452: dt=5.454545, rms=0.459 (0.161%), neg=0, invalid=766 0453: dt=5.454545, rms=0.459 (0.068%), neg=0, invalid=766 0454: dt=5.454545, rms=0.459 (-0.011%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29672.654 ms iter 0, gcam->neg = 16 after 19 iterations, nbhd size=2, neg = 0 0455: dt=11.341772, rms=0.455 (0.730%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30170.168 ms iter 0, gcam->neg = 11 after 10 iterations, nbhd size=1, neg = 0 0456: dt=5.793103, rms=0.454 (0.193%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0457: dt=5.793103, rms=0.453 (0.221%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 15 iterations, nbhd size=2, neg = 0 0458: dt=5.793103, rms=0.452 (0.216%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0459: dt=5.793103, rms=0.452 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0460: dt=5.793103, rms=0.452 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29044.170 ms iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0461: dt=9.101449, rms=0.450 (0.347%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30402.924 ms 0462: dt=4.032000, rms=0.450 (0.085%), neg=0, invalid=766 0463: dt=4.032000, rms=0.450 (0.124%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0464: dt=4.032000, rms=0.449 (0.110%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0465: dt=4.032000, rms=0.449 (0.078%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31194.174 ms 0466: dt=4.032000, rms=0.448 (0.053%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28339.562 ms 0467: dt=0.000000, rms=0.454 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28374.262 ms 0468: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28140.285 ms 0469: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=766 0470: dt=0.100000, rms=0.454 (-0.037%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29022.684 ms iter 0, gcam->neg = 391 after 10 iterations, nbhd size=1, neg = 0 0471: dt=1.696021, rms=0.419 (5.914%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28285.066 ms 0472: dt=0.000313, rms=0.419 (0.006%), neg=0, invalid=766 0473: dt=0.000313, rms=0.419 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29535.121 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0474: dt=0.005001, rms=0.418 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30202.215 ms 0475: dt=0.007000, rms=0.418 (0.002%), neg=0, invalid=766 0476: dt=0.007000, rms=0.418 (0.001%), neg=0, invalid=766 0477: dt=0.007000, rms=0.418 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29966.857 ms iter 0, gcam->neg = 354 after 11 iterations, nbhd size=1, neg = 0 0478: dt=0.920734, rms=0.397 (2.510%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28983.445 ms 0479: dt=0.000375, rms=0.397 (-0.038%), neg=0, invalid=766 0480: dt=0.000375, rms=0.397 (0.002%), neg=0, invalid=766 0481: dt=0.000375, rms=0.397 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27237.713 ms 0482: dt=0.004000, rms=0.397 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27121.791 ms iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0483: dt=0.080665, rms=0.397 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26838.795 ms 0484: dt=0.001500, rms=0.397 (0.016%), neg=0, invalid=766 0485: dt=0.001500, rms=0.397 (0.002%), neg=0, invalid=766 0486: dt=0.001500, rms=0.397 (0.003%), neg=0, invalid=766 0487: dt=0.001500, rms=0.397 (0.001%), neg=0, invalid=766 0488: dt=0.001500, rms=0.397 (0.005%), neg=0, invalid=766 0489: dt=0.001500, rms=0.397 (0.004%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26966.662 ms iter 0, gcam->neg = 178 after 10 iterations, nbhd size=1, neg = 0 0490: dt=0.412109, rms=0.390 (1.142%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28258.928 ms 0491: dt=0.000438, rms=0.390 (-0.016%), neg=0, invalid=766 0492: dt=0.000438, rms=0.390 (0.001%), neg=0, invalid=766 0493: dt=0.000438, rms=0.390 (0.000%), neg=0, invalid=766 0494: dt=0.000438, rms=0.390 (0.001%), neg=0, invalid=766 0495: dt=0.000438, rms=0.390 (0.001%), neg=0, invalid=766 0496: dt=0.000438, rms=0.390 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28184.830 ms iter 0, gcam->neg = 117 after 9 iterations, nbhd size=1, neg = 0 0497: dt=0.256000, rms=0.388 (0.684%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30302.748 ms 0498: dt=0.001750, rms=0.388 (0.017%), neg=0, invalid=766 0499: dt=0.001750, rms=0.388 (0.002%), neg=0, invalid=766 0500: dt=0.001750, rms=0.388 (0.004%), neg=0, invalid=766 0501: dt=0.001750, rms=0.387 (0.006%), neg=0, invalid=766 0502: dt=0.001750, rms=0.387 (0.010%), neg=0, invalid=766 0503: dt=0.001750, rms=0.387 (0.007%), neg=0, invalid=766 0504: dt=0.001750, rms=0.387 (0.012%), neg=0, invalid=766 0505: dt=0.001750, rms=0.387 (0.014%), neg=0, invalid=766 0506: dt=0.001750, rms=0.387 (0.017%), neg=0, invalid=766 0507: dt=0.001750, rms=0.387 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30351.564 ms iter 0, gcam->neg = 85 after 18 iterations, nbhd size=2, neg = 0 0508: dt=0.305085, rms=0.386 (0.343%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31091.703 ms 0509: dt=0.001750, rms=0.386 (-0.001%), neg=0, invalid=766 0510: dt=0.001750, rms=0.386 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0511: dt=0.001750, rms=0.386 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0512: dt=0.001750, rms=0.386 (0.001%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.385, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28539.668 ms iter 0, gcam->neg = 4 after 24 iterations, nbhd size=3, neg = 0 0513: dt=6.400000, rms=0.386 (-0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29412.604 ms iter 0, gcam->neg = 50 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17864.672 ms iter 1, dt=0.000047: new neg 0, old_neg 2, delta 2, rms=0.001 (62.556%) 0514: dt=25.600000, rms=0.384 (0.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29137.342 ms iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0515: dt=11.200000, rms=0.384 (0.084%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 28 iterations, nbhd size=3, neg = 0 0516: dt=11.200000, rms=0.384 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13980.510 ms iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.001 (75.910%) 0517: dt=11.200000, rms=0.383 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 23 iterations, nbhd size=3, neg = 0 0518: dt=11.200000, rms=0.383 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 200 iterations, nbhd size=2, neg = 3 starting rms=0.006, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17946.484 ms iter 1, dt=0.000055: new neg 0, old_neg 3, delta 3, rms=0.001 (77.823%) 0519: dt=11.200000, rms=0.383 (0.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28640.699 ms iter 0, gcam->neg = 2 after 24 iterations, nbhd size=3, neg = 0 0520: dt=11.200000, rms=0.383 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26769.482 ms iter 0, gcam->neg = 16 after 200 iterations, nbhd size=3, neg = 4 starting rms=0.006, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 16776.119 ms iter 1, dt=0.000047: new neg 0, old_neg 4, delta 4, rms=0.001 (78.750%) 0521: dt=19.200000, rms=0.383 (0.050%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28158.443 ms iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 16336.369 ms iter 1, dt=0.000039: new neg 0, old_neg 2, delta 2, rms=0.001 (61.158%) 0522: dt=1.500000, rms=0.383 (0.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26556.047 ms iter 0, gcam->neg = 14 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17810.418 ms iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.001 (80.331%) 0523: dt=1.008000, rms=0.383 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 25 iterations, nbhd size=3, neg = 0 0524: dt=1.008000, rms=0.383 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 12874.941 ms iter 1, dt=0.000156: new neg 0, old_neg 2, delta 2, rms=0.001 (78.861%) 0525: dt=1.008000, rms=0.383 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 25 iterations, nbhd size=3, neg = 0 0526: dt=1.008000, rms=0.383 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29336.500 ms iter 0, gcam->neg = 87 after 200 iterations, nbhd size=2, neg = 5 starting rms=0.006, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17164.332 ms iter 1, dt=0.000047: new neg 0, old_neg 5, delta 5, rms=0.002 (74.731%) 0527: dt=5.894737, rms=0.381 (0.405%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27869.383 ms iter 0, gcam->neg = 28 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 18009.039 ms iter 1, dt=0.000047: new neg 0, old_neg 1, delta 1, rms=0.001 (53.046%) 0528: dt=2.880000, rms=0.381 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.005, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17431.871 ms iter 1, dt=0.000055: new neg 0, old_neg 3, delta 3, rms=0.001 (77.052%) 0529: dt=2.880000, rms=0.380 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 17180.342 ms iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.001 (50.264%) 0530: dt=2.880000, rms=0.380 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13822.972 ms iter 1, dt=0.000125: new neg 0, old_neg 2, delta 2, rms=0.001 (80.485%) 0531: dt=2.880000, rms=0.380 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32598.816 ms iter 0, gcam->neg = 32 after 200 iterations, nbhd size=2, neg = 3 starting rms=0.005, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 20425.820 ms iter 1, dt=0.000047: new neg 0, old_neg 3, delta 3, rms=0.002 (70.252%) 0532: dt=5.714286, rms=0.379 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29339.434 ms iter 0, gcam->neg = 21 after 33 iterations, nbhd size=4, neg = 0 0533: dt=2.880000, rms=0.379 (0.053%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26830.717 ms 0534: dt=0.000000, rms=0.380 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.380, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26709.963 ms iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0535: dt=0.080000, rms=0.380 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27207.674 ms iter 0, gcam->neg = 17 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 18912.938 ms iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.001 (72.289%) 0536: dt=0.448000, rms=0.380 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31797.996 ms iter 0, gcam->neg = 8 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 18264.895 ms iter 1, dt=0.000030: new neg 0, old_neg 2, delta 2, rms=0.001 (86.887%) 0537: dt=0.320000, rms=0.380 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 33 iterations, nbhd size=3, neg = 0 0538: dt=0.320000, rms=0.380 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 19136.174 ms iter 1, dt=0.000080: new neg 0, old_neg 2, delta 2, rms=0.001 (82.025%) 0539: dt=0.320000, rms=0.380 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0540: dt=0.320000, rms=0.380 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 7 iterations, nbhd size=1, neg = 0 0541: dt=0.320000, rms=0.379 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 19334.215 ms iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.001 (62.283%) 0542: dt=0.320000, rms=0.379 (0.013%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.377, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33407.852 ms iter 0, gcam->neg = 41 after 6 iterations, nbhd size=1, neg = 0 0543: dt=0.112000, rms=0.376 (0.308%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30443.145 ms iter 0, gcam->neg = 16 after 7 iterations, nbhd size=1, neg = 0 0544: dt=0.048000, rms=0.376 (0.090%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 6 iterations, nbhd size=1, neg = 0 0545: dt=0.048000, rms=0.376 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 7 iterations, nbhd size=1, neg = 0 0546: dt=0.048000, rms=0.375 (0.142%), neg=0, invalid=766 iter 0, gcam->neg = 48 after 8 iterations, nbhd size=1, neg = 0 0547: dt=0.048000, rms=0.375 (0.169%), neg=0, invalid=766 iter 0, gcam->neg = 72 after 9 iterations, nbhd size=1, neg = 0 0548: dt=0.048000, rms=0.374 (0.170%), neg=0, invalid=766 iter 0, gcam->neg = 107 after 10 iterations, nbhd size=1, neg = 0 0549: dt=0.048000, rms=0.373 (0.142%), neg=0, invalid=766 iter 0, gcam->neg = 148 after 20 iterations, nbhd size=2, neg = 0 0550: dt=0.048000, rms=0.373 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 219 after 11 iterations, nbhd size=1, neg = 0 0551: dt=0.048000, rms=0.373 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29458.221 ms 0552: dt=0.000438, rms=0.373 (0.001%), neg=0, invalid=766 0553: dt=0.000438, rms=0.373 (0.000%), neg=0, invalid=766 0554: dt=0.000438, rms=0.373 (0.000%), neg=0, invalid=766 0555: dt=0.000438, rms=0.373 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28567.293 ms iter 0, gcam->neg = 38 after 19 iterations, nbhd size=2, neg = 0 0556: dt=0.112000, rms=0.372 (0.244%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30578.891 ms 0557: dt=0.001000, rms=0.372 (0.002%), neg=0, invalid=766 0558: dt=0.001000, rms=0.372 (0.002%), neg=0, invalid=766 0559: dt=0.001000, rms=0.372 (0.003%), neg=0, invalid=766 0560: dt=0.001000, rms=0.372 (0.004%), neg=0, invalid=766 0561: dt=0.001000, rms=0.372 (0.006%), neg=0, invalid=766 0562: dt=0.001000, rms=0.372 (0.007%), neg=0, invalid=766 0563: dt=0.001000, rms=0.372 (0.008%), neg=0, invalid=766 0564: dt=0.001000, rms=0.372 (0.008%), neg=0, invalid=766 0565: dt=0.001000, rms=0.372 (0.009%), neg=0, invalid=766 0566: dt=0.001000, rms=0.372 (0.010%), neg=0, invalid=766 0567: dt=0.001000, rms=0.372 (0.010%), neg=0, invalid=766 0568: dt=0.001000, rms=0.371 (0.011%), neg=0, invalid=766 0569: dt=0.001000, rms=0.371 (0.011%), neg=0, invalid=766 0570: dt=0.001000, rms=0.371 (0.011%), neg=0, invalid=766 0571: dt=0.001000, rms=0.371 (0.011%), neg=0, invalid=766 0572: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 0573: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 0574: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 0575: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 0576: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 0577: dt=0.001000, rms=0.371 (0.012%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.370, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32858.973 ms iter 0, gcam->neg = 20 after 6 iterations, nbhd size=1, neg = 0 0578: dt=0.048000, rms=0.370 (0.120%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33408.570 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0579: dt=0.016000, rms=0.370 (0.034%), neg=0, invalid=766 0580: dt=0.016000, rms=0.370 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0581: dt=0.016000, rms=0.369 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0582: dt=0.016000, rms=0.369 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 6 iterations, nbhd size=1, neg = 0 0583: dt=0.016000, rms=0.369 (0.096%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 14 iterations, nbhd size=2, neg = 0 0584: dt=0.016000, rms=0.368 (0.106%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 7 iterations, nbhd size=1, neg = 0 0585: dt=0.016000, rms=0.368 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 16 iterations, nbhd size=2, neg = 0 0586: dt=0.016000, rms=0.368 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 13 iterations, nbhd size=2, neg = 0 0587: dt=0.016000, rms=0.367 (0.097%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.367, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31606.148 ms iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0588: dt=0.004000, rms=0.367 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30982.281 ms iter 0, gcam->neg = 38 after 11 iterations, nbhd size=1, neg = 0 0589: dt=0.064000, rms=0.367 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33207.324 ms iter 0, gcam->neg = 15 after 7 iterations, nbhd size=1, neg = 0 0590: dt=0.028000, rms=0.366 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0591: dt=0.028000, rms=0.366 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 24 after 7 iterations, nbhd size=1, neg = 0 0592: dt=0.028000, rms=0.366 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 18 iterations, nbhd size=2, neg = 0 0593: dt=0.028000, rms=0.365 (0.118%), neg=0, invalid=766 iter 0, gcam->neg = 95 after 18 iterations, nbhd size=2, neg = 0 0594: dt=0.028000, rms=0.365 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 117 after 10 iterations, nbhd size=1, neg = 0 0595: dt=0.028000, rms=0.364 (0.132%), neg=0, invalid=766 iter 0, gcam->neg = 139 after 8 iterations, nbhd size=1, neg = 0 0596: dt=0.028000, rms=0.364 (0.119%), neg=0, invalid=766 iter 0, gcam->neg = 153 after 18 iterations, nbhd size=2, neg = 0 0597: dt=0.028000, rms=0.364 (0.108%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30806.998 ms 0598: dt=0.000750, rms=0.364 (0.001%), neg=0, invalid=766 0599: dt=0.000750, rms=0.364 (0.000%), neg=0, invalid=766 0600: dt=0.000750, rms=0.364 (0.001%), neg=0, invalid=766 0601: dt=0.000750, rms=0.364 (0.001%), neg=0, invalid=766 0602: dt=0.000750, rms=0.364 (0.001%), neg=0, invalid=766 0603: dt=0.000750, rms=0.364 (0.002%), neg=0, invalid=766 0604: dt=0.000750, rms=0.364 (0.002%), neg=0, invalid=766 0605: dt=0.000750, rms=0.364 (0.002%), neg=0, invalid=766 0606: dt=0.000750, rms=0.363 (0.002%), neg=0, invalid=766 0607: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0608: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0609: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0610: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0611: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0612: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0613: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0614: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0615: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0616: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 0617: dt=0.000750, rms=0.363 (0.003%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.363, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29244.719 ms iter 0, gcam->neg = 12 after 6 iterations, nbhd size=1, neg = 0 0618: dt=0.024000, rms=0.363 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28990.025 ms iter 0, gcam->neg = 11 after 6 iterations, nbhd size=1, neg = 0 0619: dt=0.024000, rms=0.362 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 6 iterations, nbhd size=1, neg = 0 0620: dt=0.024000, rms=0.362 (0.047%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0621: dt=0.024000, rms=0.362 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 31 after 10 iterations, nbhd size=1, neg = 0 0622: dt=0.024000, rms=0.361 (0.106%), neg=0, invalid=766 iter 0, gcam->neg = 40 after 13 iterations, nbhd size=2, neg = 0 0623: dt=0.024000, rms=0.361 (0.115%), neg=0, invalid=766 iter 0, gcam->neg = 41 after 17 iterations, nbhd size=2, neg = 0 0624: dt=0.024000, rms=0.361 (0.116%), neg=0, invalid=766 iter 0, gcam->neg = 57 after 23 iterations, nbhd size=3, neg = 0 0625: dt=0.024000, rms=0.360 (0.113%), neg=0, invalid=766 iter 0, gcam->neg = 63 after 18 iterations, nbhd size=2, neg = 0 0626: dt=0.024000, rms=0.360 (0.100%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.360, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28367.486 ms 0627: dt=0.001750, rms=0.360 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28517.039 ms iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0628: dt=0.012000, rms=0.360 (0.030%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28582.730 ms iter 0, gcam->neg = 11 after 7 iterations, nbhd size=1, neg = 0 0629: dt=0.028000, rms=0.359 (0.068%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29722.242 ms iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0630: dt=0.016000, rms=0.359 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0631: dt=0.016000, rms=0.359 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 20 iterations, nbhd size=2, neg = 0 0632: dt=0.016000, rms=0.359 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 16 iterations, nbhd size=2, neg = 0 0633: dt=0.016000, rms=0.359 (0.083%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 17 iterations, nbhd size=2, neg = 0 0634: dt=0.016000, rms=0.358 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 22 iterations, nbhd size=3, neg = 0 0635: dt=0.016000, rms=0.358 (0.099%), neg=0, invalid=766 iter 0, gcam->neg = 62 after 15 iterations, nbhd size=2, neg = 0 0636: dt=0.016000, rms=0.358 (0.098%), neg=0, invalid=766 iter 0, gcam->neg = 105 after 15 iterations, nbhd size=2, neg = 0 0637: dt=0.016000, rms=0.357 (0.091%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 3 hours, 56 minutes and 23 seconds. #-------------------------------------- #@# CA Reg Inv Mon Jul 23 16:51:01 BST 2012 /home/clare/subjects/subject_20/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 16:51:37 BST 2012 New invocation of recon-all Mon Jul 23 16:51:38 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -rmneck #-------------------------------------- #@# Remove Neck Mon Jul 23 16:51:38 BST 2012 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 10524987 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 42 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 16:52:20 BST 2012 New invocation of recon-all Mon Jul 23 16:52:20 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -skull-lta #-------------------------------------- #@# SkullLTA Mon Jul 23 16:52:20 BST 2012 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /home/clare/freesurfer/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/clare/freesurfer/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (45, 17, 0) --> (210, 208, 216) using (100, 81, 108) as brain centroid... mean wm in atlas = 126, using box (80,57,81) --> (120, 104,134) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10318.9, old_max_log_p =-10382.7 (thresh=-10372.4) 1.068 -0.014 0.039 -11.900; 0.021 0.928 0.081 9.396; -0.034 -0.095 1.210 -3.163; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10318.9, old_max_log_p =-10318.9 (thresh=-10308.6) 1.068 -0.014 0.039 -11.900; 0.021 0.928 0.081 9.396; -0.034 -0.095 1.210 -3.163; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10314.2, old_max_log_p =-10318.9 (thresh=-10308.6) 1.045 0.032 -0.075 -2.336; -0.016 0.962 0.092 7.441; 0.068 -0.087 1.164 -12.143; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10311.1, old_max_log_p =-10314.2 (thresh=-10303.9) 1.043 0.040 -0.083 -2.154; -0.024 0.960 0.103 7.653; 0.077 -0.095 1.162 -12.722; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04319 0.04026 -0.08315 -2.15382; -0.02384 0.95952 0.10257 7.65263; 0.07681 -0.09501 1.16241 -12.72208; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04319 0.04026 -0.08315 -2.15382; -0.02384 0.95952 0.10257 7.65263; 0.07681 -0.09501 1.16241 -12.72208; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10311.1 tol 0.000010 Resulting transform: 1.043 0.040 -0.083 -2.154; -0.024 0.960 0.103 7.653; 0.077 -0.095 1.162 -12.722; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10311.1 (old=-10382.7) transform before final EM align: 1.043 0.040 -0.083 -2.154; -0.024 0.960 0.103 7.653; 0.077 -0.095 1.162 -12.722; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04319 0.04026 -0.08315 -2.15382; -0.02384 0.95952 0.10257 7.65263; 0.07681 -0.09501 1.16241 -12.72208; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04319 0.04026 -0.08315 -2.15382; -0.02384 0.95952 0.10257 7.65263; 0.07681 -0.09501 1.16241 -12.72208; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 006: -log(p) = 1145403.0 after pass:transform: ( 1.04, 0.04, -0.08, -2.15) ( -0.02, 0.96, 0.10, 7.65) ( 0.08, -0.09, 1.16, -12.72) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1145403.0 tol 0.000000 final transform: 1.043 0.040 -0.083 -2.154; -0.023 0.960 0.103 7.653; 0.077 -0.095 1.162 -12.722; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 20 minutes and 1 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:12:21 BST 2012 New invocation of recon-all Mon Jul 23 17:12:21 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -calabel #-------------------------------------- #@# SubCort Seg Mon Jul 23 17:12:21 BST 2012 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /home/clare/subjects/subject_20/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /home/clare/freesurfer/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.10274 (24) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (439 voxels, overlap=0.809) Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (439 voxels, peak = 24), gca=24.3 gca peak = 0.14982 (20) mri peak = 0.10509 (26) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (2773 voxels, overlap=0.875) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (2773 voxels, peak = 22), gca=21.5 gca peak = 0.28003 (97) mri peak = 0.09822 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (474 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (474 voxels, peak = 97), gca=97.0 gca peak = 0.18160 (96) mri peak = 0.07187 (100) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (487 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (487 voxels, peak = 98), gca=98.4 gca peak = 0.27536 (62) mri peak = 0.05976 (77) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1063 voxels, overlap=0.001) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1063 voxels, peak = 74), gca=74.4 gca peak = 0.32745 (63) mri peak = 0.07412 (81) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1007 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1007 voxels, peak = 76), gca=75.6 gca peak = 0.08597 (105) mri peak = 0.07943 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (90570 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (90570 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.07698 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (85458 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (85458 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.05081 (84) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (72645 voxels, overlap=0.038) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (72645 voxels, peak = 82), gca=81.9 gca peak = 0.08598 (64) mri peak = 0.05416 (82) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (72586 voxels, overlap=0.021) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (72586 voxels, peak = 83), gca=83.2 gca peak = 0.24164 (71) mri peak = 0.08129 (87) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1114 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1114 voxels, peak = 83), gca=83.4 gca peak = 0.18227 (75) mri peak = 0.09484 (85) Left_Caudate (11): linear fit = 1.10 x + 0.0 (1072 voxels, overlap=0.567) Left_Caudate (11): linear fit = 1.10 x + 0.0 (1072 voxels, peak = 82), gca=82.5 gca peak = 0.10629 (62) mri peak = 0.04808 (79) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (24267 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (24267 voxels, peak = 81), gca=80.6 gca peak = 0.11668 (59) mri peak = 0.05997 (75) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (25338 voxels, overlap=0.041) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (25338 voxels, peak = 72), gca=72.3 gca peak = 0.17849 (88) mri peak = 0.08050 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6942 voxels, overlap=0.720) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6942 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.07850 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7177 voxels, overlap=0.826) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7177 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.07451 (75) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (427 voxels, overlap=0.517) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (427 voxels, peak = 74), gca=73.6 gca peak = 0.42394 (62) mri peak = 0.09207 (82) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (423 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.33 x + 0.0 (423 voxels, peak = 82), gca=82.2 gca peak = 0.10041 (96) mri peak = 0.06957 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6494 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6494 voxels, peak = 96), gca=96.0 gca peak = 0.13978 (88) mri peak = 0.07384 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6238 voxels, overlap=0.987) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6238 voxels, peak = 88), gca=88.0 gca peak = 0.08514 (81) mri peak = 0.06607 (99) Left_Putamen (12): linear fit = 1.17 x + 0.0 (2369 voxels, overlap=0.119) Left_Putamen (12): linear fit = 1.17 x + 0.0 (2369 voxels, peak = 95), gca=95.2 gca peak = 0.09624 (82) mri peak = 0.08216 (99) Right_Putamen (51): linear fit = 1.17 x + 0.0 (2388 voxels, overlap=0.078) Right_Putamen (51): linear fit = 1.17 x + 0.0 (2388 voxels, peak = 96), gca=96.3 gca peak = 0.07543 (88) mri peak = 0.06648 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14918 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14918 voxels, peak = 88), gca=88.0 gca peak = 0.12757 (95) mri peak = 0.07315 (95) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1395 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1395 voxels, peak = 97), gca=97.4 gca peak = 0.17004 (92) mri peak = 0.06965 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1686 voxels, overlap=0.886) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1686 voxels, peak = 92), gca=92.0 gca peak = 0.21361 (36) mri peak = 0.10731 (20) gca peak = 0.26069 (23) mri peak = 0.08826 (29) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (397 voxels, overlap=0.829) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (397 voxels, peak = 23), gca=23.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14649 (25) mri peak = 0.10274 (24) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (439 voxels, overlap=0.922) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (439 voxels, peak = 24), gca=23.8 gca peak = 0.18354 (22) mri peak = 0.10509 (26) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2773 voxels, overlap=0.808) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (2773 voxels, peak = 22), gca=22.0 gca peak = 0.26145 (97) mri peak = 0.09822 (99) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (474 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (474 voxels, peak = 97), gca=97.0 gca peak = 0.16128 (98) mri peak = 0.07187 (100) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (487 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (487 voxels, peak = 100), gca=100.4 gca peak = 0.20542 (75) mri peak = 0.05976 (77) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 75), gca=75.0 gca peak = 0.25795 (76) mri peak = 0.07412 (81) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1007 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1007 voxels, peak = 76), gca=76.0 gca peak = 0.08007 (112) mri peak = 0.07943 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (90570 voxels, overlap=0.745) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (90570 voxels, peak = 112), gca=112.0 gca peak = 0.08789 (111) mri peak = 0.07698 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (85458 voxels, overlap=0.754) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (85458 voxels, peak = 111), gca=111.0 gca peak = 0.05859 (82) mri peak = 0.05081 (84) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (72645 voxels, overlap=0.876) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (72645 voxels, peak = 82), gca=82.0 gca peak = 0.06762 (82) mri peak = 0.05416 (82) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (72586 voxels, overlap=0.899) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (72586 voxels, peak = 82), gca=82.0 gca peak = 0.21727 (83) mri peak = 0.08129 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1114 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1114 voxels, peak = 83), gca=83.0 gca peak = 0.13731 (82) mri peak = 0.09484 (85) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1072 voxels, overlap=0.911) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1072 voxels, peak = 82), gca=82.0 gca peak = 0.08059 (79) mri peak = 0.04808 (79) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24267 voxels, overlap=0.978) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24267 voxels, peak = 77), gca=77.0 gca peak = 0.10453 (73) mri peak = 0.05997 (75) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25338 voxels, overlap=0.970) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25338 voxels, peak = 73), gca=73.0 gca peak = 0.17137 (94) mri peak = 0.08050 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6942 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6942 voxels, peak = 94), gca=94.0 gca peak = 0.15757 (93) mri peak = 0.07850 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7177 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7177 voxels, peak = 93), gca=93.0 gca peak = 0.31087 (73) mri peak = 0.07451 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (427 voxels, overlap=0.989) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (427 voxels, peak = 73), gca=73.0 gca peak = 0.39086 (83) mri peak = 0.09207 (82) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (423 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (423 voxels, peak = 83), gca=83.0 gca peak = 0.10049 (96) mri peak = 0.06957 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6494 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6494 voxels, peak = 96), gca=96.0 gca peak = 0.13977 (88) mri peak = 0.07384 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6238 voxels, overlap=0.986) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6238 voxels, peak = 88), gca=88.0 gca peak = 0.07388 (95) mri peak = 0.06607 (99) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2369 voxels, overlap=0.906) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2369 voxels, peak = 95), gca=95.0 gca peak = 0.09706 (89) mri peak = 0.08216 (99) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2388 voxels, overlap=0.885) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2388 voxels, peak = 89), gca=89.0 gca peak = 0.07600 (85) mri peak = 0.06648 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14918 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14918 voxels, peak = 85), gca=85.0 gca peak = 0.14225 (97) mri peak = 0.07315 (95) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1395 voxels, overlap=0.837) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1395 voxels, peak = 97), gca=97.0 gca peak = 0.16834 (92) mri peak = 0.06965 (93) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1686 voxels, overlap=0.886) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1686 voxels, peak = 92), gca=92.0 gca peak = 0.21680 (36) mri peak = 0.10731 (20) gca peak = 0.26069 (23) mri peak = 0.08826 (29) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (397 voxels, overlap=0.829) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (397 voxels, peak = 23), gca=23.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26961 (42) gca peak Third_Ventricle = 0.21680 (36) gca peak CSF = 0.17920 (38) gca peak Left_Accumbens_area = 0.51393 (77) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.28322 (38) gca peak Right_Accumbens_area = 0.26229 (84) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.96365 (41) gca peak WM_hypointensities = 0.14654 (86) gca peak non_WM_hypointensities = 0.08849 (55) gca peak Optic_Chiasm = 0.34131 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.98 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 53023 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels) 512 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 102818 changed. image ll: -2.290, PF=1.000 pass 2: 18492 changed. image ll: -2.286, PF=1.000 pass 3: 6268 changed. pass 4: 2507 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 14 minutes and 53 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/clare/subjects/subject_20/mri/transforms/cc_up.lta subject_20 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/clare/subjects/subject_20/mri/transforms/cc_up.lta reading aseg from /home/clare/subjects/subject_20/mri/aseg.auto_noCCseg.mgz reading norm from /home/clare/subjects/subject_20/mri/norm.mgz 41481 voxels in left wm, 45294 in right wm, xrange [124, 132] searching rotation angles z=[-8 6], y=[-6 8] searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 global minimum found at slice 128.0, rotations (1.87, -0.16) final transformation (x=128.0, yr=1.868, zr=-0.155): 0.999 0.003 0.033 -3.571; -0.003 1.000 -0.000 36.356; -0.033 -0.000 0.999 28.229; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 152 167 eigenvectors: 0.001 0.001 1.000; 0.124 -0.992 0.001; 0.992 0.124 -0.001; error in mid anterior detected - correcting... writing aseg with callosum to /home/clare/subjects/subject_20/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Mon Jul 23 17:27:55 BST 2012 cp aseg.auto.mgz aseg.mgz #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:27:55 BST 2012 New invocation of recon-all Mon Jul 23 17:27:55 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -normalization2 #-------------------------------------------- #@# Intensity Normalization2 Mon Jul 23 17:27:55 BST 2012 /home/clare/subjects/subject_20/mri mri_normalize -f /home/clare/subjects/subject_20/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz -b 18 -n 7 norm.mgz brain.mgz using control points from file /home/clare/subjects/subject_20/tmp/control.dat... using segmentation for initial intensity normalization using control point with intensity 18.0 below target. performing 3d normalization 7 times reading from norm.mgz... normalizing image... Reading 4 control points... only using 4 control points from file, mean 93.2, scaling by 1.18... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 854 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 3 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 4 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 5 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 6 of 7 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 7 of 7 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 6 minutes and 20 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 110 gm peak at 88 (88), valley at 19 (19) csf peak at 44, setting threshold to 73 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 white matter peak found at 111 white matter peak found at 110 gm peak at 85 (85), valley at 14 (14) csf peak at 43, setting threshold to 71 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:34:18 BST 2012 New invocation of recon-all Mon Jul 23 17:34:18 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -maskbfs #-------------------------------------------- #@# Mask BFS Mon Jul 23 17:34:18 BST 2012 /home/clare/subjects/subject_20/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1908083 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:34:20 BST 2012 New invocation of recon-all Mon Jul 23 17:34:20 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -segmentation #-------------------------------------------- #@# WM Segmentation Mon Jul 23 17:34:20 BST 2012 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/clare/subjects/subject_20/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 219 values in range Counting number of voxels Found 219 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/clare/subjects/subject_20/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 3 values in range Counting number of voxels Found 3 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz Found wm edits: 3 deletes, 219 fills cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.9 +- 5.6 [80.0 --> 125.0] GM (78.0) : 75.7 +- 14.0 [30.0 --> 96.0] setting bottom of white matter range to 89.8 setting top of gray matter range to 103.8 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 13799 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2741 filled 4976 bright non-wm voxels segmented. 8385 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.41 minutes reading wm segmentation from wm.seg.mgz... 329 voxels added to wm to prevent paths from MTL structures to cortex 3613 additional wm voxels added 0 additional wm voxels added SEG EDIT: 45887 voxels turned on, 56279 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 49 found - 49 modified | TOTAL: 49 pass 2 (xy+): 0 found - 49 modified | TOTAL: 49 pass 1 (xy-): 46 found - 46 modified | TOTAL: 95 pass 2 (xy-): 0 found - 46 modified | TOTAL: 95 pass 1 (yz+): 50 found - 50 modified | TOTAL: 145 pass 2 (yz+): 0 found - 50 modified | TOTAL: 145 pass 1 (yz-): 69 found - 69 modified | TOTAL: 214 pass 2 (yz-): 0 found - 69 modified | TOTAL: 214 pass 1 (xz+): 66 found - 66 modified | TOTAL: 280 pass 2 (xz+): 0 found - 66 modified | TOTAL: 280 pass 1 (xz-): 53 found - 53 modified | TOTAL: 333 pass 2 (xz-): 0 found - 53 modified | TOTAL: 333 Iteration Number : 1 pass 1 (+++): 54 found - 54 modified | TOTAL: 54 pass 2 (+++): 0 found - 54 modified | TOTAL: 54 pass 1 (+++): 65 found - 65 modified | TOTAL: 119 pass 2 (+++): 0 found - 65 modified | TOTAL: 119 pass 1 (+++): 84 found - 84 modified | TOTAL: 203 pass 2 (+++): 0 found - 84 modified | TOTAL: 203 pass 1 (+++): 78 found - 78 modified | TOTAL: 281 pass 2 (+++): 0 found - 78 modified | TOTAL: 281 Iteration Number : 1 pass 1 (++): 264 found - 264 modified | TOTAL: 264 pass 2 (++): 0 found - 264 modified | TOTAL: 264 pass 1 (+-): 254 found - 254 modified | TOTAL: 518 pass 2 (+-): 2 found - 256 modified | TOTAL: 520 pass 3 (+-): 0 found - 256 modified | TOTAL: 520 pass 1 (--): 247 found - 247 modified | TOTAL: 767 pass 2 (--): 1 found - 248 modified | TOTAL: 768 pass 3 (--): 0 found - 248 modified | TOTAL: 768 pass 1 (-+): 255 found - 255 modified | TOTAL: 1023 pass 2 (-+): 0 found - 255 modified | TOTAL: 1023 Iteration Number : 2 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 19 found - 19 modified | TOTAL: 36 pass 2 (xy-): 0 found - 19 modified | TOTAL: 36 pass 1 (yz+): 17 found - 17 modified | TOTAL: 53 pass 2 (yz+): 0 found - 17 modified | TOTAL: 53 pass 1 (yz-): 25 found - 25 modified | TOTAL: 78 pass 2 (yz-): 0 found - 25 modified | TOTAL: 78 pass 1 (xz+): 16 found - 16 modified | TOTAL: 94 pass 2 (xz+): 0 found - 16 modified | TOTAL: 94 pass 1 (xz-): 26 found - 26 modified | TOTAL: 120 pass 2 (xz-): 0 found - 26 modified | TOTAL: 120 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 8 found - 8 modified | TOTAL: 10 pass 2 (+++): 0 found - 8 modified | TOTAL: 10 pass 1 (+++): 13 found - 13 modified | TOTAL: 23 pass 2 (+++): 0 found - 13 modified | TOTAL: 23 pass 1 (+++): 2 found - 2 modified | TOTAL: 25 pass 2 (+++): 0 found - 2 modified | TOTAL: 25 Iteration Number : 2 pass 1 (++): 15 found - 15 modified | TOTAL: 15 pass 2 (++): 0 found - 15 modified | TOTAL: 15 pass 1 (+-): 6 found - 6 modified | TOTAL: 21 pass 2 (+-): 0 found - 6 modified | TOTAL: 21 pass 1 (--): 9 found - 9 modified | TOTAL: 30 pass 2 (--): 0 found - 9 modified | TOTAL: 30 pass 1 (-+): 20 found - 20 modified | TOTAL: 50 pass 2 (-+): 0 found - 20 modified | TOTAL: 50 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 1 found - 1 modified | TOTAL: 10 pass 2 (xz-): 0 found - 1 modified | TOTAL: 10 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1843 (out of 737356: 0.249947) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 219 WM ON voxels kept 3 WM OFF voxels mri_pretess done #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:36:43 BST 2012 New invocation of recon-all Mon Jul 23 17:36:43 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -fill #-------------------------------------------- #@# Fill Mon Jul 23 17:36:43 BST 2012 /home/clare/subjects/subject_20/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.004 -0.013 0.037 -3.651; 0.023 1.003 0.088 0.338; -0.027 -0.077 0.979 17.705; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.004 -0.013 0.037 -3.651; 0.023 1.003 0.088 0.338; -0.027 -0.077 0.979 17.705; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1232 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75) no need to search using seed (127, 125, 151), TAL = (1.0, 23.0, 3.0) talairach voxel to voxel transform 0.995 0.010 -0.038 4.308; -0.025 0.990 -0.088 1.125; 0.026 0.078 1.013 -17.875; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 125, 151) --> (1.0, 23.0, 3.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (1.00, 23.00, 3.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 23.00, 3.00) SRC: (108.20, 108.84, 147.72) search lh wm seed point around talairach space (-17.00, 23.00, 3.00), SRC: (144.03, 107.93, 148.65) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:37:26 BST 2012 New invocation of recon-all Mon Jul 23 17:37:26 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -tessellate #-------------------------------------------- #@# Tessellate lh Mon Jul 23 17:37:26 BST 2012 /home/clare/subjects/subject_20/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 6 found - 6 modified | TOTAL: 13 pass 2 (xz+): 0 found - 6 modified | TOTAL: 13 pass 1 (xz-): 0 found - 0 modified | TOTAL: 13 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 4 found - 4 modified | TOTAL: 6 pass 2 (--): 0 found - 4 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 22 (out of 352937: 0.006233) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 30: 3295 vertices, 3504 faces slice 40: 10670 vertices, 10989 faces slice 50: 21609 vertices, 22008 faces slice 60: 33143 vertices, 33639 faces slice 70: 45694 vertices, 46219 faces slice 80: 58989 vertices, 59509 faces slice 90: 73085 vertices, 73691 faces slice 100: 86893 vertices, 87517 faces slice 110: 101823 vertices, 102542 faces slice 120: 116347 vertices, 117042 faces slice 130: 130464 vertices, 131122 faces slice 140: 142419 vertices, 143107 faces slice 150: 152584 vertices, 153241 faces slice 160: 161315 vertices, 161946 faces slice 170: 168678 vertices, 169292 faces slice 180: 175063 vertices, 175622 faces slice 190: 179884 vertices, 180366 faces slice 200: 181044 vertices, 181394 faces slice 210: 181044 vertices, 181394 faces slice 220: 181044 vertices, 181394 faces slice 230: 181044 vertices, 181394 faces slice 240: 181044 vertices, 181394 faces slice 250: 181044 vertices, 181394 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -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; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 181044 voxel in cpt #1: X=-350 [v=181044,e=544182,f=362788] located at (-29.463816, -25.784832, 29.626207) For the whole surface: X=-350 [v=181044,e=544182,f=362788] One single component has been found nothing to do done #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:37:33 BST 2012 New invocation of recon-all Mon Jul 23 17:37:33 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -tessellate #-------------------------------------------- #@# Tessellate rh Mon Jul 23 17:37:33 BST 2012 /home/clare/subjects/subject_20/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 1 found - 1 modified | TOTAL: 4 pass 2 (-+): 0 found - 1 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 14 (out of 361901: 0.003868) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 30: 2646 vertices, 2836 faces slice 40: 9904 vertices, 10193 faces slice 50: 19804 vertices, 20192 faces slice 60: 31163 vertices, 31684 faces slice 70: 45172 vertices, 45696 faces slice 80: 57480 vertices, 57990 faces slice 90: 71721 vertices, 72321 faces slice 100: 85789 vertices, 86367 faces slice 110: 100155 vertices, 100789 faces slice 120: 114797 vertices, 115467 faces slice 130: 129315 vertices, 130024 faces slice 140: 141118 vertices, 141718 faces slice 150: 150316 vertices, 150895 faces slice 160: 158858 vertices, 159433 faces slice 170: 166754 vertices, 167340 faces slice 180: 173287 vertices, 173811 faces slice 190: 178485 vertices, 178928 faces slice 200: 179654 vertices, 179976 faces slice 210: 179654 vertices, 179976 faces slice 220: 179654 vertices, 179976 faces slice 230: 179654 vertices, 179976 faces slice 240: 179654 vertices, 179976 faces slice 250: 179654 vertices, 179976 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -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; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 179654 voxel in cpt #1: X=-322 [v=179654,e=539928,f=359952] located at (29.881790, -25.145000, 30.295658) For the whole surface: X=-322 [v=179654,e=539928,f=359952] One single component has been found nothing to do done #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:37:40 BST 2012 New invocation of recon-all Mon Jul 23 17:37:40 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -smooth1 #-------------------------------------------- #@# Smooth1 lh Mon Jul 23 17:37:40 BST 2012 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/clare/subjects/subject_20/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:37:44 BST 2012 New invocation of recon-all Mon Jul 23 17:37:44 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -smooth1 #-------------------------------------------- #@# Smooth1 rh Mon Jul 23 17:37:44 BST 2012 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/clare/subjects/subject_20/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:37:48 BST 2012 New invocation of recon-all Mon Jul 23 17:37:48 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -inflate1 #-------------------------------------------- #@# Inflation1 lh Mon Jul 23 17:37:48 BST 2012 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/clare/subjects/subject_20/scripts avg radius = 50.6 mm, total surface area = 92292 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.091 (target=0.015) step 010: RMS=0.075 (target=0.015) step 015: RMS=0.068 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:38:24 BST 2012 New invocation of recon-all Mon Jul 23 17:38:24 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -inflate1 #-------------------------------------------- #@# Inflation1 rh Mon Jul 23 17:38:24 BST 2012 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/clare/subjects/subject_20/scripts avg radius = 51.0 mm, total surface area = 92137 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes Not saving sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.072 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.043 (target=0.015) step 050: RMS=0.042 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:38:59 BST 2012 New invocation of recon-all Mon Jul 23 17:38:59 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -qsphere #-------------------------------------------- #@# QSphere lh Mon Jul 23 17:38:59 BST 2012 /home/clare/subjects/subject_20/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.55 (0.00-->9.05) (max @ vno 120305 --> 121775) face area 0.02 +- 0.03 (-0.15-->0.53) scaling brain by 0.282... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.831, avgs=0 005/300: dt: 0.9000, rms radial error=176.570, avgs=0 010/300: dt: 0.9000, rms radial error=176.011, avgs=0 015/300: dt: 0.9000, rms radial error=175.277, avgs=0 020/300: dt: 0.9000, rms radial error=174.439, avgs=0 025/300: dt: 0.9000, rms radial error=173.542, avgs=0 030/300: dt: 0.9000, rms radial error=172.613, avgs=0 035/300: dt: 0.9000, rms radial error=171.666, avgs=0 040/300: dt: 0.9000, rms radial error=170.712, avgs=0 045/300: dt: 0.9000, rms radial error=169.755, avgs=0 050/300: dt: 0.9000, rms radial error=168.800, avgs=0 055/300: dt: 0.9000, rms radial error=167.853, avgs=0 060/300: dt: 0.9000, rms radial error=166.909, avgs=0 065/300: dt: 0.9000, rms radial error=165.970, avgs=0 070/300: dt: 0.9000, rms radial error=165.036, avgs=0 075/300: dt: 0.9000, rms radial error=164.106, avgs=0 080/300: dt: 0.9000, rms radial error=163.182, avgs=0 085/300: dt: 0.9000, rms radial error=162.263, avgs=0 090/300: dt: 0.9000, rms radial error=161.349, avgs=0 095/300: dt: 0.9000, rms radial error=160.439, avgs=0 100/300: dt: 0.9000, rms radial error=159.535, avgs=0 105/300: dt: 0.9000, rms radial error=158.636, avgs=0 110/300: dt: 0.9000, rms radial error=157.742, avgs=0 115/300: dt: 0.9000, rms radial error=156.853, avgs=0 120/300: dt: 0.9000, rms radial error=155.969, avgs=0 125/300: dt: 0.9000, rms radial error=155.090, avgs=0 130/300: dt: 0.9000, rms radial error=154.215, avgs=0 135/300: dt: 0.9000, rms radial error=153.345, avgs=0 140/300: dt: 0.9000, rms radial error=152.481, avgs=0 145/300: dt: 0.9000, rms radial error=151.621, avgs=0 150/300: dt: 0.9000, rms radial error=150.766, avgs=0 155/300: dt: 0.9000, rms radial error=149.915, avgs=0 160/300: dt: 0.9000, rms radial error=149.070, avgs=0 165/300: dt: 0.9000, rms radial error=148.229, avgs=0 170/300: dt: 0.9000, rms radial error=147.393, avgs=0 175/300: dt: 0.9000, rms radial error=146.561, avgs=0 180/300: dt: 0.9000, rms radial error=145.734, avgs=0 185/300: dt: 0.9000, rms radial error=144.914, avgs=0 190/300: dt: 0.9000, rms radial error=144.097, avgs=0 195/300: dt: 0.9000, rms radial error=143.286, avgs=0 200/300: dt: 0.9000, rms radial error=142.478, avgs=0 205/300: dt: 0.9000, rms radial error=141.675, avgs=0 210/300: dt: 0.9000, rms radial error=140.876, avgs=0 215/300: dt: 0.9000, rms radial error=140.082, avgs=0 220/300: dt: 0.9000, rms radial error=139.292, avgs=0 225/300: dt: 0.9000, rms radial error=138.507, avgs=0 230/300: dt: 0.9000, rms radial error=137.725, avgs=0 235/300: dt: 0.9000, rms radial error=136.949, avgs=0 240/300: dt: 0.9000, rms radial error=136.176, avgs=0 245/300: dt: 0.9000, rms radial error=135.408, avgs=0 250/300: dt: 0.9000, rms radial error=134.644, avgs=0 255/300: dt: 0.9000, rms radial error=133.884, avgs=0 260/300: dt: 0.9000, rms radial error=133.129, avgs=0 265/300: dt: 0.9000, rms radial error=132.377, avgs=0 270/300: dt: 0.9000, rms radial error=131.630, avgs=0 275/300: dt: 0.9000, rms radial error=130.888, avgs=0 280/300: dt: 0.9000, rms radial error=130.149, avgs=0 285/300: dt: 0.9000, rms radial error=129.415, avgs=0 290/300: dt: 0.9000, rms radial error=128.685, avgs=0 295/300: dt: 0.9000, rms radial error=127.959, avgs=0 300/300: dt: 0.9000, rms radial error=127.237, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 21970.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3984.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 497.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00344 epoch 4 (K=640.0), pass 1, starting sse = 53.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00398 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:42:45 BST 2012 New invocation of recon-all Mon Jul 23 17:42:45 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -qsphere #-------------------------------------------- #@# QSphere rh Mon Jul 23 17:42:45 BST 2012 /home/clare/subjects/subject_20/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.87 +- 0.54 (0.00-->8.24) (max @ vno 115941 --> 115942) face area 0.02 +- 0.03 (-0.19-->0.70) scaling brain by 0.283... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.647, avgs=0 005/300: dt: 0.9000, rms radial error=176.388, avgs=0 010/300: dt: 0.9000, rms radial error=175.833, avgs=0 015/300: dt: 0.9000, rms radial error=175.104, avgs=0 020/300: dt: 0.9000, rms radial error=174.275, avgs=0 025/300: dt: 0.9000, rms radial error=173.388, avgs=0 030/300: dt: 0.9000, rms radial error=172.469, avgs=0 035/300: dt: 0.9000, rms radial error=171.533, avgs=0 040/300: dt: 0.9000, rms radial error=170.589, avgs=0 045/300: dt: 0.9000, rms radial error=169.642, avgs=0 050/300: dt: 0.9000, rms radial error=168.695, avgs=0 055/300: dt: 0.9000, rms radial error=167.751, avgs=0 060/300: dt: 0.9000, rms radial error=166.809, avgs=0 065/300: dt: 0.9000, rms radial error=165.872, avgs=0 070/300: dt: 0.9000, rms radial error=164.940, avgs=0 075/300: dt: 0.9000, rms radial error=164.012, avgs=0 080/300: dt: 0.9000, rms radial error=163.089, avgs=0 085/300: dt: 0.9000, rms radial error=162.171, avgs=0 090/300: dt: 0.9000, rms radial error=161.258, avgs=0 095/300: dt: 0.9000, rms radial error=160.350, avgs=0 100/300: dt: 0.9000, rms radial error=159.447, avgs=0 105/300: dt: 0.9000, rms radial error=158.549, avgs=0 110/300: dt: 0.9000, rms radial error=157.656, avgs=0 115/300: dt: 0.9000, rms radial error=156.767, avgs=0 120/300: dt: 0.9000, rms radial error=155.883, avgs=0 125/300: dt: 0.9000, rms radial error=155.005, avgs=0 130/300: dt: 0.9000, rms radial error=154.131, avgs=0 135/300: dt: 0.9000, rms radial error=153.262, avgs=0 140/300: dt: 0.9000, rms radial error=152.397, avgs=0 145/300: dt: 0.9000, rms radial error=151.538, avgs=0 150/300: dt: 0.9000, rms radial error=150.683, avgs=0 155/300: dt: 0.9000, rms radial error=149.833, avgs=0 160/300: dt: 0.9000, rms radial error=148.987, avgs=0 165/300: dt: 0.9000, rms radial error=148.146, avgs=0 170/300: dt: 0.9000, rms radial error=147.310, avgs=0 175/300: dt: 0.9000, rms radial error=146.479, avgs=0 180/300: dt: 0.9000, rms radial error=145.654, avgs=0 185/300: dt: 0.9000, rms radial error=144.833, avgs=0 190/300: dt: 0.9000, rms radial error=144.017, avgs=0 195/300: dt: 0.9000, rms radial error=143.206, avgs=0 200/300: dt: 0.9000, rms radial error=142.399, avgs=0 205/300: dt: 0.9000, rms radial error=141.596, avgs=0 210/300: dt: 0.9000, rms radial error=140.797, avgs=0 215/300: dt: 0.9000, rms radial error=140.004, avgs=0 220/300: dt: 0.9000, rms radial error=139.214, avgs=0 225/300: dt: 0.9000, rms radial error=138.429, avgs=0 230/300: dt: 0.9000, rms radial error=137.649, avgs=0 235/300: dt: 0.9000, rms radial error=136.872, avgs=0 240/300: dt: 0.9000, rms radial error=136.100, avgs=0 245/300: dt: 0.9000, rms radial error=135.333, avgs=0 250/300: dt: 0.9000, rms radial error=134.569, avgs=0 255/300: dt: 0.9000, rms radial error=133.810, avgs=0 260/300: dt: 0.9000, rms radial error=133.055, avgs=0 265/300: dt: 0.9000, rms radial error=132.301, avgs=0 270/300: dt: 0.9000, rms radial error=131.558, avgs=0 275/300: dt: 0.9000, rms radial error=130.812, avgs=0 280/300: dt: 0.9000, rms radial error=130.077, avgs=0 285/300: dt: 0.9000, rms radial error=129.342, avgs=0 290/300: dt: 0.9000, rms radial error=128.611, avgs=0 295/300: dt: 0.9000, rms radial error=127.886, avgs=0 300/300: dt: 0.9000, rms radial error=127.164, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 21746.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3918.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 472.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00357 epoch 4 (K=640.0), pass 1, starting sse = 45.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00516 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 17:46:36 BST 2012 New invocation of recon-all Mon Jul 23 17:46:36 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -fix #-------------------------------------------- #@# Fix Topology lh Mon Jul 23 17:46:36 BST 2012 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/clare/subjects/subject_20/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject_20 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-350 (nv=181044, nf=362788, ne=544182, g=176) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 24490 ambiguous faces found in tessellation segmenting defects... 162 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 8 -merging segment 43 into 29 -merging segment 41 into 38 -merging segment 42 into 38 -merging segment 88 into 86 -merging segment 97 into 89 -merging segment 101 into 90 -merging segment 114 into 90 -merging segment 125 into 105 -merging segment 113 into 109 -merging segment 124 into 117 -merging segment 128 into 117 -merging segment 142 into 131 -merging segment 140 into 132 148 defects to be corrected 0 vertices coincident reading input surface /home/clare/subjects/subject_20/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0411 (-4.5205) -vertex loglikelihood: -5.7456 (-2.8728) -normal dot loglikelihood: -3.5615 (-3.5615) -quad curv loglikelihood: -6.3891 (-3.1946) Total Loglikelihood : -24.7374 CORRECTING DEFECT 0 (vertices=430, convex hull=223) After retessellation of defect 0, euler #=-151 (166401,493752,327200) : difference with theory (-145) = 6 CORRECTING DEFECT 1 (vertices=61, convex hull=110) After retessellation of defect 1, euler #=-150 (166426,493872,327296) : difference with theory (-144) = 6 CORRECTING DEFECT 2 (vertices=11, convex hull=33) After retessellation of defect 2, euler #=-149 (166428,493891,327314) : difference with theory (-143) = 6 CORRECTING DEFECT 3 (vertices=7, convex hull=22) After retessellation of defect 3, euler #=-148 (166429,493901,327324) : difference with theory (-142) = 6 CORRECTING DEFECT 4 (vertices=20, convex hull=19) After retessellation of defect 4, euler #=-147 (166429,493909,327333) : difference with theory (-141) = 6 CORRECTING DEFECT 5 (vertices=46, convex hull=63) After retessellation of defect 5, euler #=-146 (166448,493992,327398) : difference with theory (-140) = 6 CORRECTING DEFECT 6 (vertices=143, convex hull=25) After retessellation of defect 6, euler #=-145 (166453,494017,327419) : difference with theory (-139) = 6 CORRECTING DEFECT 7 (vertices=45, convex hull=77) After retessellation of defect 7, euler #=-144 (166473,494105,327488) : difference with theory (-138) = 6 CORRECTING DEFECT 8 (vertices=696, convex hull=254) After retessellation of defect 8, euler #=-142 (166540,494430,327748) : difference with theory (-137) = 5 CORRECTING DEFECT 9 (vertices=41, convex hull=60) After retessellation of defect 9, euler #=-141 (166557,494510,327812) : difference with theory (-136) = 5 CORRECTING DEFECT 10 (vertices=49, convex hull=36) After retessellation of defect 10, euler #=-140 (166562,494545,327843) : difference with theory (-135) = 5 CORRECTING DEFECT 11 (vertices=139, convex hull=36) After retessellation of defect 11, euler #=-139 (166568,494573,327866) : difference with theory (-134) = 5 CORRECTING DEFECT 12 (vertices=124, convex hull=56) After retessellation of defect 12, euler #=-138 (166577,494621,327906) : difference with theory (-133) = 5 CORRECTING DEFECT 13 (vertices=99, convex hull=33) After retessellation of defect 13, euler #=-137 (166583,494652,327932) : difference with theory (-132) = 5 CORRECTING DEFECT 14 (vertices=327, convex hull=282) After retessellation of defect 14, euler #=-136 (166686,495099,328277) : difference with theory (-131) = 5 CORRECTING DEFECT 15 (vertices=41, convex hull=81) After retessellation of defect 15, euler #=-135 (166697,495162,328330) : difference with theory (-130) = 5 CORRECTING DEFECT 16 (vertices=39, convex hull=68) After retessellation of defect 16, euler #=-134 (166715,495243,328394) : difference with theory (-129) = 5 CORRECTING DEFECT 17 (vertices=39, convex hull=72) After retessellation of defect 17, euler #=-133 (166731,495318,328454) : difference with theory (-128) = 5 CORRECTING DEFECT 18 (vertices=28, convex hull=64) After retessellation of defect 18, euler #=-132 (166748,495396,328516) : difference with theory (-127) = 5 CORRECTING DEFECT 19 (vertices=289, convex hull=135) After retessellation of defect 19, euler #=-131 (166796,495610,328683) : difference with theory (-126) = 5 CORRECTING DEFECT 20 (vertices=35, convex hull=44) After retessellation of defect 20, euler #=-130 (166802,495644,328712) : difference with theory (-125) = 5 CORRECTING DEFECT 21 (vertices=91, convex hull=150) After retessellation of defect 21, euler #=-129 (166842,495838,328867) : difference with theory (-124) = 5 CORRECTING DEFECT 22 (vertices=28, convex hull=69) After retessellation of defect 22, euler #=-128 (166858,495906,328920) : difference with theory (-123) = 5 CORRECTING DEFECT 23 (vertices=111, convex hull=88) After retessellation of defect 23, euler #=-127 (166877,496004,329000) : difference with theory (-122) = 5 CORRECTING DEFECT 24 (vertices=240, convex hull=46) After retessellation of defect 24, euler #=-126 (166896,496083,329061) : difference with theory (-121) = 5 CORRECTING DEFECT 25 (vertices=8, convex hull=21) After retessellation of defect 25, euler #=-125 (166897,496093,329071) : difference with theory (-120) = 5 CORRECTING DEFECT 26 (vertices=69, convex hull=119) After retessellation of defect 26, euler #=-124 (166931,496251,329196) : difference with theory (-119) = 5 CORRECTING DEFECT 27 (vertices=221, convex hull=46) After retessellation of defect 27, euler #=-123 (166950,496330,329257) : difference with theory (-118) = 5 CORRECTING DEFECT 28 (vertices=860, convex hull=618) After retessellation of defect 28, euler #=-121 (167041,496913,329751) : difference with theory (-117) = 4 CORRECTING DEFECT 29 (vertices=262, convex hull=279) After retessellation of defect 29, euler #=-120 (167170,497433,330143) : difference with theory (-116) = 4 CORRECTING DEFECT 30 (vertices=17, convex hull=25) After retessellation of defect 30, euler #=-119 (167171,497441,330151) : difference with theory (-115) = 4 CORRECTING DEFECT 31 (vertices=39, convex hull=73) After retessellation of defect 31, euler #=-118 (167195,497547,330234) : difference with theory (-114) = 4 CORRECTING DEFECT 32 (vertices=70, convex hull=74) After retessellation of defect 32, euler #=-117 (167215,497636,330304) : difference with theory (-113) = 4 CORRECTING DEFECT 33 (vertices=11, convex hull=38) After retessellation of defect 33, euler #=-116 (167220,497664,330328) : difference with theory (-112) = 4 CORRECTING DEFECT 34 (vertices=8, convex hull=29) After retessellation of defect 34, euler #=-115 (167222,497680,330343) : difference with theory (-111) = 4 CORRECTING DEFECT 35 (vertices=27, convex hull=58) After retessellation of defect 35, euler #=-114 (167237,497748,330397) : difference with theory (-110) = 4 CORRECTING DEFECT 36 (vertices=117, convex hull=128) After retessellation of defect 36, euler #=-113 (167273,497911,330525) : difference with theory (-109) = 4 CORRECTING DEFECT 37 (vertices=355, convex hull=265) After retessellation of defect 37, euler #=-110 (167300,498138,330728) : difference with theory (-108) = 2 CORRECTING DEFECT 38 (vertices=88, convex hull=126) After retessellation of defect 38, euler #=-109 (167350,498340,330881) : difference with theory (-107) = 2 CORRECTING DEFECT 39 (vertices=94, convex hull=109) After retessellation of defect 39, euler #=-108 (167375,498466,330983) : difference with theory (-106) = 2 CORRECTING DEFECT 40 (vertices=20, convex hull=28) After retessellation of defect 40, euler #=-107 (167379,498486,331000) : difference with theory (-105) = 2 CORRECTING DEFECT 41 (vertices=29, convex hull=70) After retessellation of defect 41, euler #=-106 (167395,498559,331058) : difference with theory (-104) = 2 CORRECTING DEFECT 42 (vertices=51, convex hull=63) After retessellation of defect 42, euler #=-105 (167426,498677,331146) : difference with theory (-103) = 2 CORRECTING DEFECT 43 (vertices=31, convex hull=26) After retessellation of defect 43, euler #=-104 (167432,498704,331168) : difference with theory (-102) = 2 CORRECTING DEFECT 44 (vertices=23, convex hull=31) After retessellation of defect 44, euler #=-103 (167433,498718,331182) : difference with theory (-101) = 2 CORRECTING DEFECT 45 (vertices=307, convex hull=43) After retessellation of defect 45, euler #=-103 (167437,498747,331207) : difference with theory (-100) = 3 CORRECTING DEFECT 46 (vertices=57, convex hull=84) After retessellation of defect 46, euler #=-103 (167479,498915,331333) : difference with theory (-99) = 4 CORRECTING DEFECT 47 (vertices=6, convex hull=21) After retessellation of defect 47, euler #=-102 (167480,498925,331343) : difference with theory (-98) = 4 CORRECTING DEFECT 48 (vertices=334, convex hull=160) After retessellation of defect 48, euler #=-101 (167508,499085,331476) : difference with theory (-97) = 4 CORRECTING DEFECT 49 (vertices=43, convex hull=75) After retessellation of defect 49, euler #=-100 (167536,499197,331561) : difference with theory (-96) = 4 CORRECTING DEFECT 50 (vertices=24, convex hull=57) After retessellation of defect 50, euler #=-99 (167545,499246,331602) : difference with theory (-95) = 4 CORRECTING DEFECT 51 (vertices=27, convex hull=18) After retessellation of defect 51, euler #=-98 (167546,499252,331608) : difference with theory (-94) = 4 CORRECTING DEFECT 52 (vertices=31, convex hull=75) After retessellation of defect 52, euler #=-97 (167562,499334,331675) : difference with theory (-93) = 4 CORRECTING DEFECT 53 (vertices=49, convex hull=69) After retessellation of defect 53, euler #=-96 (167582,499420,331742) : difference with theory (-92) = 4 CORRECTING DEFECT 54 (vertices=128, convex hull=100) After retessellation of defect 54, euler #=-95 (167629,499607,331883) : difference with theory (-91) = 4 CORRECTING DEFECT 55 (vertices=30, convex hull=58) After retessellation of defect 55, euler #=-94 (167644,499678,331940) : difference with theory (-90) = 4 CORRECTING DEFECT 56 (vertices=132, convex hull=136) After retessellation of defect 56, euler #=-93 (167677,499840,332070) : difference with theory (-89) = 4 CORRECTING DEFECT 57 (vertices=26, convex hull=22) After retessellation of defect 57, euler #=-92 (167680,499854,332082) : difference with theory (-88) = 4 CORRECTING DEFECT 58 (vertices=96, convex hull=113) After retessellation of defect 58, euler #=-91 (167720,500028,332217) : difference with theory (-87) = 4 CORRECTING DEFECT 59 (vertices=52, convex hull=77) After retessellation of defect 59, euler #=-90 (167738,500109,332281) : difference with theory (-86) = 4 CORRECTING DEFECT 60 (vertices=90, convex hull=94) After retessellation of defect 60, euler #=-89 (167749,500187,332349) : difference with theory (-85) = 4 CORRECTING DEFECT 61 (vertices=34, convex hull=70) After retessellation of defect 61, euler #=-88 (167769,500276,332419) : difference with theory (-84) = 4 CORRECTING DEFECT 62 (vertices=45, convex hull=74) After retessellation of defect 62, euler #=-87 (167800,500402,332515) : difference with theory (-83) = 4 CORRECTING DEFECT 63 (vertices=25, convex hull=51) After retessellation of defect 63, euler #=-86 (167809,500450,332555) : difference with theory (-82) = 4 CORRECTING DEFECT 64 (vertices=32, convex hull=57) After retessellation of defect 64, euler #=-85 (167821,500510,332604) : difference with theory (-81) = 4 CORRECTING DEFECT 65 (vertices=45, convex hull=78) After retessellation of defect 65, euler #=-84 (167847,500620,332689) : difference with theory (-80) = 4 CORRECTING DEFECT 66 (vertices=364, convex hull=125) normal vector of length zero at vertex 173624 with 3 faces After retessellation of defect 66, euler #=-84 (167880,500781,332817) : difference with theory (-79) = 5 CORRECTING DEFECT 67 (vertices=32, convex hull=26) After retessellation of defect 67, euler #=-83 (167885,500803,332835) : difference with theory (-78) = 5 CORRECTING DEFECT 68 (vertices=27, convex hull=50) After retessellation of defect 68, euler #=-82 (167894,500849,332873) : difference with theory (-77) = 5 CORRECTING DEFECT 69 (vertices=67, convex hull=75) After retessellation of defect 69, euler #=-81 (167926,500973,332966) : difference with theory (-76) = 5 CORRECTING DEFECT 70 (vertices=30, convex hull=46) After retessellation of defect 70, euler #=-80 (167944,501047,333023) : difference with theory (-75) = 5 CORRECTING DEFECT 71 (vertices=55, convex hull=78) After retessellation of defect 71, euler #=-79 (167973,501166,333114) : difference with theory (-74) = 5 CORRECTING DEFECT 72 (vertices=87, convex hull=68) After retessellation of defect 72, euler #=-78 (167995,501269,333196) : difference with theory (-73) = 5 CORRECTING DEFECT 73 (vertices=56, convex hull=53) After retessellation of defect 73, euler #=-77 (168009,501331,333245) : difference with theory (-72) = 5 CORRECTING DEFECT 74 (vertices=79, convex hull=99) After retessellation of defect 74, euler #=-77 (168046,501490,333367) : difference with theory (-71) = 6 CORRECTING DEFECT 75 (vertices=33, convex hull=81) After retessellation of defect 75, euler #=-76 (168063,501570,333431) : difference with theory (-70) = 6 CORRECTING DEFECT 76 (vertices=128, convex hull=70) After retessellation of defect 76, euler #=-76 (168089,501682,333517) : difference with theory (-69) = 7 CORRECTING DEFECT 77 (vertices=41, convex hull=105) After retessellation of defect 77, euler #=-75 (168118,501810,333617) : difference with theory (-68) = 7 CORRECTING DEFECT 78 (vertices=17, convex hull=26) After retessellation of defect 78, euler #=-74 (168123,501830,333633) : difference with theory (-67) = 7 CORRECTING DEFECT 79 (vertices=32, convex hull=85) After retessellation of defect 79, euler #=-73 (168132,501895,333690) : difference with theory (-66) = 7 CORRECTING DEFECT 80 (vertices=10, convex hull=29) After retessellation of defect 80, euler #=-72 (168135,501912,333705) : difference with theory (-65) = 7 CORRECTING DEFECT 81 (vertices=6, convex hull=19) After retessellation of defect 81, euler #=-71 (168136,501920,333713) : difference with theory (-64) = 7 CORRECTING DEFECT 82 (vertices=383, convex hull=179) After retessellation of defect 82, euler #=-70 (168176,502134,333888) : difference with theory (-63) = 7 CORRECTING DEFECT 83 (vertices=51, convex hull=70) After retessellation of defect 83, euler #=-69 (168186,502194,333939) : difference with theory (-62) = 7 CORRECTING DEFECT 84 (vertices=222, convex hull=210) After retessellation of defect 84, euler #=-67 (168210,502368,334091) : difference with theory (-61) = 6 CORRECTING DEFECT 85 (vertices=304, convex hull=214) After retessellation of defect 85, euler #=-64 (168339,502855,334452) : difference with theory (-60) = 4 CORRECTING DEFECT 86 (vertices=42, convex hull=87) After retessellation of defect 86, euler #=-63 (168361,502957,334533) : difference with theory (-59) = 4 CORRECTING DEFECT 87 (vertices=13, convex hull=15) After retessellation of defect 87, euler #=-62 (168361,502961,334538) : difference with theory (-58) = 4 CORRECTING DEFECT 88 (vertices=8, convex hull=22) After retessellation of defect 88, euler #=-61 (168363,502973,334549) : difference with theory (-57) = 4 CORRECTING DEFECT 89 (vertices=78, convex hull=109) After retessellation of defect 89, euler #=-60 (168374,503057,334623) : difference with theory (-56) = 4 CORRECTING DEFECT 90 (vertices=21, convex hull=44) After retessellation of defect 90, euler #=-59 (168384,503103,334660) : difference with theory (-55) = 4 CORRECTING DEFECT 91 (vertices=30, convex hull=67) After retessellation of defect 91, euler #=-58 (168393,503155,334704) : difference with theory (-54) = 4 CORRECTING DEFECT 92 (vertices=218, convex hull=227) After retessellation of defect 92, euler #=-57 (168414,503327,334856) : difference with theory (-53) = 4 CORRECTING DEFECT 93 (vertices=297, convex hull=186) After retessellation of defect 93, euler #=-56 (168527,503762,335179) : difference with theory (-52) = 4 CORRECTING DEFECT 94 (vertices=53, convex hull=32) After retessellation of defect 94, euler #=-55 (168532,503787,335200) : difference with theory (-51) = 4 CORRECTING DEFECT 95 (vertices=21, convex hull=28) After retessellation of defect 95, euler #=-54 (168536,503808,335218) : difference with theory (-50) = 4 CORRECTING DEFECT 96 (vertices=8, convex hull=23) After retessellation of defect 96, euler #=-53 (168539,503824,335232) : difference with theory (-49) = 4 CORRECTING DEFECT 97 (vertices=59, convex hull=59) After retessellation of defect 97, euler #=-52 (168551,503885,335282) : difference with theory (-48) = 4 CORRECTING DEFECT 98 (vertices=341, convex hull=104) After retessellation of defect 98, euler #=-50 (168594,504064,335420) : difference with theory (-47) = 3 CORRECTING DEFECT 99 (vertices=6, convex hull=20) After retessellation of defect 99, euler #=-49 (168596,504075,335430) : difference with theory (-46) = 3 CORRECTING DEFECT 100 (vertices=17, convex hull=65) After retessellation of defect 100, euler #=-48 (168605,504129,335476) : difference with theory (-45) = 3 CORRECTING DEFECT 101 (vertices=97, convex hull=65) After retessellation of defect 101, euler #=-47 (168617,504197,335533) : difference with theory (-44) = 3 CORRECTING DEFECT 102 (vertices=68, convex hull=77) After retessellation of defect 102, euler #=-45 (168650,504330,335635) : difference with theory (-43) = 2 CORRECTING DEFECT 103 (vertices=25, convex hull=75) After retessellation of defect 103, euler #=-44 (168661,504394,335689) : difference with theory (-42) = 2 CORRECTING DEFECT 104 (vertices=55, convex hull=33) After retessellation of defect 104, euler #=-43 (168670,504429,335716) : difference with theory (-41) = 2 CORRECTING DEFECT 105 (vertices=83, convex hull=72) After retessellation of defect 105, euler #=-42 (168692,504523,335789) : difference with theory (-40) = 2 CORRECTING DEFECT 106 (vertices=40, convex hull=64) After retessellation of defect 106, euler #=-41 (168714,504611,335856) : difference with theory (-39) = 2 CORRECTING DEFECT 107 (vertices=22, convex hull=62) After retessellation of defect 107, euler #=-40 (168725,504668,335903) : difference with theory (-38) = 2 CORRECTING DEFECT 108 (vertices=65, convex hull=137) After retessellation of defect 108, euler #=-37 (168758,504824,336029) : difference with theory (-37) = 0 CORRECTING DEFECT 109 (vertices=29, convex hull=49) After retessellation of defect 109, euler #=-36 (168771,504880,336073) : difference with theory (-36) = 0 CORRECTING DEFECT 110 (vertices=113, convex hull=129) After retessellation of defect 110, euler #=-35 (168819,505085,336231) : difference with theory (-35) = 0 CORRECTING DEFECT 111 (vertices=56, convex hull=70) After retessellation of defect 111, euler #=-34 (168839,505174,336301) : difference with theory (-34) = 0 CORRECTING DEFECT 112 (vertices=31, convex hull=57) After retessellation of defect 112, euler #=-33 (168853,505238,336352) : difference with theory (-33) = 0 CORRECTING DEFECT 113 (vertices=78, convex hull=83) After retessellation of defect 113, euler #=-32 (168878,505349,336439) : difference with theory (-32) = 0 CORRECTING DEFECT 114 (vertices=34, convex hull=65) After retessellation of defect 114, euler #=-31 (168893,505419,336495) : difference with theory (-31) = 0 CORRECTING DEFECT 115 (vertices=87, convex hull=76) After retessellation of defect 115, euler #=-30 (168905,505487,336552) : difference with theory (-30) = 0 CORRECTING DEFECT 116 (vertices=395, convex hull=229) After retessellation of defect 116, euler #=-29 (168964,505779,336786) : difference with theory (-29) = 0 CORRECTING DEFECT 117 (vertices=53, convex hull=87) After retessellation of defect 117, euler #=-28 (168985,505879,336866) : difference with theory (-28) = 0 CORRECTING DEFECT 118 (vertices=24, convex hull=62) After retessellation of defect 118, euler #=-27 (169000,505945,336918) : difference with theory (-27) = 0 CORRECTING DEFECT 119 (vertices=960, convex hull=391) After retessellation of defect 119, euler #=-25 (169231,506856,337600) : difference with theory (-26) = -1 CORRECTING DEFECT 120 (vertices=56, convex hull=73) After retessellation of defect 120, euler #=-23 (169260,506976,337693) : difference with theory (-25) = -2 CORRECTING DEFECT 121 (vertices=19, convex hull=52) After retessellation of defect 121, euler #=-22 (169272,507032,337738) : difference with theory (-24) = -2 CORRECTING DEFECT 122 (vertices=6, convex hull=15) After retessellation of defect 122, euler #=-21 (169273,507039,337745) : difference with theory (-23) = -2 CORRECTING DEFECT 123 (vertices=132, convex hull=124) After retessellation of defect 123, euler #=-20 (169307,507203,337876) : difference with theory (-22) = -2 CORRECTING DEFECT 124 (vertices=86, convex hull=86) After retessellation of defect 124, euler #=-19 (169334,507321,337968) : difference with theory (-21) = -2 CORRECTING DEFECT 125 (vertices=276, convex hull=145) After retessellation of defect 125, euler #=-18 (169375,507512,338119) : difference with theory (-20) = -2 CORRECTING DEFECT 126 (vertices=73, convex hull=63) After retessellation of defect 126, euler #=-17 (169388,507575,338170) : difference with theory (-19) = -2 CORRECTING DEFECT 127 (vertices=87, convex hull=73) After retessellation of defect 127, euler #=-16 (169408,507665,338241) : difference with theory (-18) = -2 CORRECTING DEFECT 128 (vertices=141, convex hull=85) After retessellation of defect 128, euler #=-15 (169426,507752,338311) : difference with theory (-17) = -2 CORRECTING DEFECT 129 (vertices=38, convex hull=40) After retessellation of defect 129, euler #=-14 (169430,507774,338330) : difference with theory (-16) = -2 CORRECTING DEFECT 130 (vertices=19, convex hull=39) After retessellation of defect 130, euler #=-13 (169440,507816,338363) : difference with theory (-15) = -2 CORRECTING DEFECT 131 (vertices=79, convex hull=39) After retessellation of defect 131, euler #=-13 (169448,507857,338396) : difference with theory (-14) = -1 CORRECTING DEFECT 132 (vertices=53, convex hull=41) After retessellation of defect 132, euler #=-12 (169457,507900,338431) : difference with theory (-13) = -1 CORRECTING DEFECT 133 (vertices=21, convex hull=52) After retessellation of defect 133, euler #=-11 (169467,507947,338469) : difference with theory (-12) = -1 CORRECTING DEFECT 134 (vertices=32, convex hull=82) After retessellation of defect 134, euler #=-10 (169487,508042,338545) : difference with theory (-11) = -1 CORRECTING DEFECT 135 (vertices=16, convex hull=35) After retessellation of defect 135, euler #=-9 (169488,508059,338562) : difference with theory (-10) = -1 CORRECTING DEFECT 136 (vertices=19, convex hull=48) After retessellation of defect 136, euler #=-8 (169499,508110,338603) : difference with theory (-9) = -1 CORRECTING DEFECT 137 (vertices=15, convex hull=24) After retessellation of defect 137, euler #=-7 (169504,508136,338625) : difference with theory (-8) = -1 CORRECTING DEFECT 138 (vertices=45, convex hull=62) After retessellation of defect 138, euler #=-6 (169525,508226,338695) : difference with theory (-7) = -1 CORRECTING DEFECT 139 (vertices=12, convex hull=24) After retessellation of defect 139, euler #=-5 (169526,508237,338706) : difference with theory (-6) = -1 CORRECTING DEFECT 140 (vertices=444, convex hull=275) After retessellation of defect 140, euler #=-4 (169601,508600,338995) : difference with theory (-5) = -1 CORRECTING DEFECT 141 (vertices=66, convex hull=83) After retessellation of defect 141, euler #=-3 (169627,508712,339082) : difference with theory (-4) = -1 CORRECTING DEFECT 142 (vertices=34, convex hull=84) After retessellation of defect 142, euler #=-2 (169639,508781,339140) : difference with theory (-3) = -1 CORRECTING DEFECT 143 (vertices=65, convex hull=32) After retessellation of defect 143, euler #=-2 (169641,508800,339157) : difference with theory (-2) = 0 CORRECTING DEFECT 144 (vertices=29, convex hull=65) After retessellation of defect 144, euler #=-1 (169652,508858,339205) : difference with theory (-1) = 0 CORRECTING DEFECT 145 (vertices=27, convex hull=68) After retessellation of defect 145, euler #=0 (169663,508914,339251) : difference with theory (0) = 0 CORRECTING DEFECT 146 (vertices=53, convex hull=95) After retessellation of defect 146, euler #=1 (169699,509065,339367) : difference with theory (1) = 0 CORRECTING DEFECT 147 (vertices=31, convex hull=61) After retessellation of defect 147, euler #=2 (169714,509136,339424) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.30 (0.04-->13.68) (max @ vno 43170 --> 47873) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.30 (0.04-->13.68) (max @ vno 43170 --> 47873) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 442 mutations (32.1%), 933 crossovers (67.9%), 1236 vertices were eliminated building final representation... 11330 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=169714, nf=339424, ne=509136, g=0) writing corrected surface to /home/clare/subjects/subject_20/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 112.1 minutes 0 defective edges removing intersecting faces 000: 1343 intersecting 001: 44 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 169714 - 509136 + 339424 = 2 --> 0 holes F =2V-4: 339424 = 339428-4 (0) 2E=3F: 1018272 = 1018272 (0) total defect index = 0 /home/clare/subjects/subject_20/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 166 intersecting 001: 13 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 19:38:48 BST 2012 New invocation of recon-all Mon Jul 23 19:38:49 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -fix #-------------------------------------------- #@# Fix Topology rh Mon Jul 23 19:38:49 BST 2012 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /home/clare/subjects/subject_20/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 subject_20 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-322 (nv=179654, nf=359952, ne=539928, g=162) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 16857 ambiguous faces found in tessellation segmenting defects... 151 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 17 into 14 -merging segment 28 into 29 -merging segment 74 into 70 -merging segment 80 into 73 -merging segment 93 into 77 -merging segment 87 into 83 -merging segment 120 into 110 -merging segment 113 into 111 143 defects to be corrected 0 vertices coincident reading input surface /home/clare/subjects/subject_20/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6961 (-4.3480) -vertex loglikelihood: -5.7149 (-2.8575) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.3095 (-3.1547) Total Loglikelihood : -24.2233 CORRECTING DEFECT 0 (vertices=24, convex hull=60) After retessellation of defect 0, euler #=-147 (169171,502740,333422) : difference with theory (-140) = 7 CORRECTING DEFECT 1 (vertices=115, convex hull=144) After retessellation of defect 1, euler #=-146 (169223,502965,333596) : difference with theory (-139) = 7 CORRECTING DEFECT 2 (vertices=18, convex hull=48) After retessellation of defect 2, euler #=-145 (169231,503007,333631) : difference with theory (-138) = 7 CORRECTING DEFECT 3 (vertices=202, convex hull=199) After retessellation of defect 3, euler #=-144 (169287,503283,333852) : difference with theory (-137) = 7 CORRECTING DEFECT 4 (vertices=5, convex hull=26) After retessellation of defect 4, euler #=-143 (169288,503292,333861) : difference with theory (-136) = 7 CORRECTING DEFECT 5 (vertices=24, convex hull=17) After retessellation of defect 5, euler #=-142 (169290,503303,333871) : difference with theory (-135) = 7 CORRECTING DEFECT 6 (vertices=83, convex hull=153) After retessellation of defect 6, euler #=-141 (169327,503487,334019) : difference with theory (-134) = 7 CORRECTING DEFECT 7 (vertices=124, convex hull=146) After retessellation of defect 7, euler #=-140 (169376,503694,334178) : difference with theory (-133) = 7 CORRECTING DEFECT 8 (vertices=25, convex hull=27) After retessellation of defect 8, euler #=-139 (169378,503714,334197) : difference with theory (-132) = 7 CORRECTING DEFECT 9 (vertices=44, convex hull=83) After retessellation of defect 9, euler #=-138 (169389,503777,334250) : difference with theory (-131) = 7 CORRECTING DEFECT 10 (vertices=8, convex hull=12) After retessellation of defect 10, euler #=-137 (169389,503778,334252) : difference with theory (-130) = 7 CORRECTING DEFECT 11 (vertices=63, convex hull=101) After retessellation of defect 11, euler #=-136 (169412,503896,334348) : difference with theory (-129) = 7 CORRECTING DEFECT 12 (vertices=81, convex hull=97) After retessellation of defect 12, euler #=-135 (169438,504016,334443) : difference with theory (-128) = 7 CORRECTING DEFECT 13 (vertices=7, convex hull=30) After retessellation of defect 13, euler #=-134 (169440,504030,334456) : difference with theory (-127) = 7 CORRECTING DEFECT 14 (vertices=163, convex hull=177) After retessellation of defect 14, euler #=-132 (169503,504302,334667) : difference with theory (-126) = 6 CORRECTING DEFECT 15 (vertices=44, convex hull=78) After retessellation of defect 15, euler #=-131 (169521,504387,334735) : difference with theory (-125) = 6 CORRECTING DEFECT 16 (vertices=91, convex hull=47) After retessellation of defect 16, euler #=-130 (169529,504426,334767) : difference with theory (-124) = 6 CORRECTING DEFECT 17 (vertices=6, convex hull=20) After retessellation of defect 17, euler #=-129 (169530,504436,334777) : difference with theory (-123) = 6 CORRECTING DEFECT 18 (vertices=47, convex hull=95) After retessellation of defect 18, euler #=-128 (169553,504547,334866) : difference with theory (-122) = 6 CORRECTING DEFECT 19 (vertices=49, convex hull=103) After retessellation of defect 19, euler #=-127 (169583,504682,334972) : difference with theory (-121) = 6 CORRECTING DEFECT 20 (vertices=259, convex hull=192) After retessellation of defect 20, euler #=-126 (169623,504892,335143) : difference with theory (-120) = 6 CORRECTING DEFECT 21 (vertices=16, convex hull=52) Warning - incorrect dp selected!!!!(-68.155796 >= -68.155797 ) After retessellation of defect 21, euler #=-125 (169631,504931,335175) : difference with theory (-119) = 6 CORRECTING DEFECT 22 (vertices=109, convex hull=57) After retessellation of defect 22, euler #=-124 (169642,504986,335220) : difference with theory (-118) = 6 CORRECTING DEFECT 23 (vertices=28, convex hull=58) After retessellation of defect 23, euler #=-123 (169651,505031,335257) : difference with theory (-117) = 6 CORRECTING DEFECT 24 (vertices=70, convex hull=107) After retessellation of defect 24, euler #=-122 (169694,505205,335389) : difference with theory (-116) = 6 CORRECTING DEFECT 25 (vertices=31, convex hull=75) After retessellation of defect 25, euler #=-121 (169712,505288,335455) : difference with theory (-115) = 6 CORRECTING DEFECT 26 (vertices=26, convex hull=60) After retessellation of defect 26, euler #=-120 (169726,505351,335505) : difference with theory (-114) = 6 CORRECTING DEFECT 27 (vertices=64, convex hull=99) After retessellation of defect 27, euler #=-118 (169748,505457,335591) : difference with theory (-113) = 5 CORRECTING DEFECT 28 (vertices=83, convex hull=60) After retessellation of defect 28, euler #=-117 (169762,505522,335643) : difference with theory (-112) = 5 CORRECTING DEFECT 29 (vertices=188, convex hull=123) After retessellation of defect 29, euler #=-116 (169802,505694,335776) : difference with theory (-111) = 5 CORRECTING DEFECT 30 (vertices=47, convex hull=71) After retessellation of defect 30, euler #=-115 (169831,505811,335865) : difference with theory (-110) = 5 CORRECTING DEFECT 31 (vertices=98, convex hull=75) After retessellation of defect 31, euler #=-114 (169854,505915,335947) : difference with theory (-109) = 5 CORRECTING DEFECT 32 (vertices=22, convex hull=18) After retessellation of defect 32, euler #=-113 (169856,505929,335960) : difference with theory (-108) = 5 CORRECTING DEFECT 33 (vertices=314, convex hull=182) After retessellation of defect 33, euler #=-112 (169907,506169,336150) : difference with theory (-107) = 5 CORRECTING DEFECT 34 (vertices=124, convex hull=171) After retessellation of defect 34, euler #=-111 (169965,506423,336347) : difference with theory (-106) = 5 CORRECTING DEFECT 35 (vertices=114, convex hull=100) After retessellation of defect 35, euler #=-110 (170007,506597,336480) : difference with theory (-105) = 5 CORRECTING DEFECT 36 (vertices=25, convex hull=18) After retessellation of defect 36, euler #=-109 (170007,506600,336484) : difference with theory (-104) = 5 CORRECTING DEFECT 37 (vertices=11, convex hull=16) After retessellation of defect 37, euler #=-108 (170010,506613,336495) : difference with theory (-103) = 5 CORRECTING DEFECT 38 (vertices=38, convex hull=44) After retessellation of defect 38, euler #=-107 (170019,506657,336531) : difference with theory (-102) = 5 CORRECTING DEFECT 39 (vertices=85, convex hull=130) After retessellation of defect 39, euler #=-106 (170046,506799,336647) : difference with theory (-101) = 5 CORRECTING DEFECT 40 (vertices=20, convex hull=50) After retessellation of defect 40, euler #=-105 (170059,506858,336694) : difference with theory (-100) = 5 CORRECTING DEFECT 41 (vertices=33, convex hull=69) After retessellation of defect 41, euler #=-104 (170070,506918,336744) : difference with theory (-99) = 5 CORRECTING DEFECT 42 (vertices=84, convex hull=86) After retessellation of defect 42, euler #=-103 (170090,507017,336824) : difference with theory (-98) = 5 CORRECTING DEFECT 43 (vertices=115, convex hull=171) After retessellation of defect 43, euler #=-102 (170163,507311,337046) : difference with theory (-97) = 5 CORRECTING DEFECT 44 (vertices=22, convex hull=52) After retessellation of defect 44, euler #=-101 (170172,507354,337081) : difference with theory (-96) = 5 CORRECTING DEFECT 45 (vertices=299, convex hull=201) After retessellation of defect 45, euler #=-100 (170188,507497,337209) : difference with theory (-95) = 5 CORRECTING DEFECT 46 (vertices=25, convex hull=27) After retessellation of defect 46, euler #=-99 (170190,507511,337222) : difference with theory (-94) = 5 CORRECTING DEFECT 47 (vertices=355, convex hull=98) After retessellation of defect 47, euler #=-98 (170205,507600,337297) : difference with theory (-93) = 5 CORRECTING DEFECT 48 (vertices=697, convex hull=349) After retessellation of defect 48, euler #=-98 (170324,508153,337731) : difference with theory (-92) = 6 CORRECTING DEFECT 49 (vertices=24, convex hull=47) After retessellation of defect 49, euler #=-97 (170333,508194,337764) : difference with theory (-91) = 6 CORRECTING DEFECT 50 (vertices=26, convex hull=69) After retessellation of defect 50, euler #=-96 (170348,508264,337820) : difference with theory (-90) = 6 CORRECTING DEFECT 51 (vertices=18, convex hull=61) After retessellation of defect 51, euler #=-95 (170361,508325,337869) : difference with theory (-89) = 6 CORRECTING DEFECT 52 (vertices=34, convex hull=67) After retessellation of defect 52, euler #=-94 (170373,508390,337923) : difference with theory (-88) = 6 CORRECTING DEFECT 53 (vertices=39, convex hull=66) After retessellation of defect 53, euler #=-93 (170387,508459,337979) : difference with theory (-87) = 6 CORRECTING DEFECT 54 (vertices=19, convex hull=23) After retessellation of defect 54, euler #=-92 (170390,508475,337993) : difference with theory (-86) = 6 CORRECTING DEFECT 55 (vertices=33, convex hull=56) After retessellation of defect 55, euler #=-91 (170403,508536,338042) : difference with theory (-85) = 6 CORRECTING DEFECT 56 (vertices=71, convex hull=78) After retessellation of defect 56, euler #=-90 (170428,508649,338131) : difference with theory (-84) = 6 CORRECTING DEFECT 57 (vertices=26, convex hull=49) After retessellation of defect 57, euler #=-89 (170437,508695,338169) : difference with theory (-83) = 6 CORRECTING DEFECT 58 (vertices=33, convex hull=56) After retessellation of defect 58, euler #=-88 (170459,508783,338236) : difference with theory (-82) = 6 CORRECTING DEFECT 59 (vertices=42, convex hull=79) After retessellation of defect 59, euler #=-87 (170480,508877,338310) : difference with theory (-81) = 6 CORRECTING DEFECT 60 (vertices=40, convex hull=73) After retessellation of defect 60, euler #=-86 (170506,508981,338389) : difference with theory (-80) = 6 CORRECTING DEFECT 61 (vertices=6, convex hull=19) After retessellation of defect 61, euler #=-85 (170507,508991,338399) : difference with theory (-79) = 6 CORRECTING DEFECT 62 (vertices=109, convex hull=97) After retessellation of defect 62, euler #=-84 (170544,509148,338520) : difference with theory (-78) = 6 CORRECTING DEFECT 63 (vertices=109, convex hull=126) After retessellation of defect 63, euler #=-83 (170558,509253,338612) : difference with theory (-77) = 6 CORRECTING DEFECT 64 (vertices=29, convex hull=27) After retessellation of defect 64, euler #=-82 (170564,509278,338632) : difference with theory (-76) = 6 CORRECTING DEFECT 65 (vertices=45, convex hull=68) After retessellation of defect 65, euler #=-81 (170574,509338,338683) : difference with theory (-75) = 6 CORRECTING DEFECT 66 (vertices=21, convex hull=21) After retessellation of defect 66, euler #=-80 (170576,509352,338696) : difference with theory (-74) = 6 CORRECTING DEFECT 67 (vertices=45, convex hull=69) After retessellation of defect 67, euler #=-79 (170595,509439,338765) : difference with theory (-73) = 6 CORRECTING DEFECT 68 (vertices=244, convex hull=94) After retessellation of defect 68, euler #=-77 (170607,509520,338836) : difference with theory (-72) = 5 CORRECTING DEFECT 69 (vertices=18, convex hull=21) After retessellation of defect 69, euler #=-76 (170608,509529,338845) : difference with theory (-71) = 5 CORRECTING DEFECT 70 (vertices=32, convex hull=20) After retessellation of defect 70, euler #=-75 (170613,509551,338863) : difference with theory (-70) = 5 CORRECTING DEFECT 71 (vertices=136, convex hull=154) After retessellation of defect 71, euler #=-73 (170679,509815,339063) : difference with theory (-69) = 4 CORRECTING DEFECT 72 (vertices=38, convex hull=61) After retessellation of defect 72, euler #=-72 (170695,509886,339119) : difference with theory (-68) = 4 CORRECTING DEFECT 73 (vertices=28, convex hull=74) After retessellation of defect 73, euler #=-71 (170711,509961,339179) : difference with theory (-67) = 4 CORRECTING DEFECT 74 (vertices=325, convex hull=383) After retessellation of defect 74, euler #=-69 (170885,510684,339730) : difference with theory (-66) = 3 CORRECTING DEFECT 75 (vertices=112, convex hull=111) After retessellation of defect 75, euler #=-68 (170894,510762,339800) : difference with theory (-65) = 3 CORRECTING DEFECT 76 (vertices=20, convex hull=60) After retessellation of defect 76, euler #=-67 (170903,510811,339841) : difference with theory (-64) = 3 CORRECTING DEFECT 77 (vertices=382, convex hull=305) After retessellation of defect 77, euler #=-66 (171050,511406,340290) : difference with theory (-63) = 3 CORRECTING DEFECT 78 (vertices=5, convex hull=32) After retessellation of defect 78, euler #=-65 (171052,511422,340305) : difference with theory (-62) = 3 CORRECTING DEFECT 79 (vertices=444, convex hull=260) After retessellation of defect 79, euler #=-63 (171144,511840,340633) : difference with theory (-61) = 2 CORRECTING DEFECT 80 (vertices=39, convex hull=86) After retessellation of defect 80, euler #=-62 (171155,511907,340690) : difference with theory (-60) = 2 CORRECTING DEFECT 81 (vertices=39, convex hull=85) After retessellation of defect 81, euler #=-61 (171169,511982,340752) : difference with theory (-59) = 2 CORRECTING DEFECT 82 (vertices=23, convex hull=29) After retessellation of defect 82, euler #=-60 (171172,511999,340767) : difference with theory (-58) = 2 CORRECTING DEFECT 83 (vertices=23, convex hull=61) After retessellation of defect 83, euler #=-59 (171185,512056,340812) : difference with theory (-57) = 2 CORRECTING DEFECT 84 (vertices=133, convex hull=130) After retessellation of defect 84, euler #=-58 (171208,512189,340923) : difference with theory (-56) = 2 CORRECTING DEFECT 85 (vertices=6, convex hull=14) After retessellation of defect 85, euler #=-57 (171208,512191,340926) : difference with theory (-55) = 2 CORRECTING DEFECT 86 (vertices=12, convex hull=36) After retessellation of defect 86, euler #=-56 (171211,512212,340945) : difference with theory (-54) = 2 CORRECTING DEFECT 87 (vertices=721, convex hull=327) After retessellation of defect 87, euler #=-55 (171368,512842,341419) : difference with theory (-53) = 2 CORRECTING DEFECT 88 (vertices=64, convex hull=31) After retessellation of defect 88, euler #=-54 (171373,512869,341442) : difference with theory (-52) = 2 CORRECTING DEFECT 89 (vertices=89, convex hull=121) After retessellation of defect 89, euler #=-53 (171399,513004,341552) : difference with theory (-51) = 2 CORRECTING DEFECT 90 (vertices=46, convex hull=86) After retessellation of defect 90, euler #=-52 (171417,513095,341626) : difference with theory (-50) = 2 CORRECTING DEFECT 91 (vertices=25, convex hull=25) After retessellation of defect 91, euler #=-51 (171423,513119,341645) : difference with theory (-49) = 2 CORRECTING DEFECT 92 (vertices=6, convex hull=20) After retessellation of defect 92, euler #=-50 (171424,513129,341655) : difference with theory (-48) = 2 CORRECTING DEFECT 93 (vertices=11, convex hull=25) After retessellation of defect 93, euler #=-49 (171428,513149,341672) : difference with theory (-47) = 2 CORRECTING DEFECT 94 (vertices=19, convex hull=45) After retessellation of defect 94, euler #=-48 (171437,513191,341706) : difference with theory (-46) = 2 CORRECTING DEFECT 95 (vertices=14, convex hull=26) After retessellation of defect 95, euler #=-47 (171441,513214,341726) : difference with theory (-45) = 2 CORRECTING DEFECT 96 (vertices=25, convex hull=37) After retessellation of defect 96, euler #=-46 (171444,513233,341743) : difference with theory (-44) = 2 CORRECTING DEFECT 97 (vertices=54, convex hull=79) After retessellation of defect 97, euler #=-45 (171459,513311,341807) : difference with theory (-43) = 2 CORRECTING DEFECT 98 (vertices=63, convex hull=32) After retessellation of defect 98, euler #=-44 (171467,513345,341834) : difference with theory (-42) = 2 CORRECTING DEFECT 99 (vertices=36, convex hull=62) After retessellation of defect 99, euler #=-43 (171490,513443,341910) : difference with theory (-41) = 2 CORRECTING DEFECT 100 (vertices=5, convex hull=21) After retessellation of defect 100, euler #=-42 (171492,513454,341920) : difference with theory (-40) = 2 CORRECTING DEFECT 101 (vertices=9, convex hull=16) After retessellation of defect 101, euler #=-41 (171493,513461,341927) : difference with theory (-39) = 2 CORRECTING DEFECT 102 (vertices=27, convex hull=66) After retessellation of defect 102, euler #=-40 (171505,513522,341977) : difference with theory (-38) = 2 CORRECTING DEFECT 103 (vertices=6, convex hull=21) After retessellation of defect 103, euler #=-39 (171506,513531,341986) : difference with theory (-37) = 2 CORRECTING DEFECT 104 (vertices=96, convex hull=143) After retessellation of defect 104, euler #=-37 (171539,513691,342115) : difference with theory (-36) = 1 CORRECTING DEFECT 105 (vertices=60, convex hull=65) After retessellation of defect 105, euler #=-35 (171559,513777,342183) : difference with theory (-35) = 0 CORRECTING DEFECT 106 (vertices=49, convex hull=58) After retessellation of defect 106, euler #=-34 (171576,513855,342245) : difference with theory (-34) = 0 CORRECTING DEFECT 107 (vertices=24, convex hull=50) After retessellation of defect 107, euler #=-33 (171585,513902,342284) : difference with theory (-33) = 0 CORRECTING DEFECT 108 (vertices=30, convex hull=26) Warning - incorrect dp selected!!!!(-64.894102 >= -64.894103 ) After retessellation of defect 108, euler #=-32 (171588,513919,342299) : difference with theory (-32) = 0 CORRECTING DEFECT 109 (vertices=12, convex hull=29) After retessellation of defect 109, euler #=-31 (171590,513935,342314) : difference with theory (-31) = 0 CORRECTING DEFECT 110 (vertices=26, convex hull=31) After retessellation of defect 110, euler #=-30 (171595,513961,342336) : difference with theory (-30) = 0 CORRECTING DEFECT 111 (vertices=205, convex hull=87) After retessellation of defect 111, euler #=-29 (171614,514058,342415) : difference with theory (-29) = 0 CORRECTING DEFECT 112 (vertices=67, convex hull=88) After retessellation of defect 112, euler #=-28 (171648,514203,342527) : difference with theory (-28) = 0 CORRECTING DEFECT 113 (vertices=30, convex hull=60) After retessellation of defect 113, euler #=-27 (171663,514275,342585) : difference with theory (-27) = 0 CORRECTING DEFECT 114 (vertices=129, convex hull=75) After retessellation of defect 114, euler #=-26 (171695,514404,342683) : difference with theory (-26) = 0 CORRECTING DEFECT 115 (vertices=51, convex hull=69) After retessellation of defect 115, euler #=-25 (171708,514472,342739) : difference with theory (-25) = 0 CORRECTING DEFECT 116 (vertices=19, convex hull=48) After retessellation of defect 116, euler #=-24 (171716,514515,342775) : difference with theory (-24) = 0 CORRECTING DEFECT 117 (vertices=43, convex hull=80) After retessellation of defect 117, euler #=-23 (171745,514639,342871) : difference with theory (-23) = 0 CORRECTING DEFECT 118 (vertices=21, convex hull=59) After retessellation of defect 118, euler #=-22 (171754,514690,342914) : difference with theory (-22) = 0 CORRECTING DEFECT 119 (vertices=38, convex hull=59) After retessellation of defect 119, euler #=-21 (171763,514743,342959) : difference with theory (-21) = 0 CORRECTING DEFECT 120 (vertices=28, convex hull=67) After retessellation of defect 120, euler #=-20 (171773,514800,343007) : difference with theory (-20) = 0 CORRECTING DEFECT 121 (vertices=38, convex hull=75) After retessellation of defect 121, euler #=-19 (171793,514892,343080) : difference with theory (-19) = 0 CORRECTING DEFECT 122 (vertices=38, convex hull=65) After retessellation of defect 122, euler #=-18 (171813,514979,343148) : difference with theory (-18) = 0 CORRECTING DEFECT 123 (vertices=36, convex hull=40) After retessellation of defect 123, euler #=-17 (171819,515013,343177) : difference with theory (-17) = 0 CORRECTING DEFECT 124 (vertices=32, convex hull=64) After retessellation of defect 124, euler #=-16 (171837,515093,343240) : difference with theory (-16) = 0 CORRECTING DEFECT 125 (vertices=28, convex hull=25) After retessellation of defect 125, euler #=-15 (171842,515115,343258) : difference with theory (-15) = 0 CORRECTING DEFECT 126 (vertices=29, convex hull=76) After retessellation of defect 126, euler #=-14 (171860,515200,343326) : difference with theory (-14) = 0 CORRECTING DEFECT 127 (vertices=42, convex hull=66) After retessellation of defect 127, euler #=-13 (171869,515254,343372) : difference with theory (-13) = 0 CORRECTING DEFECT 128 (vertices=39, convex hull=59) After retessellation of defect 128, euler #=-12 (171884,515321,343425) : difference with theory (-12) = 0 CORRECTING DEFECT 129 (vertices=38, convex hull=65) After retessellation of defect 129, euler #=-11 (171899,515391,343481) : difference with theory (-11) = 0 CORRECTING DEFECT 130 (vertices=56, convex hull=41) After retessellation of defect 130, euler #=-10 (171902,515415,343503) : difference with theory (-10) = 0 CORRECTING DEFECT 131 (vertices=53, convex hull=77) After retessellation of defect 131, euler #=-9 (171914,515489,343566) : difference with theory (-9) = 0 CORRECTING DEFECT 132 (vertices=39, convex hull=30) After retessellation of defect 132, euler #=-8 (171917,515506,343581) : difference with theory (-8) = 0 CORRECTING DEFECT 133 (vertices=23, convex hull=68) After retessellation of defect 133, euler #=-7 (171927,515561,343627) : difference with theory (-7) = 0 CORRECTING DEFECT 134 (vertices=50, convex hull=68) After retessellation of defect 134, euler #=-6 (171936,515616,343674) : difference with theory (-6) = 0 CORRECTING DEFECT 135 (vertices=38, convex hull=83) After retessellation of defect 135, euler #=-5 (171952,515700,343743) : difference with theory (-5) = 0 CORRECTING DEFECT 136 (vertices=31, convex hull=26) After retessellation of defect 136, euler #=-4 (171954,515712,343754) : difference with theory (-4) = 0 CORRECTING DEFECT 137 (vertices=28, convex hull=23) After retessellation of defect 137, euler #=-3 (171955,515721,343763) : difference with theory (-3) = 0 CORRECTING DEFECT 138 (vertices=45, convex hull=78) After retessellation of defect 138, euler #=-2 (171978,515817,343837) : difference with theory (-2) = 0 CORRECTING DEFECT 139 (vertices=40, convex hull=61) After retessellation of defect 139, euler #=-1 (171991,515881,343889) : difference with theory (-1) = 0 CORRECTING DEFECT 140 (vertices=36, convex hull=70) After retessellation of defect 140, euler #=0 (172000,515940,343940) : difference with theory (0) = 0 CORRECTING DEFECT 141 (vertices=107, convex hull=99) After retessellation of defect 141, euler #=1 (172013,516023,344011) : difference with theory (1) = 0 CORRECTING DEFECT 142 (vertices=20, convex hull=31) After retessellation of defect 142, euler #=2 (172013,516033,344022) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.07-->10.58) (max @ vno 128573 --> 137581) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.07-->10.58) (max @ vno 128573 --> 137581) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 462 mutations (34.1%), 891 crossovers (65.9%), 764 vertices were eliminated building final representation... 7641 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=172013, nf=344022, ne=516033, g=0) writing corrected surface to /home/clare/subjects/subject_20/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 86.8 minutes 0 defective edges removing intersecting faces 000: 947 intersecting 001: 46 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 172013 - 516033 + 344022 = 2 --> 0 holes F =2V-4: 344022 = 344026-4 (0) 2E=3F: 1032066 = 1032066 (0) total defect index = 0 /home/clare/subjects/subject_20/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 94 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:05:44 BST 2012 New invocation of recon-all Mon Jul 23 21:05:44 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -white #-------------------------------------------- #@# Make White Surf lh Mon Jul 23 21:05:44 BST 2012 /home/clare/subjects/subject_20/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs subject_20 lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /home/clare/subjects/subject_20/mri/filled.mgz... reading volume /home/clare/subjects/subject_20/mri/brain.finalsurfs.mgz... reading volume /home/clare/subjects/subject_20/mri/wm.mgz... 24707 bright wm thresholded. 6489 bright non-wm voxels segmented. reading original surface position from /home/clare/subjects/subject_20/surf/lh.orig... computing class statistics... border white: 366408 voxels (2.18%) border gray 384424 voxels (2.29%) WM (101.0): 101.1 +- 6.0 [70.0 --> 110.0] GM (91.0) : 89.2 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.7 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 62.4 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 79.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/clare/subjects/subject_20/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.24 (0.02-->5.94) (max @ vno 43170 --> 44312) face area 0.28 +- 0.14 (0.00-->6.56) mean absolute distance = 0.85 +- 1.07 4881 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=85 using class modes intead of means.... mean inside = 100.6, mean outside = 88.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=92.1, 213 (213) missing vertices, mean dist 0.3 [0.8 (%31.8)->0.9 (%68.2))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=clare, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.28 (0.07-->6.17) (max @ vno 43170 --> 44312) face area 0.28 +- 0.15 (0.00-->5.58) mean absolute distance = 0.50 +- 0.75 7335 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4778393.0, rms=6.84 001: dt: 0.5000, sse=6202551.5, rms=4.90 002: dt: 0.5000, sse=6464974.5, rms=3.72 003: dt: 0.5000, sse=6757829.0, rms=3.03 004: dt: 0.5000, sse=6878498.5, rms=2.64 005: dt: 0.5000, sse=6993255.5, rms=2.43 006: dt: 0.5000, sse=7035743.0, rms=2.31 007: dt: 0.5000, sse=7120135.5, rms=2.23 rms = 2.19, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=7157755.0, rms=2.19 009: dt: 0.2500, sse=5273778.0, rms=1.84 010: dt: 0.2500, sse=5092636.0, rms=1.78 rms = 1.77, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=5019073.0, rms=1.77 rms = 1.76, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=4978413.5, rms=1.76 positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.1, 156 (50) missing vertices, mean dist -0.3 [0.6 (%66.6)->0.3 (%33.4))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=clare, 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 0.88 +- 0.27 (0.06-->5.92) (max @ vno 43170 --> 44312) face area 0.33 +- 0.18 (0.00-->7.25) mean absolute distance = 0.38 +- 0.52 6869 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5353161.0, rms=3.32 013: dt: 0.5000, sse=5794343.5, rms=2.22 014: dt: 0.5000, sse=6377732.0, rms=1.89 rms = 1.85, time step reduction 1 of 3 to 0.250... 015: dt: 0.5000, sse=6341356.5, rms=1.85 016: dt: 0.2500, sse=5591537.0, rms=1.56 rms = 1.53, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=5408690.5, rms=1.53 rms = 1.51, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=5358833.5, rms=1.51 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=95.6, 164 (26) missing vertices, mean dist -0.2 [0.4 (%67.1)->0.3 (%32.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=clare, 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 0.87 +- 0.27 (0.06-->5.83) (max @ vno 43170 --> 44312) face area 0.32 +- 0.17 (0.00-->7.18) mean absolute distance = 0.30 +- 0.41 5778 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5486829.0, rms=2.64 019: dt: 0.5000, sse=5844946.5, rms=1.77 020: dt: 0.5000, sse=6533688.5, rms=1.61 rms = 1.67, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=5935804.5, rms=1.45 022: dt: 0.2500, sse=5632151.5, rms=1.38 rms = 1.38, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5588877.5, rms=1.38 rms = 1.37, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5550793.0, rms=1.37 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=96.1, 180 (16) missing vertices, mean dist -0.1 [0.3 (%55.9)->0.3 (%44.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=clare, 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 writing white matter surface to /home/clare/subjects/subject_20/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5564364.5, rms=1.60 025: dt: 0.5000, sse=7023869.5, rms=1.16 rms = 1.44, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=6513250.5, rms=1.09 rms = 1.12, time step reduction 2 of 3 to 0.125... rms = 1.09, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=6459854.0, rms=1.09 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 17 non-cortical segments detected only using segment with 2332 vertices erasing segment 1 (vno[0] = 59977) erasing segment 2 (vno[0] = 61151) erasing segment 3 (vno[0] = 101215) erasing segment 4 (vno[0] = 106342) erasing segment 5 (vno[0] = 112606) erasing segment 6 (vno[0] = 115004) erasing segment 7 (vno[0] = 115024) erasing segment 8 (vno[0] = 116233) erasing segment 9 (vno[0] = 119676) erasing segment 10 (vno[0] = 119711) erasing segment 11 (vno[0] = 120780) erasing segment 12 (vno[0] = 122846) erasing segment 13 (vno[0] = 128080) erasing segment 14 (vno[0] = 130109) erasing segment 15 (vno[0] = 168223) erasing segment 16 (vno[0] = 168646) writing cortex label to /home/clare/subjects/subject_20/label/lh.cortex.label... LabelWrite: saving to /home/clare/subjects/subject_20/label/lh.cortex.label writing curvature file /home/clare/subjects/subject_20/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/clare/subjects/subject_20/surf/lh.area vertex spacing 0.88 +- 0.27 (0.05-->5.86) (max @ vno 43170 --> 44312) face area 0.32 +- 0.17 (0.00-->7.17) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=74.2, 233 (233) missing vertices, mean dist 1.8 [0.9 (%0.0)->2.8 (%100.0))] %22 local maxima, %39 large gradients and %35 min vals, 2877 gradients ignored tol=1.0e-04, sigma=2.0, host=clare, 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=20260852.0, rms=22.91 001: dt: 0.5000, sse=16998156.0, rms=20.57 002: dt: 0.5000, sse=14335322.0, rms=18.46 003: dt: 0.5000, sse=12258637.0, rms=16.61 004: dt: 0.5000, sse=10783048.0, rms=15.02 005: dt: 0.5000, sse=9875497.0, rms=13.69 006: dt: 0.5000, sse=9338493.0, rms=12.56 007: dt: 0.5000, sse=9023683.0, rms=11.56 008: dt: 0.5000, sse=8785719.0, rms=10.63 009: dt: 0.5000, sse=8579005.0, rms=9.71 010: dt: 0.5000, sse=8400669.0, rms=8.79 011: dt: 0.5000, sse=8118566.0, rms=7.79 012: dt: 0.5000, sse=7997866.5, rms=6.80 013: dt: 0.5000, sse=7851627.5, rms=5.89 014: dt: 0.5000, sse=7935861.0, rms=5.24 015: dt: 0.5000, sse=7966941.5, rms=4.82 016: dt: 0.5000, sse=8088352.0, rms=4.59 017: dt: 0.5000, sse=8080166.0, rms=4.43 018: dt: 0.5000, sse=8144178.5, rms=4.34 019: dt: 0.5000, sse=8172537.5, rms=4.25 rms = 4.22, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=8184962.5, rms=4.22 021: dt: 0.2500, sse=5730115.5, rms=3.40 022: dt: 0.2500, sse=5547395.5, rms=3.19 rms = 3.17, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5395775.5, rms=3.17 024: dt: 0.1250, sse=5052248.0, rms=2.93 rms = 2.88, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5002784.0, rms=2.88 positioning took 2.7 minutes mean border=72.3, 1735 (63) missing vertices, mean dist 0.1 [0.2 (%42.3)->0.5 (%57.7))] %43 local maxima, %23 large gradients and %28 min vals, 1383 gradients ignored tol=1.0e-04, sigma=1.0, host=clare, 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=5653221.5, rms=4.48 026: dt: 0.5000, sse=6204301.0, rms=4.23 027: dt: 0.5000, sse=7580146.0, rms=4.17 rms = 4.28, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6315792.5, rms=3.38 029: dt: 0.2500, sse=5882006.0, rms=3.14 rms = 3.16, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=5752261.0, rms=3.02 031: dt: 0.1250, sse=5554493.5, rms=2.86 032: dt: 0.1250, sse=5504427.5, rms=2.81 rms = 2.79, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5473935.5, rms=2.79 positioning took 1.0 minutes mean border=71.4, 2282 (55) missing vertices, mean dist 0.1 [0.2 (%41.6)->0.3 (%58.4))] %54 local maxima, %12 large gradients and %28 min vals, 1428 gradients ignored tol=1.0e-04, sigma=0.5, host=clare, 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=5576025.5, rms=3.24 rms = 3.78, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5421109.5, rms=2.94 035: dt: 0.2500, sse=5525400.5, rms=2.84 rms = 2.86, time step reduction 2 of 3 to 0.125... rms = 2.79, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5473990.5, rms=2.79 positioning took 0.5 minutes mean border=71.0, 4610 (55) missing vertices, mean dist 0.0 [0.2 (%47.8)->0.3 (%52.2))] %55 local maxima, %11 large gradients and %27 min vals, 1248 gradients ignored tol=1.0e-04, sigma=0.2, host=clare, 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/clare/subjects/subject_20/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5489998.0, rms=2.90 rms = 3.46, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5427958.5, rms=2.73 038: dt: 0.2500, sse=5695925.5, rms=2.68 rms = 2.71, time step reduction 2 of 3 to 0.125... rms = 2.63, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5641151.0, rms=2.63 positioning took 0.5 minutes writing curvature file /home/clare/subjects/subject_20/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/clare/subjects/subject_20/surf/lh.area.pial vertex spacing 0.98 +- 0.44 (0.05-->7.20) (max @ vno 81286 --> 82733) face area 0.38 +- 0.31 (0.00-->7.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 169714 vertices processed 25000 of 169714 vertices processed 50000 of 169714 vertices processed 75000 of 169714 vertices processed 100000 of 169714 vertices processed 125000 of 169714 vertices processed 150000 of 169714 vertices processed 0 of 169714 vertices processed 25000 of 169714 vertices processed 50000 of 169714 vertices processed 75000 of 169714 vertices processed 100000 of 169714 vertices processed 125000 of 169714 vertices processed 150000 of 169714 vertices processed thickness calculation complete, 1463:1292 truncations. 64792 vertices at 0 distance 96463 vertices at 1 distance 87756 vertices at 2 distance 45308 vertices at 3 distance 18764 vertices at 4 distance 7137 vertices at 5 distance 2791 vertices at 6 distance 1220 vertices at 7 distance 711 vertices at 8 distance 393 vertices at 9 distance 217 vertices at 10 distance 162 vertices at 11 distance 133 vertices at 12 distance 98 vertices at 13 distance 89 vertices at 14 distance 60 vertices at 15 distance 36 vertices at 16 distance 39 vertices at 17 distance 27 vertices at 18 distance 24 vertices at 19 distance 24 vertices at 20 distance writing curvature file /home/clare/subjects/subject_20/surf/lh.thickness positioning took 11.5 minutes #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:17:12 BST 2012 New invocation of recon-all Mon Jul 23 21:17:12 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -white #-------------------------------------------- #@# Make White Surf rh Mon Jul 23 21:17:12 BST 2012 /home/clare/subjects/subject_20/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs subject_20 rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /home/clare/subjects/subject_20/mri/filled.mgz... reading volume /home/clare/subjects/subject_20/mri/brain.finalsurfs.mgz... reading volume /home/clare/subjects/subject_20/mri/wm.mgz... 23284 bright wm thresholded. 6486 bright non-wm voxels segmented. reading original surface position from /home/clare/subjects/subject_20/surf/rh.orig... computing class statistics... border white: 366408 voxels (2.18%) border gray 384424 voxels (2.29%) WM (101.0): 101.1 +- 5.9 [70.0 --> 110.0] GM (91.0) : 89.2 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.7 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 62.4 (was 40) setting MAX_GRAY to 100.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 79.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/clare/subjects/subject_20/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.24 (0.02-->4.63) (max @ vno 71474 --> 170232) face area 0.28 +- 0.13 (0.00-->3.63) mean absolute distance = 0.85 +- 1.09 5350 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=85 using class modes intead of means.... mean inside = 100.4, mean outside = 88.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=91.9, 181 (181) missing vertices, mean dist 0.3 [0.8 (%32.8)->0.8 (%67.2))] %61 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=clare, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.27 (0.05-->5.57) (max @ vno 171295 --> 121275) face area 0.28 +- 0.14 (0.00-->3.97) mean absolute distance = 0.49 +- 0.74 6365 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4824574.0, rms=6.73 001: dt: 0.5000, sse=6180500.5, rms=4.81 002: dt: 0.5000, sse=6444126.0, rms=3.66 003: dt: 0.5000, sse=6738948.0, rms=2.99 004: dt: 0.5000, sse=6876621.0, rms=2.60 005: dt: 0.5000, sse=7010420.0, rms=2.39 006: dt: 0.5000, sse=7053918.5, rms=2.26 007: dt: 0.5000, sse=7131980.5, rms=2.20 rms = 2.15, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=7166407.0, rms=2.15 009: dt: 0.2500, sse=5258155.0, rms=1.81 rms = 1.77, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=5081461.0, rms=1.77 rms = 1.76, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=5005777.0, rms=1.76 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.9, 101 (20) missing vertices, mean dist -0.3 [0.6 (%66.8)->0.3 (%33.2))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=clare, 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 0.87 +- 0.26 (0.06-->6.27) (max @ vno 60678 --> 60687) face area 0.33 +- 0.17 (0.00-->5.35) mean absolute distance = 0.37 +- 0.51 6227 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5368068.5, rms=3.27 012: dt: 0.5000, sse=5803903.0, rms=2.13 013: dt: 0.5000, sse=6370490.5, rms=1.83 rms = 1.78, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=6357126.5, rms=1.78 015: dt: 0.2500, sse=5607592.5, rms=1.52 rms = 1.49, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=5430587.0, rms=1.49 rms = 1.48, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=5362842.0, rms=1.48 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=95.4, 108 (10) missing vertices, mean dist -0.2 [0.4 (%67.3)->0.3 (%32.7))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=clare, 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 0.87 +- 0.26 (0.03-->6.52) (max @ vno 60678 --> 60687) face area 0.32 +- 0.17 (0.00-->5.54) mean absolute distance = 0.29 +- 0.40 5368 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5487763.5, rms=2.60 018: dt: 0.5000, sse=5910651.0, rms=1.72 019: dt: 0.5000, sse=6529936.5, rms=1.57 rms = 1.63, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=5954838.5, rms=1.42 021: dt: 0.2500, sse=5660814.5, rms=1.36 rms = 1.36, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5620666.5, rms=1.36 rms = 1.35, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5563122.5, rms=1.35 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=96.0, 148 (7) missing vertices, mean dist -0.1 [0.3 (%56.2)->0.2 (%43.8))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=clare, 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 writing white matter surface to /home/clare/subjects/subject_20/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5578021.5, rms=1.57 024: dt: 0.5000, sse=7039545.5, rms=1.13 rms = 1.40, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=6542378.5, rms=1.07 rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=6491681.0, rms=1.07 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 13 non-cortical segments detected only using segment with 2077 vertices erasing segment 1 (vno[0] = 113982) erasing segment 2 (vno[0] = 114032) erasing segment 3 (vno[0] = 118863) erasing segment 4 (vno[0] = 121127) erasing segment 5 (vno[0] = 121155) erasing segment 6 (vno[0] = 121188) erasing segment 7 (vno[0] = 124995) erasing segment 8 (vno[0] = 128525) erasing segment 9 (vno[0] = 129509) erasing segment 10 (vno[0] = 130461) erasing segment 11 (vno[0] = 130509) erasing segment 12 (vno[0] = 131276) writing cortex label to /home/clare/subjects/subject_20/label/rh.cortex.label... LabelWrite: saving to /home/clare/subjects/subject_20/label/rh.cortex.label writing curvature file /home/clare/subjects/subject_20/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/clare/subjects/subject_20/surf/rh.area vertex spacing 0.87 +- 0.26 (0.03-->6.62) (max @ vno 60678 --> 60687) face area 0.32 +- 0.17 (0.00-->5.54) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=74.2, 224 (224) missing vertices, mean dist 1.8 [0.9 (%0.1)->2.8 (%99.9))] %22 local maxima, %41 large gradients and %33 min vals, 2841 gradients ignored tol=1.0e-04, sigma=2.0, host=clare, 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=20206308.0, rms=22.62 001: dt: 0.5000, sse=16950430.0, rms=20.31 002: dt: 0.5000, sse=14353959.0, rms=18.27 003: dt: 0.5000, sse=12330980.0, rms=16.51 004: dt: 0.5000, sse=10903656.0, rms=14.99 005: dt: 0.5000, sse=9946260.0, rms=13.67 006: dt: 0.5000, sse=9342304.0, rms=12.53 007: dt: 0.5000, sse=8980877.0, rms=11.51 008: dt: 0.5000, sse=8802188.0, rms=10.59 009: dt: 0.5000, sse=8617149.0, rms=9.72 010: dt: 0.5000, sse=8450026.0, rms=8.85 011: dt: 0.5000, sse=8267906.5, rms=7.92 012: dt: 0.5000, sse=8099744.0, rms=6.98 013: dt: 0.5000, sse=7984556.0, rms=6.08 014: dt: 0.5000, sse=7975648.0, rms=5.40 015: dt: 0.5000, sse=8038995.5, rms=4.93 016: dt: 0.5000, sse=8134121.5, rms=4.64 017: dt: 0.5000, sse=8169526.5, rms=4.44 018: dt: 0.5000, sse=8205510.0, rms=4.34 019: dt: 0.5000, sse=8215001.0, rms=4.24 rms = 4.20, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=8217488.0, rms=4.20 021: dt: 0.2500, sse=5703502.5, rms=3.36 022: dt: 0.2500, sse=5498784.5, rms=3.13 rms = 3.11, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5353651.0, rms=3.11 024: dt: 0.1250, sse=5003972.5, rms=2.86 rms = 2.81, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4961619.0, rms=2.81 positioning took 2.6 minutes mean border=72.2, 1661 (31) missing vertices, mean dist 0.1 [0.2 (%41.1)->0.5 (%58.9))] %46 local maxima, %23 large gradients and %26 min vals, 1005 gradients ignored tol=1.0e-04, sigma=1.0, host=clare, 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=5677690.0, rms=4.60 026: dt: 0.5000, sse=6155203.5, rms=4.29 027: dt: 0.5000, sse=7589874.5, rms=4.18 rms = 4.29, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=6300382.5, rms=3.38 029: dt: 0.2500, sse=5827962.5, rms=3.10 rms = 3.10, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=5701427.5, rms=2.99 031: dt: 0.1250, sse=5511283.5, rms=2.82 032: dt: 0.1250, sse=5448056.0, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5434984.0, rms=2.74 positioning took 1.1 minutes mean border=71.2, 2261 (24) missing vertices, mean dist 0.1 [0.2 (%39.8)->0.3 (%60.2))] %58 local maxima, %12 large gradients and %26 min vals, 1162 gradients ignored tol=1.0e-04, sigma=0.5, host=clare, 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=5552311.5, rms=3.26 rms = 3.82, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=5374626.0, rms=2.91 035: dt: 0.2500, sse=5474530.5, rms=2.80 rms = 2.80, time step reduction 2 of 3 to 0.125... 036: dt: 0.1250, sse=5428506.5, rms=2.75 037: dt: 0.1250, sse=5420672.5, rms=2.67 rms = 2.63, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5435647.5, rms=2.63 positioning took 0.7 minutes mean border=70.7, 4489 (23) missing vertices, mean dist 0.0 [0.2 (%47.0)->0.3 (%53.0))] %58 local maxima, %11 large gradients and %25 min vals, 946 gradients ignored tol=1.0e-04, sigma=0.2, host=clare, 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/clare/subjects/subject_20/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5449090.5, rms=2.73 rms = 3.26, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5413482.5, rms=2.59 rms = 2.54, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=5686812.0, rms=2.54 041: dt: 0.1250, sse=5566505.5, rms=2.46 rms = 2.43, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5605754.0, rms=2.43 positioning took 0.5 minutes writing curvature file /home/clare/subjects/subject_20/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/clare/subjects/subject_20/surf/rh.area.pial vertex spacing 0.98 +- 0.44 (0.03-->8.21) (max @ vno 60678 --> 60687) face area 0.38 +- 0.31 (0.00-->8.74) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 172013 vertices processed 25000 of 172013 vertices processed 50000 of 172013 vertices processed 75000 of 172013 vertices processed 100000 of 172013 vertices processed 125000 of 172013 vertices processed 150000 of 172013 vertices processed 0 of 172013 vertices processed 25000 of 172013 vertices processed 50000 of 172013 vertices processed 75000 of 172013 vertices processed 100000 of 172013 vertices processed 125000 of 172013 vertices processed 150000 of 172013 vertices processed thickness calculation complete, 1636:1677 truncations. 69020 vertices at 0 distance 91782 vertices at 1 distance 88324 vertices at 2 distance 48170 vertices at 3 distance 20434 vertices at 4 distance 7729 vertices at 5 distance 3088 vertices at 6 distance 1330 vertices at 7 distance 633 vertices at 8 distance 387 vertices at 9 distance 233 vertices at 10 distance 202 vertices at 11 distance 153 vertices at 12 distance 122 vertices at 13 distance 88 vertices at 14 distance 57 vertices at 15 distance 45 vertices at 16 distance 46 vertices at 17 distance 42 vertices at 18 distance 53 vertices at 19 distance 64 vertices at 20 distance writing curvature file /home/clare/subjects/subject_20/surf/rh.thickness positioning took 11.2 minutes #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:28:21 BST 2012 New invocation of recon-all Mon Jul 23 21:28:22 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -smooth2 #-------------------------------------------- #@# Smooth2 lh Mon Jul 23 21:28:22 BST 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/clare/subjects/subject_20/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:28:26 BST 2012 New invocation of recon-all Mon Jul 23 21:28:26 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -smooth2 #-------------------------------------------- #@# Smooth2 rh Mon Jul 23 21:28:26 BST 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/clare/subjects/subject_20/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:28:30 BST 2012 New invocation of recon-all Mon Jul 23 21:28:30 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -inflate2 #-------------------------------------------- #@# Inflation2 lh Mon Jul 23 21:28:30 BST 2012 /home/clare/subjects/subject_20/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 50.5 mm, total surface area = 98863 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.084 (target=0.015) step 010: RMS=0.065 (target=0.015) step 015: RMS=0.053 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.038 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.020 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 428 vertices thresholded to be in k1 ~ [-0.22 0.31], k2 ~ [-0.11 0.07] total integrated curvature = 0.359*4pi (4.514) --> 1 handles ICI = 1.6, FI = 10.7, variation=184.144 189 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 191 vertices thresholded to be in [-0.13 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.022 done. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:30:33 BST 2012 New invocation of recon-all Mon Jul 23 21:30:33 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -inflate2 #-------------------------------------------- #@# Inflation2 rh Mon Jul 23 21:30:33 BST 2012 /home/clare/subjects/subject_20/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 99884 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.085 (target=0.015) step 010: RMS=0.064 (target=0.015) step 015: RMS=0.053 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 419 vertices thresholded to be in k1 ~ [-0.18 0.31], k2 ~ [-0.08 0.05] total integrated curvature = 0.478*4pi (6.006) --> 1 handles ICI = 1.5, FI = 10.8, variation=180.422 203 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 183 vertices thresholded to be in [-0.11 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.022 done. #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 21:32:37 BST 2012 New invocation of recon-all Mon Jul 23 21:32:37 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -sphere #-------------------------------------------- #@# Sphere lh Mon Jul 23 21:32:37 BST 2012 /home/clare/subjects/subject_20/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.00 hours scaling brain by 0.268... pass 1: epoch 1 of 3 starting distance error %20.60 pass 1: epoch 2 of 3 starting distance error %20.60 unfolding complete - removing small folds... starting distance error %20.53 removing remaining folds... final distance error %20.54 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 22:32:25 BST 2012 New invocation of recon-all Mon Jul 23 22:32:25 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -sphere #-------------------------------------------- #@# Sphere rh Mon Jul 23 22:32:25 BST 2012 /home/clare/subjects/subject_20/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.12 hours scaling brain by 0.270... pass 1: epoch 1 of 3 starting distance error %20.13 pass 1: epoch 2 of 3 starting distance error %20.06 unfolding complete - removing small folds... starting distance error %19.98 removing remaining folds... final distance error %20.00 expanding nbhd size to 1 #------------------------------------------ recon-all -s subject_20 finished without error at Mon Jul 23 23:39:24 BST 2012 New invocation of recon-all Mon Jul 23 23:39:24 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -surfreg #-------------------------------------------- #@# Surf Reg lh Mon Jul 23 23:39:24 BST 2012 /home/clare/subjects/subject_20/scripts mris_register -curv ../surf/lh.sphere /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /home/clare/freesurfer/freesurfer/average/lh.average.curvature.filled.buckner40.tif... singular matrix in quadratic form writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.599 curvature mean = 0.023, std = 0.929 curvature mean = 0.022, std = 0.845 curvature mean = -0.012, std = 0.940 curvature mean = 0.009, std = 0.934 curvature mean = -0.018, std = 0.950 curvature mean = 0.004, std = 0.969 curvature mean = -0.022, std = 0.950 curvature mean = 0.001, std = 0.985 curvature mean = -0.032, std = 0.379 curvature mean = 0.002, std = 0.066 curvature mean = 0.058, std = 0.245 curvature mean = 0.002, std = 0.078 curvature mean = 0.036, std = 0.380 curvature mean = 0.002, std = 0.083 curvature mean = 0.024, std = 0.490 curvature mean = 0.002, std = 0.086 curvature mean = 0.009, std = 0.596 #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:17:21 BST 2012 New invocation of recon-all Tue Jul 24 00:17:21 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -surfreg #-------------------------------------------- #@# Surf Reg rh Tue Jul 24 00:17:21 BST 2012 /home/clare/subjects/subject_20/scripts mris_register -curv ../surf/rh.sphere /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /home/clare/freesurfer/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.595 curvature mean = 0.036, std = 0.927 curvature mean = 0.025, std = 0.840 curvature mean = -0.003, std = 0.930 curvature mean = 0.008, std = 0.927 curvature mean = -0.010, std = 0.936 curvature mean = 0.004, std = 0.965 curvature mean = -0.013, std = 0.935 curvature mean = 0.001, std = 0.983 curvature mean = -0.030, std = 0.333 curvature mean = 0.005, std = 0.069 curvature mean = 0.065, std = 0.273 curvature mean = 0.005, std = 0.081 curvature mean = 0.043, std = 0.430 curvature mean = 0.005, std = 0.087 curvature mean = 0.026, std = 0.559 curvature mean = 0.005, std = 0.088 curvature mean = 0.009, std = 0.673 expanding nbhd size to 1 #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:02 BST 2012 New invocation of recon-all Tue Jul 24 00:49:02 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -jacobian_white #-------------------------------------------- #@# Jacobian white lh Tue Jul 24 00:49:02 BST 2012 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 #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:04 BST 2012 New invocation of recon-all Tue Jul 24 00:49:04 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Jul 24 00:49:04 BST 2012 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 #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:06 BST 2012 New invocation of recon-all Tue Jul 24 00:49:06 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -avgcurv #-------------------------------------------- #@# AvgCurv lh Tue Jul 24 00:49:06 BST 2012 /home/clare/subjects/subject_20/scripts mrisp_paint -a 5 /home/clare/freesurfer/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 /home/clare/freesurfer/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:08 BST 2012 New invocation of recon-all Tue Jul 24 00:49:08 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -avgcurv #-------------------------------------------- #@# AvgCurv rh Tue Jul 24 00:49:08 BST 2012 /home/clare/subjects/subject_20/scripts mrisp_paint -a 5 /home/clare/freesurfer/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 /home/clare/freesurfer/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:10 BST 2012 New invocation of recon-all Tue Jul 24 00:49:10 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortparc #----------------------------------------- #@# Cortical Parc lh Tue Jul 24 00:49:10 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 lh ../surf/lh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 1677 labels changed using aseg relabeling using gibbs priors... 000: 3546 changed, 169714 examined... 001: 839 changed, 15153 examined... 002: 216 changed, 4639 examined... 003: 76 changed, 1253 examined... 004: 35 changed, 467 examined... 005: 14 changed, 201 examined... 006: 2 changed, 60 examined... 007: 2 changed, 14 examined... 008: 2 changed, 13 examined... 009: 2 changed, 15 examined... 010: 0 changed, 10 examined... 297 labels changed using aseg 000: 153 total segments, 100 labels (452 vertices) changed 001: 54 total segments, 10 labels (23 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 57 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2102 vertices marked for relabeling... 2102 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 44 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:49:54 BST 2012 New invocation of recon-all Tue Jul 24 00:49:54 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -cortparc #----------------------------------------- #@# Cortical Parc rh Tue Jul 24 00:49:54 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 rh ../surf/rh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 1309 labels changed using aseg relabeling using gibbs priors... 000: 3488 changed, 172013 examined... 001: 797 changed, 14880 examined... 002: 182 changed, 4365 examined... 003: 61 changed, 1115 examined... 004: 18 changed, 356 examined... 005: 8 changed, 113 examined... 006: 1 changed, 53 examined... 007: 4 changed, 9 examined... 008: 0 changed, 17 examined... 165 labels changed using aseg 000: 120 total segments, 78 labels (509 vertices) changed 001: 42 total segments, 1 labels (6 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1943 vertices marked for relabeling... 1943 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 44 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:50:38 BST 2012 New invocation of recon-all Tue Jul 24 00:50:38 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -parcstats #----------------------------------------- #@# Parcellation Stats lh Tue Jul 24 00:50:38 BST 2012 /home/clare/subjects/subject_20/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 subject_20 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/lh.white... reading input pial surface /home/clare/subjects/subject_20/surf/lh.pial... reading input white surface /home/clare/subjects/subject_20/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 2073 1429 3838 2.778 0.555 0.110 0.029 14 2.5 bankssts 1821 1115 3881 3.057 0.906 0.158 0.070 35 5.2 caudalanteriorcingulate 4164 2481 7242 2.676 0.510 0.152 0.176 448 23.6 caudalmiddlefrontal 2578 1602 2806 1.691 0.489 0.171 0.086 56 10.3 cuneus 687 466 2117 3.320 0.926 0.227 0.256 34 9.0 entorhinal 5272 3501 11231 2.780 0.777 0.192 0.140 208 32.1 fusiform 8268 5298 16096 2.698 0.577 0.148 0.110 200 46.4 inferiorparietal 6149 3966 14516 2.987 0.769 0.155 0.077 145 18.8 inferiortemporal 1907 1164 3326 2.666 0.861 0.164 0.101 48 7.8 isthmuscingulate 10072 6164 15147 2.238 0.682 0.171 0.128 457 69.6 lateraloccipital 4449 2911 9297 2.826 0.792 0.180 0.116 130 22.9 lateralorbitofrontal 5381 3483 7500 2.023 0.572 0.200 0.131 191 31.6 lingual 3588 2314 7402 2.761 0.900 0.171 0.106 144 16.4 medialorbitofrontal 6447 4308 16430 3.037 0.680 0.154 0.070 128 19.9 middletemporal 1298 841 3321 3.278 0.800 0.181 0.266 84 5.9 parahippocampal 2771 1704 3798 2.161 0.633 0.164 0.140 184 16.4 paracentral 2597 1735 5657 2.872 0.560 0.135 0.061 45 7.1 parsopercularis 1123 778 2985 3.097 0.597 0.159 0.082 23 3.0 parsorbitalis 2224 1457 4971 2.901 0.609 0.140 0.058 34 5.5 parstriangularis 1792 1265 1748 1.493 0.372 0.198 0.125 157 9.9 pericalcarine 9470 5860 12477 2.000 0.721 0.153 0.094 280 38.4 postcentral 2482 1614 5224 2.890 0.865 0.172 0.091 63 8.8 posteriorcingulate 11747 7252 16403 2.201 0.728 0.162 0.114 435 54.3 precentral 6552 4262 11851 2.510 0.619 0.176 0.146 309 37.9 precuneus 1585 1004 3723 3.457 0.585 0.159 0.078 43 5.0 rostralanteriorcingulate 11701 7699 24144 2.725 0.591 0.153 0.068 268 33.8 rostralmiddlefrontal 12560 7926 26082 2.953 0.642 0.154 0.089 406 49.9 superiorfrontal 9898 6367 17262 2.407 0.640 0.166 0.148 629 49.2 superiorparietal 6472 4344 16306 3.197 0.700 0.151 0.067 113 17.8 superiortemporal 7460 4991 14199 2.604 0.559 0.163 0.126 268 51.6 supramarginal 333 207 963 3.274 0.616 0.175 0.089 8 1.2 frontalpole 881 624 2924 3.432 0.915 0.247 0.162 53 6.1 temporalpole 862 476 1059 2.127 0.593 0.168 0.199 71 5.3 transversetemporal 3863 2466 8219 3.310 0.850 0.157 0.127 86 16.8 insula #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:50:53 BST 2012 New invocation of recon-all Tue Jul 24 00:50:53 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -parcstats #----------------------------------------- #@# Parcellation Stats rh Tue Jul 24 00:50:53 BST 2012 /home/clare/subjects/subject_20/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 subject_20 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/rh.white... reading input pial surface /home/clare/subjects/subject_20/surf/rh.pial... reading input white surface /home/clare/subjects/subject_20/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 1577 1122 2908 2.606 0.368 0.113 0.029 12 1.9 bankssts 1484 962 3238 2.823 0.806 0.158 0.072 27 3.9 caudalanteriorcingulate 3773 2373 7014 2.618 0.524 0.150 0.115 244 17.7 caudalmiddlefrontal 2851 1723 3103 1.717 0.462 0.163 0.092 81 10.0 cuneus 675 435 2110 3.813 0.733 0.221 0.249 202 5.6 entorhinal 5415 3599 11889 2.824 0.789 0.183 0.117 178 27.4 fusiform 10744 7197 22186 2.727 0.619 0.143 0.064 198 28.8 inferiorparietal 6225 4078 14920 3.037 0.784 0.157 0.087 165 21.6 inferiortemporal 1522 905 2540 2.575 0.755 0.156 0.133 68 5.7 isthmuscingulate 10071 6069 15121 2.244 0.670 0.180 0.136 390 56.7 lateraloccipital 4836 3094 10149 2.882 0.839 0.188 0.258 255 29.4 lateralorbitofrontal 5454 3559 8486 2.164 0.680 0.207 0.242 388 64.8 lingual 3133 2069 6925 2.923 0.736 0.163 0.392 245 10.4 medialorbitofrontal 6602 4423 17216 3.104 0.673 0.154 0.080 157 18.9 middletemporal 1212 756 2750 2.976 0.876 0.171 0.139 33 6.3 parahippocampal 3709 2173 4865 2.255 0.594 0.149 0.468 205 19.9 paracentral 2255 1498 4858 2.924 0.450 0.142 0.058 37 5.3 parsopercularis 1574 982 3552 2.852 0.668 0.170 0.120 50 6.8 parsorbitalis 2833 1855 6336 2.947 0.635 0.144 0.057 47 6.6 parstriangularis 2228 1535 2240 1.577 0.458 0.199 0.118 56 10.6 pericalcarine 8701 5247 11564 2.052 0.677 0.145 0.076 186 29.2 postcentral 2161 1389 4562 2.902 0.795 0.161 0.078 41 7.3 posteriorcingulate 10185 6350 15233 2.305 0.682 0.159 0.374 357 53.4 precentral 7240 4606 12489 2.424 0.689 0.160 0.101 252 31.7 precuneus 1094 735 2844 3.181 0.654 0.176 0.070 25 3.2 rostralanteriorcingulate 12337 8049 24812 2.705 0.660 0.159 0.093 352 39.5 rostralmiddlefrontal 14537 8742 29059 2.960 0.666 0.157 0.643 835 72.4 superiorfrontal 10007 6218 16989 2.411 0.643 0.162 0.120 1137 49.6 superiorparietal 6753 4532 16631 3.110 0.738 0.140 0.061 108 17.7 superiortemporal 6005 3883 11300 2.691 0.594 0.146 0.087 145 16.3 supramarginal 479 336 1478 3.330 0.507 0.209 0.166 15 1.9 frontalpole 811 535 2840 3.947 0.771 0.192 0.315 41 15.4 temporalpole 727 440 909 2.089 0.679 0.158 0.089 13 2.7 transversetemporal 4336 2794 8943 3.254 0.791 0.167 0.123 132 22.5 insula #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:51:09 BST 2012 New invocation of recon-all Tue Jul 24 00:51:10 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortparc2 #----------------------------------------- #@# Cortical Parc 2 lh Tue Jul 24 00:51:10 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 lh ../surf/lh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 45 labels changed using aseg relabeling using gibbs priors... 000: 10926 changed, 169714 examined... 001: 2827 changed, 42059 examined... 002: 882 changed, 14364 examined... 003: 363 changed, 4828 examined... 004: 191 changed, 2037 examined... 005: 102 changed, 1003 examined... 006: 51 changed, 603 examined... 007: 32 changed, 294 examined... 008: 18 changed, 171 examined... 009: 13 changed, 98 examined... 010: 10 changed, 67 examined... 011: 7 changed, 58 examined... 012: 3 changed, 31 examined... 013: 0 changed, 15 examined... 1 labels changed using aseg 000: 317 total segments, 238 labels (4426 vertices) changed 001: 104 total segments, 26 labels (138 vertices) changed 002: 78 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 155 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1315 vertices marked for relabeling... 1315 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 48 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:51:57 BST 2012 New invocation of recon-all Tue Jul 24 00:51:57 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -cortparc2 #----------------------------------------- #@# Cortical Parc 2 rh Tue Jul 24 00:51:57 BST 2012 /home/clare/subjects/subject_20/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subject_20 rh ../surf/rh.sphere.reg /home/clare/freesurfer/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /home/clare/freesurfer/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... 40 labels changed using aseg relabeling using gibbs priors... 000: 11751 changed, 172013 examined... 001: 2731 changed, 44957 examined... 002: 862 changed, 13995 examined... 003: 410 changed, 4695 examined... 004: 192 changed, 2221 examined... 005: 99 changed, 1079 examined... 006: 52 changed, 514 examined... 007: 24 changed, 293 examined... 008: 21 changed, 146 examined... 009: 11 changed, 113 examined... 010: 5 changed, 71 examined... 011: 4 changed, 32 examined... 012: 1 changed, 19 examined... 013: 0 changed, 7 examined... 18 labels changed using aseg 000: 358 total segments, 271 labels (3565 vertices) changed 001: 104 total segments, 18 labels (36 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 158 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1286 vertices marked for relabeling... 1286 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 50 seconds. #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:52:47 BST 2012 New invocation of recon-all Tue Jul 24 00:52:47 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -parcstats2 #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jul 24 00:52:47 BST 2012 /home/clare/subjects/subject_20/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 subject_20 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/lh.white... reading input pial surface /home/clare/subjects/subject_20/surf/lh.pial... reading input white surface /home/clare/subjects/subject_20/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 1446 960 2811 2.723 0.554 0.159 0.077 28 4.4 G_and_S_frontomargin 2410 1505 4459 2.562 0.762 0.169 0.096 54 10.8 G_and_S_occipital_inf 1907 1174 2391 1.825 0.585 0.171 0.145 140 11.2 G_and_S_paracentral 1953 1189 3192 2.523 0.669 0.173 0.101 84 8.0 G_and_S_subcentral 1122 705 2454 2.814 0.551 0.169 0.081 38 4.1 G_and_S_transv_frontopol 2951 1937 6237 3.109 0.636 0.139 0.057 43 7.0 G_and_S_cingul-Ant 2180 1428 4606 3.098 0.766 0.156 0.062 34 6.0 G_and_S_cingul-Mid-Ant 1799 1159 3584 2.880 0.662 0.157 0.087 41 5.5 G_and_S_cingul-Mid-Post 819 518 2003 3.230 0.812 0.190 0.109 22 3.7 G_cingul-Post-dorsal 395 236 763 2.969 0.983 0.154 0.101 10 1.8 G_cingul-Post-ventral 2095 1341 2427 1.655 0.495 0.179 0.097 51 9.1 G_cuneus 1726 1104 4450 2.961 0.614 0.167 0.133 75 8.1 G_front_inf-Opercular 377 240 949 2.876 0.446 0.172 0.089 9 1.4 G_front_inf-Orbital 1253 823 3682 3.213 0.569 0.167 0.085 31 4.5 G_front_inf-Triangul 6445 3973 14390 2.858 0.583 0.164 0.138 526 29.9 G_front_middle 8913 5430 20214 3.045 0.682 0.172 0.117 424 47.8 G_front_sup 554 365 1407 3.708 0.704 0.175 0.142 17 3.6 G_Ins_lg_and_S_cent_ins 847 515 2598 3.912 0.700 0.199 0.158 28 6.1 G_insular_short 3421 2019 7206 2.797 0.637 0.171 0.220 344 46.5 G_occipital_middle 1891 1084 2922 2.247 0.649 0.163 0.183 50 18.1 G_occipital_sup 1821 1231 4630 2.950 0.753 0.225 0.162 81 12.2 G_oc-temp_lat-fusifor 3802 2431 5471 1.996 0.589 0.214 0.149 163 25.4 G_oc-temp_med-Lingual 1575 993 4420 3.448 0.896 0.208 0.277 101 10.0 G_oc-temp_med-Parahip 3076 2049 7909 2.947 0.720 0.199 0.139 121 18.5 G_orbital 3208 2011 8113 2.957 0.585 0.171 0.171 115 29.5 G_pariet_inf-Angular 3725 2481 7802 2.607 0.588 0.178 0.196 211 42.5 G_pariet_inf-Supramar 3646 2436 8319 2.662 0.695 0.184 0.210 435 16.1 G_parietal_sup 4157 2388 5730 2.056 0.683 0.162 0.128 163 23.4 G_postcentral 5002 2804 7082 2.160 0.787 0.166 0.144 221 28.4 G_precentral 3257 2102 7119 2.673 0.644 0.199 0.175 250 24.3 G_precuneus 927 602 2545 2.988 0.824 0.199 0.091 34 3.3 G_rectus 764 474 1603 3.233 0.788 0.188 0.180 62 5.5 G_subcallosal 756 417 1229 2.386 0.742 0.169 0.222 70 5.0 G_temp_sup-G_T_transv 2507 1690 9020 3.637 0.643 0.182 0.088 67 9.7 G_temp_sup-Lateral 501 332 1307 3.769 0.502 0.196 0.131 12 2.7 G_temp_sup-Plan_polar 1386 897 2583 2.713 0.700 0.140 0.060 26 3.7 G_temp_sup-Plan_tempo 3476 2222 9935 3.199 0.798 0.174 0.126 160 19.0 G_temporal_inf 4052 2717 12515 3.214 0.688 0.166 0.075 93 12.7 G_temporal_middle 378 248 547 2.456 0.408 0.110 0.031 2 0.6 Lat_Fis-ant-Horizont 419 275 725 2.855 0.521 0.114 0.035 3 0.5 Lat_Fis-ant-Vertical 1492 990 2027 2.529 0.493 0.139 0.048 15 2.9 Lat_Fis-post 2945 1796 3417 1.810 0.564 0.190 0.104 75 13.5 Pole_occipital 2432 1650 7058 3.188 0.854 0.210 0.161 115 17.0 Pole_temporal 2481 1664 2811 1.852 0.766 0.182 0.114 168 12.5 S_calcarine 3735 2631 3355 1.489 0.435 0.162 0.073 69 12.1 S_central 1233 827 1984 2.437 0.528 0.166 0.106 26 4.2 S_cingul-Marginalis 670 430 1172 2.898 0.517 0.130 0.064 7 1.9 S_circular_insula_ant 1638 1089 2960 3.094 0.767 0.124 0.078 20 3.9 S_circular_insula_inf 2049 1346 3246 2.818 0.510 0.123 0.078 25 4.1 S_circular_insula_sup 1379 928 2523 2.692 0.710 0.131 0.051 13 3.2 S_collat_transv_ant 545 353 580 1.951 0.495 0.189 0.119 12 2.7 S_collat_transv_post 2191 1424 3486 2.506 0.431 0.113 0.037 17 3.4 S_front_inf 2518 1734 4488 2.535 0.534 0.139 0.048 42 5.0 S_front_middle 3332 2209 6080 2.695 0.617 0.144 0.063 47 8.8 S_front_sup 522 357 754 2.523 0.281 0.115 0.033 3 0.7 S_interm_prim-Jensen 3596 2341 4960 2.319 0.418 0.144 0.084 76 13.1 S_intrapariet_and_P_trans 1381 886 1809 2.158 0.474 0.153 0.064 20 3.7 S_oc_middle_and_Lunatus 1695 1088 2226 2.181 0.452 0.125 0.042 14 3.1 S_oc_sup_and_transversal 822 547 1108 2.314 0.419 0.126 0.040 6 1.4 S_occipital_ant 1027 673 1718 2.801 0.469 0.153 0.063 15 2.7 S_oc-temp_lat 2404 1625 3791 2.391 0.599 0.160 0.080 40 8.7 S_oc-temp_med_and_Lingual 646 462 927 2.254 0.330 0.102 0.023 4 0.7 S_orbital_lateral 1090 717 1925 2.529 0.970 0.174 0.115 34 6.3 S_orbital_med-olfact 1525 970 2861 2.965 0.907 0.148 0.080 28 5.0 S_orbital-H_Shaped 2391 1526 3075 2.189 0.544 0.147 0.069 33 7.5 S_parieto_occipital 1622 956 1639 2.148 0.814 0.152 0.091 47 5.8 S_pericallosal 4693 3098 6642 2.235 0.591 0.140 0.058 63 11.7 S_postcentral 2548 1643 4026 2.597 0.392 0.135 0.076 95 9.7 S_precentral-inf-part 1734 1136 2326 2.417 0.469 0.143 0.083 31 6.4 S_precentral-sup-part 868 566 1322 2.366 0.838 0.149 0.064 18 2.3 S_suborbital 1465 956 2442 2.466 0.643 0.162 0.149 80 7.5 S_subparietal 1878 1212 2511 2.511 0.471 0.122 0.042 16 3.4 S_temporal_inf 6594 4448 10950 2.698 0.498 0.127 0.047 76 13.4 S_temporal_sup 447 291 598 2.500 0.546 0.147 0.088 8 1.3 S_temporal_transverse #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:53:04 BST 2012 New invocation of recon-all Tue Jul 24 00:53:04 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi rh -parcstats2 #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jul 24 00:53:04 BST 2012 /home/clare/subjects/subject_20/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 subject_20 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/clare/subjects/subject_20/mri/wm.mgz... reading input surface /home/clare/subjects/subject_20/surf/rh.white... reading input pial surface /home/clare/subjects/subject_20/surf/rh.pial... reading input white surface /home/clare/subjects/subject_20/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 1249 859 3029 2.788 0.700 0.176 0.073 28 3.8 G_and_S_frontomargin 1403 908 3045 2.712 0.707 0.180 0.107 36 6.4 G_and_S_occipital_inf 2058 1234 2352 1.831 0.567 0.154 0.085 47 7.6 G_and_S_paracentral 1818 1193 3531 2.690 0.642 0.156 0.067 32 5.1 G_and_S_subcentral 1570 1023 3617 2.872 0.650 0.182 0.136 56 6.4 G_and_S_transv_frontopol 3456 2325 7543 2.982 0.567 0.146 0.057 58 7.8 G_and_S_cingul-Ant 1871 1239 4416 3.110 0.646 0.157 0.075 30 6.1 G_and_S_cingul-Mid-Ant 2126 1371 4037 2.755 0.629 0.151 0.078 33 7.4 G_and_S_cingul-Mid-Post 690 421 1655 3.096 0.706 0.176 0.099 55 2.7 G_cingul-Post-dorsal 288 161 600 2.940 0.536 0.170 0.115 6 1.5 G_cingul-Post-ventral 2636 1608 2947 1.699 0.491 0.166 0.096 77 9.3 G_cuneus 1470 974 3870 3.030 0.486 0.155 0.072 34 4.0 G_front_inf-Opercular 523 329 1554 3.281 0.565 0.181 0.085 16 1.7 G_front_inf-Orbital 1478 970 4084 3.206 0.588 0.168 0.075 32 4.7 G_front_inf-Triangul 5702 3529 13249 2.922 0.606 0.176 0.123 219 27.3 G_front_middle 9385 5210 19382 3.011 0.706 0.171 1.084 870 67.6 G_front_sup 712 445 1856 3.976 0.708 0.179 0.232 30 6.0 G_Ins_lg_and_S_cent_ins 729 453 2187 3.555 0.741 0.192 0.119 24 3.8 G_insular_short 4076 2338 8437 2.798 0.687 0.172 0.158 234 24.5 G_occipital_middle 2144 1214 3592 2.418 0.693 0.160 0.105 60 9.7 G_occipital_sup 2042 1315 4876 2.935 0.679 0.208 0.144 77 12.3 G_oc-temp_lat-fusifor 3744 2493 6371 2.126 0.750 0.220 0.307 347 57.0 G_oc-temp_med-Lingual 1957 1221 5416 3.582 0.766 0.209 0.192 98 13.1 G_oc-temp_med-Parahip 3459 2162 8500 3.005 0.844 0.209 0.328 227 24.4 G_orbital 4243 2805 10682 3.016 0.544 0.178 0.099 130 17.3 G_pariet_inf-Angular 3368 2114 7199 2.874 0.552 0.159 0.121 114 11.8 G_pariet_inf-Supramar 3008 1851 6136 2.628 0.631 0.171 0.176 951 20.7 G_parietal_sup 3658 1890 5012 2.159 0.595 0.155 0.103 114 17.0 G_postcentral 3977 2171 6327 2.379 0.745 0.180 0.845 263 31.6 G_precentral 3225 2012 7275 2.682 0.768 0.188 0.152 130 19.9 G_precuneus 845 542 2321 3.068 0.652 0.199 1.285 197 4.7 G_rectus 417 270 951 3.186 0.904 0.131 0.133 19 2.2 G_subcallosal 530 333 807 2.290 1.055 0.167 0.105 11 2.3 G_temp_sup-G_T_transv 2434 1659 8125 3.406 0.823 0.167 0.090 63 9.4 G_temp_sup-Lateral 951 632 2679 3.630 0.655 0.164 0.284 60 17.2 G_temp_sup-Plan_polar 926 614 1719 2.603 0.561 0.115 0.033 10 1.1 G_temp_sup-Plan_tempo 3380 2215 9977 3.290 0.853 0.176 0.111 129 14.5 G_temporal_inf 4004 2684 12493 3.302 0.595 0.171 0.103 129 14.2 G_temporal_middle 531 343 790 2.568 0.452 0.089 0.020 2 0.4 Lat_Fis-ant-Horizont 206 139 404 2.741 0.499 0.132 0.052 4 0.4 Lat_Fis-ant-Vertical 1379 940 2047 2.572 0.497 0.129 0.041 11 2.5 Lat_Fis-post 3864 2307 4592 1.828 0.581 0.198 0.138 118 23.8 Pole_occipital 2248 1528 7295 3.477 0.917 0.199 0.134 212 13.0 Pole_temporal 2540 1726 3100 2.043 0.721 0.186 0.099 59 10.9 S_calcarine 4048 2812 4156 1.685 0.503 0.146 0.060 45 11.0 S_central 1634 1072 2522 2.470 0.434 0.120 0.044 12 3.2 S_cingul-Marginalis 651 421 1168 3.106 0.386 0.122 0.050 5 1.3 S_circular_insula_ant 1619 1049 2667 3.033 0.599 0.123 0.054 15 3.8 S_circular_insula_inf 1846 1241 2843 2.679 0.499 0.123 0.037 15 2.9 S_circular_insula_sup 1165 793 2035 2.564 0.685 0.125 0.052 12 2.6 S_collat_transv_ant 810 553 1032 2.065 0.517 0.195 0.140 46 5.6 S_collat_transv_post 2748 1825 4520 2.454 0.548 0.133 0.050 35 6.3 S_front_inf 3140 2102 5045 2.549 0.544 0.129 0.044 41 5.0 S_front_middle 4221 2697 7602 2.616 0.664 0.152 0.206 317 16.6 S_front_sup 308 194 376 2.326 0.531 0.125 0.039 2 0.6 S_interm_prim-Jensen 3816 2448 5350 2.228 0.519 0.150 0.089 101 15.3 S_intrapariet_and_P_trans 1750 1135 2319 2.208 0.427 0.141 0.059 21 4.5 S_oc_middle_and_Lunatus 1909 1268 2986 2.264 0.672 0.139 0.063 34 5.5 S_oc_sup_and_transversal 1253 826 2150 2.598 0.573 0.161 0.083 26 3.7 S_occipital_ant 1209 796 1793 2.583 0.576 0.135 0.060 21 3.6 S_oc-temp_lat 2368 1557 3530 2.448 0.579 0.161 0.092 46 9.1 S_oc-temp_med_and_Lingual 586 388 894 2.600 0.540 0.138 0.041 7 1.1 S_orbital_lateral 916 632 1613 2.442 0.848 0.135 0.065 14 2.5 S_orbital_med-olfact 1923 1253 3379 2.751 0.700 0.165 0.110 49 7.8 S_orbital-H_Shaped 2608 1649 3165 2.107 0.552 0.148 0.070 35 7.9 S_parieto_occipital 1968 1176 2296 2.295 0.828 0.149 0.097 36 5.0 S_pericallosal 3201 2108 3774 2.055 0.513 0.128 0.047 33 6.2 S_postcentral 1931 1324 3060 2.544 0.401 0.122 0.049 18 4.3 S_precentral-inf-part 1956 1281 2713 2.443 0.535 0.140 0.089 37 9.7 S_precentral-sup-part 399 262 794 3.254 0.663 0.171 0.066 13 1.2 S_suborbital 1402 948 2274 2.380 0.597 0.139 0.072 97 4.9 S_subparietal 1802 1173 2570 2.648 0.494 0.122 0.041 16 3.0 S_temporal_inf 7614 5255 12890 2.573 0.449 0.115 0.035 70 10.5 S_temporal_sup 425 253 467 2.221 0.360 0.130 0.050 5 0.9 S_temporal_transverse #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 00:53:20 BST 2012 New invocation of recon-all Tue Jul 24 00:53:20 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -hemi lh -cortribbon #-------------------------------------------- #@# Cortical ribbon mask Tue Jul 24 00:53:20 BST 2012 /home/clare/subjects/subject_20/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon subject_20 SUBJECTS_DIR is /home/clare/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 28 writing volume /home/clare/subjects/subject_20/mri/ribbon.mgz writing ribbon files #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 01:10:13 BST 2012 New invocation of recon-all Tue Jul 24 01:10:13 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -segstats #-------------------------------------------- #@# ASeg Stats Tue Jul 24 01:10:13 BST 2012 /home/clare/subjects/subject_20 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /home/clare/freesurfer/freesurfer/ASegStatsLUT.txt --subject subject_20 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /home/clare/freesurfer/freesurfer/ASegStatsLUT.txt --subject subject_20 sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare atlas_icv (eTIV) = 1896950 mm^3 (det: 1.026967 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 323297 rh white matter volume 329060 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 342335.761549, pTot = 639289.716386 c = 296953.954837 rh surface-based volumes (mm3): wTot = 350495.604031, pTot = 654875.841711 c = 304380.237680 Computing SupraTentVolCor SupraTentVolCor = 73862.000 SupraTentVol = 1368027.558 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 3598 3598 4 5 Left-Inf-Lat-Vent 145 145 5 7 Left-Cerebellum-White-Matter 17982 17982 6 8 Left-Cerebellum-Cortex 54941 54941 7 10 Left-Thalamus-Proper 10801 10801 8 11 Left-Caudate 4127 4127 9 12 Left-Putamen 6083 6083 10 13 Left-Pallidum 1800 1800 11 14 3rd-Ventricle 1205 1205 12 15 4th-Ventricle 2523 2523 13 16 Brain-Stem 26221 26221 14 17 Left-Hippocampus 4642 4642 15 18 Left-Amygdala 1669 1669 16 24 CSF 1246 1246 17 26 Left-Accumbens-area 882 882 18 28 Left-VentralDC 5289 5289 19 30 Left-vessel 67 67 20 31 Left-choroid-plexus 1790 1790 23 43 Right-Lateral-Ventricle 8551 8551 24 44 Right-Inf-Lat-Vent 302 302 25 46 Right-Cerebellum-White-Matter 15335 15335 26 47 Right-Cerebellum-Cortex 57355 57355 27 49 Right-Thalamus-Proper 9818 9818 28 50 Right-Caudate 4220 4220 29 51 Right-Putamen 5668 5668 30 52 Right-Pallidum 1953 1953 31 53 Right-Hippocampus 4694 4694 32 54 Right-Amygdala 1785 1785 33 58 Right-Accumbens-area 475 475 34 60 Right-VentralDC 4752 4752 35 62 Right-vessel 37 37 36 63 Right-choroid-plexus 1966 1966 37 72 5th-Ventricle 0 38 77 WM-hypointensities 1919 1919 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 29 29 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 241 241 45 251 CC_Posterior 1269 1269 46 252 CC_Mid_Posterior 835 835 47 253 CC_Central 618 618 48 254 CC_Mid_Anterior 706 706 49 255 CC_Anterior 1119 1119 Reporting on 45 segmentations SubCortGrayVol = 207175 #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 01:18:09 BST 2012 New invocation of recon-all Tue Jul 24 01:18:09 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -aparc2aseg #----------------------------------------- #@# AParc-to-ASeg Tue Jul 24 01:18:09 BST 2012 /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --volmask SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol /home/clare/subjects/subject_20/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 593324 Used brute-force search on 0 voxels Writing output aseg to /home/clare/subjects/subject_20/mri/aparc+aseg.mgz /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --volmask --a2009s SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol /home/clare/subjects/subject_20/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.a2009s.annot 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) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.a2009s.annot 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) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 593324 Used brute-force search on 0 voxels Writing output aseg to /home/clare/subjects/subject_20/mri/aparc.a2009s+aseg.mgz #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 01:21:36 BST 2012 New invocation of recon-all Tue Jul 24 01:21:36 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s /home/clare/subjects/subject_20 -wmparc #----------------------------------------- #@# WMParc Tue Jul 24 01:21:36 BST 2012 /home/clare/subjects/subject_20 mri_aparc2aseg --s subject_20 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/clare/subjects subject subject_20 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/clare/subjects/subject_20/mri/aparc+aseg.mgz Reading lh white surface /home/clare/subjects/subject_20/surf/lh.white Reading lh pial surface /home/clare/subjects/subject_20/surf/lh.pial Loading lh annotations from /home/clare/subjects/subject_20/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /home/clare/subjects/subject_20/surf/rh.white Reading rh pial surface /home/clare/subjects/subject_20/surf/rh.pial Loading rh annotations from /home/clare/subjects/subject_20/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/clare/subjects/subject_20/mri/ribbon.mgz Loading filled from /home/clare/subjects/subject_20/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9187 vertices from left hemi Ripped 8467 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/clare/subjects/subject_20/mri/aseg.mgz Loading Ctx Seg File /home/clare/subjects/subject_20/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -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; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1208511 Used brute-force search on 170 voxels Fixing Parahip LH WM Found 15 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 5.000000 5 k 1857.000000 6 k 2.000000 7 k 4.000000 8 k 2.000000 9 k 1.000000 10 k 5.000000 11 k 1.000000 12 k 2.000000 13 k 2.000000 14 k 2.000000 Fixing Parahip RH WM Found 12 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 3.000000 7 k 6.000000 8 k 16.000000 9 k 2.000000 10 k 1.000000 11 k 1801.000000 Writing output aseg to mri/wmparc.mgz /home/clare/subjects/subject_20 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject_20 --surf-wm-vol --ctab /home/clare/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject_20 --surf-wm-vol --ctab /home/clare/freesurfer/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname clare-OptiPlex-990 machine x86_64 user clare atlas_icv (eTIV) = 1896950 mm^3 (det: 1.026967 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 323297 rh white matter volume 329060 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1912590 # brainmaskvolume 1912590.0 # nbrainsegvoxels 262955 # brainsegvolume 262955.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 4047 4047 2 3002 wm-lh-caudalanteriorcingulate 4164 4164 3 3003 wm-lh-caudalmiddlefrontal 7029 7029 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 3387 3387 6 3006 wm-lh-entorhinal 899 899 7 3007 wm-lh-fusiform 8948 8948 8 3008 wm-lh-inferiorparietal 12267 12267 9 3009 wm-lh-inferiortemporal 7512 7512 10 3010 wm-lh-isthmuscingulate 4589 4589 11 3011 wm-lh-lateraloccipital 13334 13334 12 3012 wm-lh-lateralorbitofrontal 7533 7533 13 3013 wm-lh-lingual 6754 6754 14 3014 wm-lh-medialorbitofrontal 4617 4617 15 3015 wm-lh-middletemporal 7739 7739 16 3016 wm-lh-parahippocampal 2081 2081 17 3017 wm-lh-paracentral 5410 5410 18 3018 wm-lh-parsopercularis 4530 4530 19 3019 wm-lh-parsorbitalis 1217 1217 20 3020 wm-lh-parstriangularis 3677 3677 21 3021 wm-lh-pericalcarine 3946 3946 22 3022 wm-lh-postcentral 12177 12177 23 3023 wm-lh-posteriorcingulate 5618 5618 24 3024 wm-lh-precentral 21368 21368 25 3025 wm-lh-precuneus 11065 11065 26 3026 wm-lh-rostralanteriorcingulate 3329 3329 27 3027 wm-lh-rostralmiddlefrontal 17925 17925 28 3028 wm-lh-superiorfrontal 21521 21521 29 3029 wm-lh-superiorparietal 15935 15935 30 3030 wm-lh-superiortemporal 9869 9869 31 3031 wm-lh-supramarginal 11231 11231 32 3032 wm-lh-frontalpole 251 251 33 3033 wm-lh-temporalpole 1001 1001 34 3034 wm-lh-transversetemporal 944 944 35 3035 wm-lh-insula 10159 10159 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 3474 3474 120 4002 wm-rh-caudalanteriorcingulate 4027 4027 121 4003 wm-rh-caudalmiddlefrontal 5922 5922 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 3084 3084 124 4006 wm-rh-entorhinal 845 845 125 4007 wm-rh-fusiform 8483 8483 126 4008 wm-rh-inferiorparietal 16655 16655 127 4009 wm-rh-inferiortemporal 8041 8041 128 4010 wm-rh-isthmuscingulate 3751 3751 129 4011 wm-rh-lateraloccipital 12758 12758 130 4012 wm-rh-lateralorbitofrontal 7801 7801 131 4013 wm-rh-lingual 7044 7044 132 4014 wm-rh-medialorbitofrontal 4874 4874 133 4015 wm-rh-middletemporal 8086 8086 134 4016 wm-rh-parahippocampal 1978 1978 135 4017 wm-rh-paracentral 7555 7555 136 4018 wm-rh-parsopercularis 4162 4162 137 4019 wm-rh-parsorbitalis 1486 1486 138 4020 wm-rh-parstriangularis 4334 4334 139 4021 wm-rh-pericalcarine 3625 3625 140 4022 wm-rh-postcentral 11376 11376 141 4023 wm-rh-posteriorcingulate 5450 5450 142 4024 wm-rh-precentral 19470 19470 143 4025 wm-rh-precuneus 13033 13033 144 4026 wm-rh-rostralanteriorcingulate 2211 2211 145 4027 wm-rh-rostralmiddlefrontal 20044 20044 146 4028 wm-rh-superiorfrontal 22969 22969 147 4029 wm-rh-superiorparietal 15559 15559 148 4030 wm-rh-superiortemporal 9344 9344 149 4031 wm-rh-supramarginal 9422 9422 150 4032 wm-rh-frontalpole 466 466 151 4033 wm-rh-temporalpole 1009 1009 152 4034 wm-rh-transversetemporal 991 991 153 4035 wm-rh-insula 11497 11497 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 51847 51847 237 5002 Right-UnsegmentedWhiteMatter 51694 51694 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations #------------------------------------------ recon-all -s subject_20 finished without error at Tue Jul 24 01:35:30 BST 2012 New invocation of recon-all Tue Jul 24 18:12:40 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s subject_20 -qcache subjid subject_20 setenv SUBJECTS_DIR /home/clare/subjects FREESURFER_HOME /home/clare/freesurfer/freesurfer Actual FREESURFER_HOME /home/clare/freesurfer/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 16422708 15862228 560480 0 150252 14508724 -/+ buffers/cache: 1203252 15219456 Swap: 19795964 0 19795964 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/24-17:12:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/clare/freesurfer/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/clare/freesurfer/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/clare/subjects/subject_20/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Tue Jul 24 18:12:43 BST 2012 mris_preproc --s subject_20 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.29130 /home/clare/subjects/subject_20/surf Log file is lh.thickness.fsaverage.mris_preproc.log Tue Jul 24 18:12:43 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.29130 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Tue Jul 24 18:12:43 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.29130/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.29130/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.thickness Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.29130/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.29130/subject_20.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.29130 Tue Jul 24 18:12:48 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh thickness fwhm0 fsaverage Tue Jul 24 18:12:48 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm5 fsaverage Tue Jul 24 18:12:50 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm10 fsaverage Tue Jul 24 18:12:54 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm15 fsaverage Tue Jul 24 18:13:01 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm20 fsaverage Tue Jul 24 18:13:11 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm25 fsaverage Tue Jul 24 18:13:28 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fsaverage Tue Jul 24 18:13:52 BST 2012 mris_preproc --s subject_20 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.29375 /home/clare/subjects/subject_20/surf Log file is lh.area.fsaverage.mris_preproc.log Tue Jul 24 18:13:52 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.29375 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Tue Jul 24 18:13:52 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.29375/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.area --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.29375/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.area Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.29375/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.29375/subject_20.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.29375 Tue Jul 24 18:13:57 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area fwhm0 fsaverage Tue Jul 24 18:13:57 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm5 fsaverage Tue Jul 24 18:13:59 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm10 fsaverage Tue Jul 24 18:14:03 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm15 fsaverage Tue Jul 24 18:14:10 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm20 fsaverage Tue Jul 24 18:14:21 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm25 fsaverage Tue Jul 24 18:14:37 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Tue Jul 24 18:15:01 BST 2012 mris_preproc --s subject_20 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.29618 /home/clare/subjects/subject_20/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Tue Jul 24 18:15:01 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.29618 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Tue Jul 24 18:15:01 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.29618/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.area.pial --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.29618/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.area.pial Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.29618/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.29618/subject_20.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.29618 Tue Jul 24 18:15:07 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm0 fsaverage Tue Jul 24 18:15:07 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm5 fsaverage Tue Jul 24 18:15:08 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm10 fsaverage Tue Jul 24 18:15:12 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm15 fsaverage Tue Jul 24 18:15:19 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm20 fsaverage Tue Jul 24 18:15:30 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm25 fsaverage Tue Jul 24 18:15:46 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Tue Jul 24 18:16:10 BST 2012 mris_preproc --s subject_20 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.29862 /home/clare/subjects/subject_20/surf Log file is lh.volume.fsaverage.mris_preproc.log Tue Jul 24 18:16:10 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.29862 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Tue Jul 24 18:16:10 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.29862/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.29862/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.volume ERROR: number of vertices in /home/clare/subjects/subject_20/surf/lh.volume does not match surface (173473,169714) ERROR: reading curvature file Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s subject_20 exited with ERRORS at Tue Jul 24 18:16:12 BST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Wed Jul 25 10:01:02 BST 2012 /home/clare/subjects/subject_20 /home/clare/freesurfer/freesurfer/bin/recon-all -s subject_20 -qcache subjid subject_20 setenv SUBJECTS_DIR /home/clare/subjects FREESURFER_HOME /home/clare/freesurfer/freesurfer Actual FREESURFER_HOME /home/clare/freesurfer/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 16422708 16214848 207860 0 3291208 11453628 -/+ buffers/cache: 1470012 14952696 Swap: 19795964 0 19795964 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/25-09:01:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: clare Machine: clare-OptiPlex-990 Platform: Linux PlatformVersion: 2.6.35-32-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/clare/freesurfer/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/clare/freesurfer/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/clare/subjects/subject_20/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Wed Jul 25 10:01:07 BST 2012 mris_preproc --s subject_20 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.15396 /home/clare/subjects/subject_20/surf Log file is lh.thickness.fsaverage.mris_preproc.log Wed Jul 25 10:01:08 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.15396 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Wed Jul 25 10:01:08 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15396/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15396/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.thickness Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.15396/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15396/subject_20.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15396 Wed Jul 25 10:01:13 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh thickness fwhm0 fsaverage Wed Jul 25 10:01:13 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm5 fsaverage Wed Jul 25 10:01:15 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm10 fsaverage Wed Jul 25 10:01:19 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm15 fsaverage Wed Jul 25 10:01:26 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm20 fsaverage Wed Jul 25 10:01:37 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm25 fsaverage Wed Jul 25 10:01:53 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fsaverage Wed Jul 25 10:02:17 BST 2012 mris_preproc --s subject_20 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.15644 /home/clare/subjects/subject_20/surf Log file is lh.area.fsaverage.mris_preproc.log Wed Jul 25 10:02:17 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.15644 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Wed Jul 25 10:02:17 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15644/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.area --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15644/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.area Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.15644/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15644/subject_20.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15644 Wed Jul 25 10:02:23 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area fwhm0 fsaverage Wed Jul 25 10:02:23 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm5 fsaverage Wed Jul 25 10:02:24 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm10 fsaverage Wed Jul 25 10:02:28 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm15 fsaverage Wed Jul 25 10:02:35 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm20 fsaverage Wed Jul 25 10:02:46 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm25 fsaverage Wed Jul 25 10:03:03 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Wed Jul 25 10:03:27 BST 2012 mris_preproc --s subject_20 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.15892 /home/clare/subjects/subject_20/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Wed Jul 25 10:03:27 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.15892 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Wed Jul 25 10:03:27 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.15892/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.area.pial --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.15892/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.area.pial Reading target surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169714) Reverse Loop had 46153 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 132526, nTrgMulti = 31316, MnTrgMultiHits = 2.47378 nSrc121 = 138541, nSrcLost = 0, nSrcMulti = 31173, MnSrcMultiHits = 2.29218 Saving target data Saving to ./tmp.mris_preproc.15892/subject_20.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.15892/subject_20.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.15892 Wed Jul 25 10:03:32 BST 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm0 fsaverage Wed Jul 25 10:03:32 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm5 fsaverage Wed Jul 25 10:03:34 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm10 fsaverage Wed Jul 25 10:03:38 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm15 fsaverage Wed Jul 25 10:03:45 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm20 fsaverage Wed Jul 25 10:03:56 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm25 fsaverage Wed Jul 25 10:04:12 BST 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Wed Jul 25 10:04:37 BST 2012 mris_preproc --s subject_20 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.16138 /home/clare/subjects/subject_20/surf Log file is lh.volume.fsaverage.mris_preproc.log Wed Jul 25 10:04:37 BST 2012 setenv SUBJECTS_DIR /home/clare/subjects cd /home/clare/subjects/subject_20/surf /home/clare/freesurfer/freesurfer/bin/mris_preproc --s subject_20 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.16138 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 subject_20 Wed Jul 25 10:04:37 BST 2012 -------------- ----------------------- mri_surf2surf --srcsubject subject_20 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.16138/subject_20.1.mgh --sval /home/clare/subjects/subject_20/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = subject_20 srcval = /home/clare/subjects/subject_20/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.16138/subject_20.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /home/clare/subjects/subject_20/surf/lh.sphere.reg Loading source data Reading curvature file /home/clare/subjects/subject_20/surf/lh.volume ERROR: number of vertices in /home/clare/subjects/subject_20/surf/lh.volume does not match surface (173473,169714) ERROR: reading curvature file Linux clare-OptiPlex-990 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s subject_20 exited with ERRORS at Wed Jul 25 10:04:38 BST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting