INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /prod3/allegra/barcs_fs/tmp Actual FREESURFER_HOME /opt/freesurfer -rwxrwxrwx 1 Skhadka2 users 288305 Feb 25 11:42 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts/recon-all.log Linux compute11 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #------------------------------------- #@# EM Registration Tue Feb 25 12:37:57 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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 '/opt/freesurfer/average/RB_all_2008-03-26.gca'... 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 = (56, 65, 19) --> (196, 211, 196) using (103, 114, 108) as brain centroid... mean wm in atlas = 107, using box (86,96,86) --> (120, 131,129) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.193229 @ (0.000, 0.000, 0.000) max log p = -3.997432 @ (-4.545, -22.727, 4.545) max log p = -3.824323 @ (2.273, 6.818, -6.818) max log p = -3.822296 @ (-1.136, -1.136, 3.409) max log p = -3.801689 @ (1.705, -0.568, -0.568) max log p = -3.801689 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -17.6, 0.6): log p = -3.802 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8) 1.000 0.000 0.000 -1.705; 0.000 0.992 0.372 -55.522; 0.000 -0.390 0.833 71.303; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.000 0.000 0.000 -1.705; 0.000 0.992 0.372 -55.522; 0.000 -0.390 0.833 71.303; 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=-3.3, old_max_log_p =-3.4 (thresh=-3.4) 1.037 0.033 0.014 -12.409; -0.033 0.995 0.408 -53.510; 0.000 -0.412 0.806 79.012; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.037 0.033 0.014 -12.409; -0.034 0.999 0.442 -57.525; 0.001 -0.453 0.807 84.279; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.018 0.033 0.013 -9.798; -0.035 1.017 0.450 -60.709; 0.001 -0.453 0.807 84.279; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.018 0.033 0.013 -9.798; -0.035 1.017 0.450 -60.709; 0.001 -0.453 0.807 84.279; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 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 1.01656 0.02417 0.00971 -8.63257; -0.02620 1.02000 0.44332 -61.42802; 0.00083 -0.44376 0.80955 83.30574; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.01656 0.02417 0.00971 -8.63257; -0.02620 1.02000 0.44332 -61.42802; 0.00083 -0.44376 0.80955 83.30574; 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: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.2) transform before final EM align: 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 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 1.01656 0.02417 0.00971 -8.63257; -0.02620 1.02000 0.44332 -61.42802; 0.00083 -0.44376 0.80955 83.30574; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.01656 0.02417 0.00971 -8.63257; -0.02620 1.02000 0.44332 -61.42802; 0.00083 -0.44376 0.80955 83.30574; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 51 minutes and 53 seconds. #-------------------------------------- #@# CA Normalize Tue Feb 25 13:29:50 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2008-03-26.gca'... 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 = (56, 65, 19) --> (196, 211, 196) using (103, 114, 108) as brain centroid... mean wm in atlas = 107, using box (86,96,86) --> (120, 131,129) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 244171 sample points... INFO: compute sample coordinates transform 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 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 (126, 75, 22) --> (193, 193, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 248.0 1 of 5265 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 75, 24) --> (129, 185, 197) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 248.0 0 of 4905 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 162, 62) --> (176, 203, 118) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 248.0 0 of 134 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 161, 58) --> (128, 202, 119) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 248.0 0 of 167 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 146, 93) --> (143, 207, 128) Brain_Stem: limiting intensities to 93.0 --> 248.0 0 of 431 (0.0%) samples deleted using 10902 total control points for intensity normalization... bias field = 1.011 +- 0.059 12 of 10901 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 75, 22) --> (193, 193, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 240.0 5 of 5228 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 75, 24) --> (129, 185, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 240.0 0 of 4901 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 162, 62) --> (176, 203, 118) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 240.0 0 of 131 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 161, 58) --> (128, 202, 119) Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 240.0 0 of 167 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 146, 93) --> (143, 207, 128) Brain_Stem: limiting intensities to 84.0 --> 240.0 0 of 428 (0.0%) samples deleted using 10855 total control points for intensity normalization... bias field = 1.020 +- 0.039 12 of 10850 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 75, 22) --> (193, 193, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 241.0 1 of 5150 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 75, 24) --> (129, 185, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 241.0 4 of 4803 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 162, 62) --> (176, 203, 118) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 241.0 8 of 131 (6.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 161, 58) --> (128, 202, 119) Right_Cerebellum_White_Matter: limiting intensities to 86.0 --> 241.0 0 of 145 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 146, 93) --> (143, 207, 128) Brain_Stem: limiting intensities to 78.0 --> 241.0 0 of 419 (0.0%) samples deleted using 10648 total control points for intensity normalization... bias field = 1.016 +- 0.030 18 of 10635 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 30 seconds. #-------------------------------------- #@# CA Reg Tue Feb 25 13:32:20 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/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 ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.04 (predicted orig area = 7.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.769, neg=0, invalid=96777 0001: dt=129.472000, rms=0.704 (8.423%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.681 (3.382%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.671 (1.348%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.669 (0.340%), neg=0, invalid=96777 0005: dt=443.904000, rms=0.661 (1.188%), neg=0, invalid=96777 0006: dt=73.984000, rms=0.658 (0.405%), neg=0, invalid=96777 0007: dt=517.888000, rms=0.656 (0.380%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.652 (0.596%), neg=0, invalid=96777 0009: dt=110.976000, rms=0.651 (0.096%), neg=0, invalid=96777 0010: dt=110.976000, rms=0.650 (0.164%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.649 (0.226%), neg=0, invalid=96777 0012: dt=110.976000, rms=0.647 (0.259%), neg=0, invalid=96777 0013: dt=110.976000, rms=0.645 (0.310%), neg=0, invalid=96777 0014: dt=110.976000, rms=0.643 (0.336%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.641 (0.348%), neg=0, invalid=96777 0016: dt=110.976000, rms=0.639 (0.347%), neg=0, invalid=96777 0017: dt=110.976000, rms=0.637 (0.317%), neg=0, invalid=96777 0018: dt=110.976000, rms=0.635 (0.266%), neg=0, invalid=96777 0019: dt=110.976000, rms=0.633 (0.256%), neg=0, invalid=96777 0020: dt=110.976000, rms=0.632 (0.270%), neg=0, invalid=96777 0021: dt=110.976000, rms=0.630 (0.258%), neg=0, invalid=96777 0022: dt=110.976000, rms=0.629 (0.212%), neg=0, invalid=96777 0023: dt=110.976000, rms=0.627 (0.168%), neg=0, invalid=96777 0024: dt=110.976000, rms=0.626 (0.194%), neg=0, invalid=96777 0025: dt=110.976000, rms=0.625 (0.198%), neg=0, invalid=96777 0026: dt=110.976000, rms=0.624 (0.166%), neg=0, invalid=96777 0027: dt=110.976000, rms=0.623 (0.127%), neg=0, invalid=96777 0028: dt=110.976000, rms=0.622 (0.129%), neg=0, invalid=96777 0029: dt=110.976000, rms=0.621 (0.153%), neg=0, invalid=96777 0030: dt=110.976000, rms=0.621 (0.133%), neg=0, invalid=96777 0031: dt=110.976000, rms=0.620 (0.078%), neg=0, invalid=96777 0032: dt=110.976000, rms=0.620 (0.080%), neg=0, invalid=96777 0033: dt=110.976000, rms=0.619 (0.116%), neg=0, invalid=96777 0034: dt=110.976000, rms=0.618 (0.098%), neg=0, invalid=96777 0035: dt=0.000000, rms=0.618 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.618, neg=0, invalid=96777 0036: dt=129.472000, rms=0.618 (0.045%), neg=0, invalid=96777 0037: dt=443.904000, rms=0.617 (0.141%), neg=0, invalid=96777 0038: dt=92.480000, rms=0.617 (0.021%), neg=0, invalid=96777 0039: dt=92.480000, rms=0.617 (0.034%), neg=0, invalid=96777 0040: dt=92.480000, rms=0.617 (0.022%), neg=0, invalid=96777 0041: dt=92.480000, rms=0.617 (0.012%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=96777 0042: dt=145.152000, rms=0.616 (1.069%), neg=0, invalid=96777 0043: dt=62.208000, rms=0.613 (0.573%), neg=0, invalid=96777 0044: dt=103.680000, rms=0.608 (0.788%), neg=0, invalid=96777 0045: dt=25.920000, rms=0.606 (0.233%), neg=0, invalid=96777 0046: dt=25.920000, rms=0.605 (0.183%), neg=0, invalid=96777 0047: dt=25.920000, rms=0.604 (0.287%), neg=0, invalid=96777 0048: dt=25.920000, rms=0.601 (0.369%), neg=0, invalid=96777 0049: dt=25.920000, rms=0.599 (0.412%), neg=0, invalid=96777 0050: dt=25.920000, rms=0.596 (0.461%), neg=0, invalid=96777 0051: dt=25.920000, rms=0.593 (0.470%), neg=0, invalid=96777 0052: dt=25.920000, rms=0.590 (0.471%), neg=0, invalid=96777 0053: dt=25.920000, rms=0.588 (0.461%), neg=0, invalid=96777 0054: dt=25.920000, rms=0.585 (0.433%), neg=0, invalid=96777 0055: dt=25.920000, rms=0.583 (0.381%), neg=0, invalid=96777 0056: dt=25.920000, rms=0.581 (0.345%), neg=0, invalid=96777 0057: dt=25.920000, rms=0.579 (0.319%), neg=0, invalid=96777 0058: dt=25.920000, rms=0.578 (0.280%), neg=0, invalid=96777 0059: dt=25.920000, rms=0.576 (0.265%), neg=0, invalid=96777 0060: dt=25.920000, rms=0.574 (0.262%), neg=0, invalid=96777 0061: dt=25.920000, rms=0.573 (0.235%), neg=0, invalid=96777 0062: dt=25.920000, rms=0.572 (0.199%), neg=0, invalid=96777 0063: dt=25.920000, rms=0.571 (0.177%), neg=0, invalid=96777 0064: dt=25.920000, rms=0.570 (0.143%), neg=0, invalid=96777 0065: dt=25.920000, rms=0.570 (0.115%), neg=0, invalid=96777 0066: dt=25.920000, rms=0.569 (0.109%), neg=0, invalid=96777 0067: dt=82.944000, rms=0.569 (0.038%), neg=0, invalid=96777 0068: dt=82.944000, rms=0.569 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0069: dt=82.944000, rms=0.567 (0.229%), neg=0, invalid=96777 0070: dt=31.104000, rms=0.567 (0.061%), neg=0, invalid=96777 0071: dt=31.104000, rms=0.567 (0.044%), neg=0, invalid=96777 0072: dt=31.104000, rms=0.567 (0.037%), neg=0, invalid=96777 0073: dt=31.104000, rms=0.566 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=96777 0074: dt=7.587629, rms=0.591 (0.105%), neg=0, invalid=96777 0075: dt=2.400000, rms=0.591 (0.007%), neg=0, invalid=96777 0076: dt=2.400000, rms=0.591 (0.003%), neg=0, invalid=96777 0077: dt=2.400000, rms=0.591 (-0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.591, neg=0, invalid=96777 0078: dt=0.300000, rms=0.591 (0.000%), neg=0, invalid=96777 0079: dt=0.300000, rms=0.591 (0.000%), neg=0, invalid=96777 0080: dt=0.115000, rms=0.591 (0.000%), neg=0, invalid=96777 0081: dt=0.001563, rms=0.591 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=96777 0082: dt=5.941973, rms=0.636 (2.681%), neg=0, invalid=96777 0083: dt=3.456000, rms=0.635 (0.131%), neg=0, invalid=96777 0084: dt=3.456000, rms=0.635 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0085: dt=0.000105, rms=0.635 (0.000%), neg=0, invalid=96777 0086: dt=0.000105, rms=0.635 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.694, neg=0, invalid=96777 0087: dt=1.026954, rms=0.691 (0.426%), neg=0, invalid=96777 0088: dt=2.764706, rms=0.684 (1.024%), neg=0, invalid=96777 0089: dt=0.465909, rms=0.684 (0.084%), neg=0, invalid=96777 0090: dt=0.465909, rms=0.683 (0.062%), neg=0, invalid=96777 0091: dt=0.465909, rms=0.682 (0.091%), neg=0, invalid=96777 0092: dt=0.465909, rms=0.682 (0.109%), neg=0, invalid=96777 0093: dt=0.465909, rms=0.681 (0.112%), neg=0, invalid=96777 0094: dt=0.465909, rms=0.681 (0.066%), neg=0, invalid=96777 0095: dt=0.465909, rms=0.680 (-0.038%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.680, neg=0, invalid=96777 0096: dt=1.536000, rms=0.679 (0.170%), neg=0, invalid=96777 0097: dt=0.028000, rms=0.679 (-0.002%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.646, neg=0, invalid=96777 0098: dt=0.448000, rms=0.632 (2.078%), neg=0, invalid=96777 0099: dt=0.000000, rms=0.632 (0.006%), neg=0, invalid=96777 0100: dt=0.050000, rms=0.632 (-0.281%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.632, neg=0, invalid=96777 0101: dt=0.000000, rms=0.632 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08611 (24) Left_Lateral_Ventricle (4): linear fit = 0.83 x + 0.0 (2483 voxels, overlap=0.778) Left_Lateral_Ventricle (4): linear fit = 0.83 x + 0.0 (2483 voxels, peak = 20), gca=20.0 gca peak = 0.14022 (22) mri peak = 0.14286 (23) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (980 voxels, overlap=0.471) Right_Lateral_Ventricle (43): linear fit = 0.87 x + 0.0 (980 voxels, peak = 19), gca=19.0 gca peak = 0.24234 (100) mri peak = 0.11584 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (584 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (584 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.07551 (85) Left_Pallidum (13): linear fit = 0.87 x + 0.0 (521 voxels, overlap=0.052) Left_Pallidum (13): linear fit = 0.87 x + 0.0 (521 voxels, peak = 84), gca=83.9 gca peak = 0.24007 (63) mri peak = 0.09714 (69) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (968 voxels, overlap=0.280) Right_Hippocampus (53): linear fit = 1.09 x + 0.0 (968 voxels, peak = 68), gca=68.4 gca peak = 0.29892 (64) mri peak = 0.15481 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (955 voxels, overlap=0.556) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (955 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.14034 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (88085 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (88085 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.12408 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (90385 voxels, overlap=0.583) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (90385 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.04124 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (37544 voxels, overlap=0.989) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (37544 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.04032 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (43423 voxels, overlap=0.996) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (43423 voxels, peak = 61), gca=60.8 gca peak = 0.15182 (70) mri peak = 0.12240 (76) Right_Caudate (50): linear fit = 1.02 x + 0.0 (506 voxels, overlap=0.765) Right_Caudate (50): linear fit = 1.02 x + 0.0 (506 voxels, peak = 72), gca=71.8 gca peak = 0.14251 (76) mri peak = 0.09004 (78) Left_Caudate (11): linear fit = 0.99 x + 0.0 (970 voxels, overlap=0.972) Left_Caudate (11): linear fit = 0.99 x + 0.0 (970 voxels, peak = 75), gca=74.9 gca peak = 0.12116 (60) mri peak = 0.03313 (68) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27345 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27345 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.03426 (63) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (35986 voxels, overlap=0.963) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (35986 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.11042 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9900 voxels, overlap=0.021) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9900 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.13380 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9444 voxels, overlap=0.378) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9444 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.10766 (68) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (417 voxels, overlap=0.415) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (417 voxels, peak = 67), gca=67.3 gca peak = 0.39668 (62) mri peak = 0.13115 (68) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (271 voxels, overlap=0.879) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (271 voxels, peak = 67), gca=66.7 gca peak = 0.10129 (93) mri peak = 0.06042 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (6474 voxels, overlap=0.803) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (6474 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.05682 (88) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4973 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4973 voxels, peak = 90), gca=90.3 gca peak = 0.13716 (82) mri peak = 0.07423 (88) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3343 voxels, overlap=0.969) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3343 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.06810 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3205 voxels, overlap=0.983) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3205 voxels, peak = 84), gca=83.6 gca peak = 0.08983 (85) mri peak = 0.09572 (92) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12674 voxels, overlap=0.467) Brain_Stem (16): linear fit = 1.09 x + 0.0 (12674 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.10929 (101) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1030 voxels, overlap=0.242) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1030 voxels, peak = 100), gca=99.8 gca peak = 0.12914 (94) mri peak = 0.16272 (103) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1367 voxels, overlap=0.140) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1367 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.14508 (17) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (422 voxels, overlap=0.130) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (422 voxels, peak = 16), gca=16.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) 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) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.05 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.85 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=96777 0102: dt=129.472000, rms=0.645 (1.293%), neg=0, invalid=96777 0103: dt=129.472000, rms=0.642 (0.381%), neg=0, invalid=96777 0104: dt=221.952000, rms=0.639 (0.579%), neg=0, invalid=96777 0105: dt=55.488000, rms=0.638 (0.152%), neg=0, invalid=96777 0106: dt=517.888000, rms=0.635 (0.458%), neg=0, invalid=96777 0107: dt=110.976000, rms=0.632 (0.430%), neg=0, invalid=96777 0108: dt=32.368000, rms=0.632 (0.045%), neg=0, invalid=96777 0109: dt=32.368000, rms=0.632 (0.023%), neg=0, invalid=96777 0110: dt=32.368000, rms=0.631 (0.028%), neg=0, invalid=96777 0111: dt=32.368000, rms=0.631 (0.041%), neg=0, invalid=96777 0112: dt=32.368000, rms=0.631 (0.084%), neg=0, invalid=96777 0113: dt=32.368000, rms=0.630 (0.130%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.629 (0.139%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.628 (0.128%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.627 (0.118%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.627 (0.104%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.626 (0.093%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.626 (0.081%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.625 (0.084%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.625 (0.100%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.624 (0.122%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.623 (0.114%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.622 (0.103%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.622 (0.090%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.621 (0.082%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.621 (0.073%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.620 (0.072%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.620 (0.074%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.619 (0.085%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.619 (0.091%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.618 (0.087%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.618 (0.074%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.618 (0.059%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.617 (0.053%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.617 (0.056%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.617 (0.057%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.616 (0.064%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.616 (0.067%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.615 (0.067%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.615 (0.060%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.615 (0.055%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.614 (0.049%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.614 (0.046%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.614 (0.047%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.613 (0.050%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.613 (0.050%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.613 (0.055%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.612 (0.051%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.612 (0.047%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.612 (0.042%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.612 (0.036%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.611 (0.039%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.611 (0.038%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.611 (0.039%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.611 (0.037%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.611 (0.037%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.610 (0.034%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.610 (0.030%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.610 (0.027%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.610 (0.025%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.610 (0.027%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.609 (0.033%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.609 (0.033%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.609 (0.031%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.609 (0.028%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.609 (0.026%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.609 (0.025%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.608 (0.027%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.608 (0.027%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.608 (0.028%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.608 (0.022%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.608 (0.023%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.608 (0.021%), neg=0, invalid=96777 0175: dt=5918.720000, rms=0.606 (0.320%), neg=0, invalid=96777 0176: dt=73.984000, rms=0.605 (0.092%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.605 (0.040%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.605 (-0.025%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=96777 0179: dt=92.480000, rms=0.605 (0.034%), neg=0, invalid=96777 0180: dt=129.472000, rms=0.604 (0.037%), neg=0, invalid=96777 0181: dt=517.888000, rms=0.604 (0.095%), neg=0, invalid=96777 0182: dt=92.480000, rms=0.604 (0.035%), neg=0, invalid=96777 0183: dt=92.480000, rms=0.604 (0.000%), neg=0, invalid=96777 0184: dt=92.480000, rms=0.604 (0.006%), neg=0, invalid=96777 0185: dt=92.480000, rms=0.604 (0.019%), neg=0, invalid=96777 0186: dt=92.480000, rms=0.603 (0.021%), neg=0, invalid=96777 0187: dt=92.480000, rms=0.603 (0.024%), neg=0, invalid=96777 0188: dt=92.480000, rms=0.603 (0.026%), neg=0, invalid=96777 0189: dt=92.480000, rms=0.603 (0.027%), neg=0, invalid=96777 0190: dt=92.480000, rms=0.603 (0.036%), neg=0, invalid=96777 0191: dt=92.480000, rms=0.603 (0.023%), neg=0, invalid=96777 0192: dt=92.480000, rms=0.602 (0.030%), neg=0, invalid=96777 0193: dt=92.480000, rms=0.602 (0.024%), neg=0, invalid=96777 0194: dt=92.480000, rms=0.602 (0.018%), neg=0, invalid=96777 0195: dt=73.984000, rms=0.602 (0.010%), neg=0, invalid=96777 0196: dt=73.984000, rms=0.602 (0.005%), neg=0, invalid=96777 0197: dt=73.984000, rms=0.602 (0.010%), neg=0, invalid=96777 0198: dt=73.984000, rms=0.602 (0.012%), neg=0, invalid=96777 0199: dt=73.984000, rms=0.602 (0.009%), neg=0, invalid=96777 0200: dt=73.984000, rms=0.602 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0201: dt=2.268000, rms=0.603 (0.036%), neg=0, invalid=96777 0202: dt=0.567000, rms=0.603 (0.008%), neg=0, invalid=96777 0203: dt=0.035437, rms=0.603 (0.000%), neg=0, invalid=96777 0204: dt=0.017719, rms=0.603 (0.000%), neg=0, invalid=96777 0205: dt=0.004430, rms=0.603 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0206: dt=0.000000, rms=0.603 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.607, neg=0, invalid=96777 0207: dt=0.000000, rms=0.607 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=96777 0208: dt=0.000000, rms=0.607 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.619, neg=0, invalid=96777 0209: dt=4.032000, rms=0.600 (3.084%), neg=0, invalid=96777 0210: dt=4.032000, rms=0.586 (2.311%), neg=0, invalid=96777 0211: dt=4.032000, rms=0.576 (1.765%), neg=0, invalid=96777 0212: dt=11.520000, rms=0.554 (3.774%), neg=0, invalid=96777 0213: dt=16.128000, rms=0.542 (2.095%), neg=0, invalid=96777 0214: dt=11.520000, rms=0.539 (0.531%), neg=0, invalid=96777 0215: dt=6.976744, rms=0.537 (0.408%), neg=0, invalid=96777 0216: dt=4.074074, rms=0.536 (0.163%), neg=0, invalid=96777 0217: dt=4.032000, rms=0.536 (0.156%), neg=0, invalid=96777 0218: dt=13.824000, rms=0.534 (0.320%), neg=0, invalid=96777 0219: dt=3.456000, rms=0.533 (0.081%), neg=0, invalid=96777 0220: dt=11.520000, rms=0.532 (0.180%), neg=0, invalid=96777 0221: dt=2.634146, rms=0.532 (0.070%), neg=0, invalid=96777 0222: dt=13.824000, rms=0.531 (0.232%), neg=0, invalid=96777 0223: dt=3.456000, rms=0.531 (0.029%), neg=0, invalid=96777 0224: dt=3.456000, rms=0.530 (0.061%), neg=0, invalid=96777 0225: dt=3.456000, rms=0.530 (0.081%), neg=0, invalid=96777 0226: dt=3.456000, rms=0.529 (0.101%), neg=0, invalid=96777 0227: dt=3.456000, rms=0.529 (0.093%), neg=0, invalid=96777 0228: dt=3.456000, rms=0.528 (0.121%), neg=0, invalid=96777 0229: dt=3.456000, rms=0.528 (0.134%), neg=0, invalid=96777 0230: dt=3.456000, rms=0.527 (0.141%), neg=0, invalid=96777 0231: dt=3.456000, rms=0.526 (0.124%), neg=0, invalid=96777 0232: dt=3.456000, rms=0.526 (0.096%), neg=0, invalid=96777 0233: dt=3.456000, rms=0.525 (0.083%), neg=0, invalid=96777 0234: dt=3.456000, rms=0.525 (0.075%), neg=0, invalid=96777 0235: dt=3.456000, rms=0.525 (0.058%), neg=0, invalid=96777 0236: dt=3.456000, rms=0.524 (0.061%), neg=0, invalid=96777 0237: dt=3.456000, rms=0.524 (0.050%), neg=0, invalid=96777 0238: dt=3.456000, rms=0.524 (0.039%), neg=0, invalid=96777 0239: dt=3.456000, rms=0.524 (0.019%), neg=0, invalid=96777 0240: dt=3.456000, rms=0.524 (0.026%), neg=0, invalid=96777 0241: dt=3.456000, rms=0.523 (0.026%), neg=0, invalid=96777 0242: dt=3.456000, rms=0.523 (0.044%), neg=0, invalid=96777 0243: dt=3.456000, rms=0.523 (0.041%), neg=0, invalid=96777 0244: dt=3.456000, rms=0.523 (0.021%), neg=0, invalid=96777 0245: dt=3.456000, rms=0.523 (0.008%), neg=0, invalid=96777 0246: dt=9.216000, rms=0.523 (0.024%), neg=0, invalid=96777 0247: dt=2.880000, rms=0.523 (0.008%), neg=0, invalid=96777 0248: dt=2.880000, rms=0.523 (0.002%), neg=0, invalid=96777 0249: dt=2.880000, rms=0.523 (0.010%), neg=0, invalid=96777 0250: dt=2.880000, rms=0.523 (0.010%), neg=0, invalid=96777 0251: dt=2.880000, rms=0.522 (0.008%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=96777 0252: dt=5.333333, rms=0.522 (0.085%), neg=0, invalid=96777 0253: dt=1.008000, rms=0.522 (0.002%), neg=0, invalid=96777 0254: dt=1.008000, rms=0.522 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=96777 0255: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=96777 0256: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777 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=96777 0257: dt=0.148913, rms=0.502 (0.900%), neg=0, invalid=96777 0258: dt=0.129348, rms=0.499 (0.564%), neg=0, invalid=96777 0259: dt=0.117325, rms=0.497 (0.392%), neg=0, invalid=96777 0260: dt=0.320000, rms=0.493 (0.853%), neg=0, invalid=96777 0261: dt=0.112000, rms=0.492 (0.154%), neg=0, invalid=96777 0262: dt=0.112000, rms=0.491 (0.131%), neg=0, invalid=96777 0263: dt=0.112000, rms=0.491 (0.119%), neg=0, invalid=96777 0264: dt=0.112000, rms=0.490 (0.105%), neg=0, invalid=96777 0265: dt=0.384000, rms=0.489 (0.313%), neg=0, invalid=96777 0266: dt=0.028000, rms=0.489 (0.016%), neg=0, invalid=96777 0267: dt=0.028000, rms=0.489 (0.013%), neg=0, invalid=96777 0268: dt=0.028000, rms=0.488 (0.028%), neg=0, invalid=96777 0269: dt=0.028000, rms=0.488 (0.041%), neg=0, invalid=96777 0270: dt=0.028000, rms=0.488 (0.049%), neg=0, invalid=96777 0271: dt=0.028000, rms=0.488 (0.057%), neg=0, invalid=96777 0272: dt=0.028000, rms=0.487 (0.062%), neg=0, invalid=96777 0273: dt=0.028000, rms=0.487 (0.065%), neg=0, invalid=96777 0274: dt=0.028000, rms=0.487 (0.068%), neg=0, invalid=96777 0275: dt=0.028000, rms=0.486 (0.070%), neg=0, invalid=96777 0276: dt=0.028000, rms=0.486 (0.068%), neg=0, invalid=96777 0277: dt=0.028000, rms=0.486 (0.071%), neg=0, invalid=96777 0278: dt=0.028000, rms=0.485 (0.064%), neg=0, invalid=96777 0279: dt=0.028000, rms=0.485 (0.063%), neg=0, invalid=96777 0280: dt=0.028000, rms=0.485 (0.061%), neg=0, invalid=96777 0281: dt=0.028000, rms=0.484 (0.059%), neg=0, invalid=96777 0282: dt=0.028000, rms=0.484 (0.051%), neg=0, invalid=96777 0283: dt=0.028000, rms=0.484 (0.049%), neg=0, invalid=96777 0284: dt=0.028000, rms=0.484 (0.045%), neg=0, invalid=96777 0285: dt=0.028000, rms=0.484 (0.038%), neg=0, invalid=96777 0286: dt=0.028000, rms=0.483 (0.037%), neg=0, invalid=96777 0287: dt=0.028000, rms=0.483 (0.031%), neg=0, invalid=96777 0288: dt=0.028000, rms=0.483 (0.033%), neg=0, invalid=96777 0289: dt=0.028000, rms=0.483 (0.027%), neg=0, invalid=96777 0290: dt=0.028000, rms=0.483 (0.023%), neg=0, invalid=96777 0291: dt=0.028000, rms=0.483 (0.022%), neg=0, invalid=96777 0292: dt=0.112000, rms=0.483 (0.003%), neg=0, invalid=96777 0293: dt=0.112000, rms=0.483 (0.001%), neg=0, invalid=96777 0294: dt=0.112000, rms=0.483 (0.003%), neg=0, invalid=96777 0295: dt=0.056000, rms=0.483 (0.000%), neg=0, invalid=96777 0296: dt=0.056000, rms=0.483 (0.001%), neg=0, invalid=96777 0297: dt=0.056000, rms=0.483 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=96777 0298: dt=0.112000, rms=0.481 (0.260%), neg=0, invalid=96777 0299: dt=0.448000, rms=0.478 (0.748%), neg=0, invalid=96777 0300: dt=0.007000, rms=0.478 (-0.002%), neg=0, invalid=96777 0301: dt=0.007000, rms=0.478 (0.000%), neg=0, invalid=96777 0302: dt=0.007000, rms=0.478 (0.000%), neg=0, invalid=96777 0303: dt=0.007000, rms=0.478 (0.001%), neg=0, invalid=96777 0304: dt=0.007000, rms=0.478 (0.001%), neg=0, invalid=96777 0305: dt=0.007000, rms=0.478 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=96777 0306: dt=18.496000, rms=0.475 (0.002%), neg=0, invalid=96777 0307: dt=0.014462, rms=0.475 (0.001%), neg=0, invalid=96777 0308: dt=0.014462, rms=0.475 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=96777 0309: dt=129.472000, rms=0.475 (0.096%), neg=0, invalid=96777 0310: dt=369.920000, rms=0.474 (0.096%), neg=0, invalid=96777 0311: dt=369.920000, rms=0.475 (-0.479%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=96777 0312: dt=36.288000, rms=0.474 (0.181%), neg=0, invalid=96777 0313: dt=82.944000, rms=0.473 (0.232%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.472 (0.165%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.471 (0.097%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.471 (0.119%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.470 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0318: dt=36.288000, rms=0.469 (0.086%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0319: dt=36.288000, rms=0.469 (0.055%), neg=0, invalid=96777 0320: dt=414.720000, rms=0.468 (0.319%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.467 (0.080%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.467 (0.026%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.467 (0.015%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.467 (0.012%), neg=0, invalid=96777 0325: dt=124.416000, rms=0.467 (0.032%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.467 (0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 0327: dt=62.208000, rms=0.465 (0.428%), neg=0, invalid=96777 0328: dt=36.288000, rms=0.464 (0.130%), neg=0, invalid=96777 0329: dt=36.288000, rms=0.464 (0.076%), neg=0, invalid=96777 0330: dt=36.288000, rms=0.463 (0.134%), neg=0, invalid=96777 0331: dt=36.288000, rms=0.463 (0.133%), neg=0, invalid=96777 0332: dt=36.288000, rms=0.462 (0.118%), neg=0, invalid=96777 0333: dt=36.288000, rms=0.462 (0.097%), neg=0, invalid=96777 0334: dt=103.680000, rms=0.462 (0.033%), neg=0, invalid=96777 0335: dt=103.680000, rms=0.461 (-0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0336: dt=11.200000, rms=0.461 (0.205%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0337: dt=38.400000, rms=0.460 (0.301%), neg=0, invalid=96777 0338: dt=11.200000, rms=0.459 (0.239%), neg=0, invalid=96777 0339: dt=11.200000, rms=0.458 (0.158%), neg=0, invalid=96777 0340: dt=11.200000, rms=0.457 (0.250%), neg=0, invalid=96777 0341: dt=11.200000, rms=0.456 (0.325%), neg=0, invalid=96777 0342: dt=11.200000, rms=0.454 (0.310%), neg=0, invalid=96777 0343: dt=11.200000, rms=0.453 (0.302%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0344: dt=11.200000, rms=0.452 (0.267%), neg=0, invalid=96777 0345: dt=11.200000, rms=0.450 (0.269%), neg=0, invalid=96777 0346: dt=11.200000, rms=0.449 (0.238%), neg=0, invalid=96777 0347: dt=11.200000, rms=0.448 (0.246%), neg=0, invalid=96777 0348: dt=11.200000, rms=0.447 (0.215%), neg=0, invalid=96777 0349: dt=11.200000, rms=0.446 (0.211%), neg=0, invalid=96777 0350: dt=11.200000, rms=0.445 (0.184%), neg=0, invalid=96777 0351: dt=11.200000, rms=0.445 (0.178%), neg=0, invalid=96777 0352: dt=11.200000, rms=0.444 (0.144%), neg=0, invalid=96777 0353: dt=11.200000, rms=0.443 (0.141%), neg=0, invalid=96777 0354: dt=11.200000, rms=0.443 (0.103%), neg=0, invalid=96777 0355: dt=11.200000, rms=0.443 (0.079%), neg=0, invalid=96777 0356: dt=19.200000, rms=0.442 (0.030%), neg=0, invalid=96777 0357: dt=19.200000, rms=0.442 (0.007%), neg=0, invalid=96777 0358: dt=19.200000, rms=0.442 (0.020%), neg=0, invalid=96777 0359: dt=19.200000, rms=0.442 (0.037%), neg=0, invalid=96777 0360: dt=19.200000, rms=0.442 (0.016%), neg=0, invalid=96777 0361: dt=19.200000, rms=0.442 (0.015%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0362: dt=25.600000, rms=0.440 (0.443%), neg=0, invalid=96777 0363: dt=8.000000, rms=0.439 (0.166%), neg=0, invalid=96777 0364: dt=8.000000, rms=0.439 (0.107%), neg=0, invalid=96777 0365: dt=8.000000, rms=0.438 (0.120%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0366: dt=8.000000, rms=0.438 (0.135%), neg=0, invalid=96777 0367: dt=8.000000, rms=0.437 (0.100%), neg=0, invalid=96777 0368: dt=8.000000, rms=0.437 (0.079%), neg=0, invalid=96777 0369: dt=11.200000, rms=0.437 (0.040%), neg=0, invalid=96777 0370: dt=11.200000, rms=0.437 (0.018%), neg=0, invalid=96777 0371: dt=11.200000, rms=0.436 (0.038%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.436 (0.058%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.436 (0.038%), neg=0, invalid=96777 0374: dt=11.200000, rms=0.436 (0.033%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 0375: dt=0.720000, rms=0.444 (0.004%), neg=0, invalid=96777 0376: dt=0.252000, rms=0.444 (0.001%), neg=0, invalid=96777 0377: dt=0.252000, rms=0.444 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0378: dt=4.032000, rms=0.444 (0.053%), neg=0, invalid=96777 0379: dt=0.180000, rms=0.444 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=96777 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0380: dt=0.518519, rms=0.458 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0381: dt=0.518519, rms=0.457 (0.098%), neg=0, invalid=96777 0382: dt=0.518519, rms=0.457 (0.047%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0383: dt=0.518519, rms=0.457 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=96777 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0384: dt=1.905660, rms=0.455 (0.360%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0385: dt=0.320000, rms=0.455 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0386: dt=0.320000, rms=0.455 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0387: dt=0.320000, rms=0.455 (0.013%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0388: dt=0.320000, rms=0.455 (-0.009%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 iter 0, gcam->neg = 510 after 27 iterations, nbhd size=3, neg = 0 0389: dt=1.787280, rms=0.417 (6.041%), neg=0, invalid=96777 0390: dt=0.000109, rms=0.417 (-0.002%), neg=0, invalid=96777 0391: dt=0.000109, rms=0.417 (0.000%), neg=0, invalid=96777 0392: dt=0.000109, rms=0.417 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=96777 0393: dt=0.001750, rms=0.417 (0.002%), neg=0, invalid=96777 0394: dt=0.003000, rms=0.417 (0.000%), neg=0, invalid=96777 0395: dt=0.003000, rms=0.417 (0.001%), neg=0, invalid=96777 0396: dt=0.003000, rms=0.417 (-0.002%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0397: dt=0.000000, rms=0.406 (-0.182%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0398: dt=92.480000, rms=0.406 (0.015%), neg=0, invalid=96777 0399: dt=129.472000, rms=0.406 (0.009%), neg=0, invalid=96777 0400: dt=129.472000, rms=0.406 (0.004%), neg=0, invalid=96777 0401: dt=129.472000, rms=0.406 (0.009%), neg=0, invalid=96777 0402: dt=129.472000, rms=0.406 (0.006%), neg=0, invalid=96777 0403: dt=129.472000, rms=0.406 (0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0404: dt=0.567000, rms=0.406 (0.000%), neg=0, invalid=96777 0405: dt=0.060750, rms=0.406 (0.000%), neg=0, invalid=96777 0406: dt=0.060750, rms=0.406 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 39 iterations, nbhd size=2, neg = 0 0407: dt=145.152000, rms=0.405 (0.143%), neg=0, invalid=96777 0408: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0409: dt=0.010937, rms=0.406 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0410: dt=11.200000, rms=0.405 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0411: dt=11.200000, rms=0.405 (0.063%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.405 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0413: dt=11.200000, rms=0.404 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0414: dt=11.200000, rms=0.404 (-0.045%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 10 iterations, nbhd size=1, neg = 0 0415: dt=25.600000, rms=0.402 (0.644%), neg=0, invalid=96777 0416: dt=19.200000, rms=0.401 (0.250%), neg=0, invalid=96777 0417: dt=19.200000, rms=0.400 (0.178%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 32 iterations, nbhd size=4, neg = 0 0418: dt=19.200000, rms=0.399 (0.217%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0419: dt=19.200000, rms=0.399 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0420: dt=19.200000, rms=0.398 (0.184%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 28 iterations, nbhd size=4, neg = 0 0421: dt=19.200000, rms=0.398 (0.131%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0422: dt=19.200000, rms=0.397 (0.216%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0423: dt=19.200000, rms=0.396 (0.236%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 23 iterations, nbhd size=3, neg = 0 0424: dt=19.200000, rms=0.395 (0.178%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0425: dt=19.200000, rms=0.395 (0.108%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0426: dt=19.200000, rms=0.394 (0.124%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0427: dt=19.200000, rms=0.393 (0.207%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.003 (29.673%) 0428: dt=19.200000, rms=0.393 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.002 (49.573%) 0429: dt=19.200000, rms=0.392 (0.083%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 12 iterations, nbhd size=2, neg = 0 0430: dt=19.200000, rms=0.392 (0.073%), neg=0, invalid=96777 0431: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.397, neg=0, invalid=96777 0432: dt=0.000984, rms=0.397 (0.000%), neg=0, invalid=96777 0433: dt=0.000984, rms=0.397 (0.000%), neg=0, invalid=96777 0434: dt=0.000984, rms=0.397 (0.000%), neg=0, invalid=96777 0435: dt=0.000984, rms=0.397 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=96777 0436: dt=0.252000, rms=0.397 (0.003%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.002 (59.174%) 0437: dt=4.500000, rms=0.396 (0.141%), neg=0, invalid=96777 0438: dt=1.008000, rms=0.396 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0439: dt=1.008000, rms=0.396 (0.019%), neg=0, invalid=96777 0440: dt=1.008000, rms=0.396 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0441: dt=1.008000, rms=0.396 (0.026%), neg=0, invalid=96777 0442: dt=1.008000, rms=0.396 (0.014%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 0 iterations, nbhd size=0, neg = 0 0443: dt=1.008000, rms=0.396 (-0.008%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0444: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0445: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 315 after 17 iterations, nbhd size=2, neg = 0 0446: dt=0.768000, rms=0.382 (2.399%), neg=0, invalid=96777 0447: dt=0.000188, rms=0.382 (0.002%), neg=0, invalid=96777 0448: dt=0.000188, rms=0.382 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.382, neg=0, invalid=96777 0449: dt=0.001750, rms=0.382 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 7 iterations, nbhd size=1, neg = 0 0450: dt=0.096000, rms=0.382 (0.046%), neg=0, invalid=96777 0451: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0452: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0453: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0454: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0455: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0456: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0457: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0458: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0459: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0460: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0461: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0462: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0463: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0464: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0465: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0466: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0467: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0468: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0469: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0470: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0471: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0472: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0473: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0474: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0475: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0476: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0477: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0478: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 0479: dt=0.000047, rms=0.382 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 8 hours, 13 minutes and 52 seconds. #-------------------------------------- #@# CA Reg Inv Tue Feb 25 21:46:13 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Feb 25 21:47:59 EST 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10395992 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 2 minutes and 0 seconds. #-------------------------------------- #@# SkullLTA Tue Feb 25 21:50:01 EST 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= 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_2.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... 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=6.0 skull bounding box = (38, 51, 0) --> (211, 219, 223) using (96, 107, 112) as brain centroid... mean wm in atlas = 126, using box (75,86,84) --> (117, 127,139) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.017 0.024 0.010 -8.633; -0.030 1.173 0.510 -88.809; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.017 0.024 0.010 -8.633; -0.030 1.173 0.510 -88.809; 0.001 -0.444 0.810 83.306; 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=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.017 -0.013 -0.006 -1.975; 0.004 1.142 0.466 -82.572; -0.000 -0.404 0.826 76.194; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.016 -0.026 0.021 -2.883; 0.004 1.164 0.475 -86.391; -0.034 -0.411 0.842 79.909; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.016 -0.020 0.008 -1.297; 0.005 1.170 0.461 -86.873; -0.017 -0.391 0.848 73.515; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.016 -0.020 0.008 -1.297; 0.005 1.170 0.461 -86.873; -0.017 -0.391 0.848 73.515; 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 1.01564 -0.01998 0.00759 -1.29651; 0.00490 1.17009 0.46094 -86.87330; -0.01737 -0.39141 0.84848 73.51492; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.01564 -0.01998 0.00759 -1.29651; 0.00490 1.17009 0.46094 -86.87330; -0.01737 -0.39141 0.84848 73.51492; 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) = -0.0 tol 0.000010 Resulting transform: 1.016 -0.020 0.008 -1.297; 0.005 1.170 0.461 -86.873; -0.017 -0.391 0.848 73.515; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.016 -0.020 0.008 -1.297; 0.005 1.170 0.461 -86.873; -0.017 -0.391 0.848 73.515; 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 1.01564 -0.01998 0.00759 -1.29651; 0.00490 1.17009 0.46094 -86.87330; -0.01737 -0.39141 0.84848 73.51492; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.01564 -0.01998 0.00759 -1.29651; 0.00490 1.17009 0.46094 -86.87330; -0.01737 -0.39141 0.84848 73.51492; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000 final transform: 1.016 -0.020 0.008 -1.297; 0.005 1.170 0.461 -86.873; -0.017 -0.391 0.848 73.515; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 58 minutes and 16 seconds. #-------------------------------------- #@# SubCort Seg Tue Feb 25 22:48:17 EST 2014 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute11 machine x86_64 user Skhadka2 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 norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute11 machine x86_64 setenv SUBJECTS_DIR /prod3/allegra/barcs_fs/tmp cd /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/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 reading 1 input volumes... reading classifier array from /opt/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /opt/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 = 0.14762 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (421 voxels, overlap=0.593) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (421 voxels, peak = 22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.13913 (20) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (343 voxels, overlap=0.621) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (343 voxels, peak = 18), gca=17.7 gca peak = 0.28003 (97) mri peak = 0.20812 (102) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (394 voxels, overlap=1.009) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (394 voxels, peak = 100), gca=100.4 gca peak = 0.18160 (96) mri peak = 0.11388 (98) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (137 voxels, overlap=0.849) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (137 voxels, peak = 93), gca=92.6 gca peak = 0.27536 (62) mri peak = 0.12446 (67) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (787 voxels, overlap=0.397) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (787 voxels, peak = 67), gca=66.7 gca peak = 0.32745 (63) mri peak = 0.16222 (68) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (968 voxels, overlap=0.520) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (968 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.15822 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52014 voxels, overlap=0.579) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52014 voxels, peak = 106), gca=105.5 gca peak = 0.09209 (106) mri peak = 0.14047 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (44298 voxels, overlap=0.544) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (44298 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04857 (63) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (52774 voxels, overlap=0.955) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (52774 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04695 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (48344 voxels, overlap=0.911) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (48344 voxels, peak = 62), gca=61.8 gca peak = 0.24164 (71) mri peak = 0.17433 (75) Right_Caudate (50): linear fit = 1.03 x + 0.0 (631 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.03 x + 0.0 (631 voxels, peak = 73), gca=73.5 gca peak = 0.18227 (75) mri peak = 0.13846 (79) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1103 voxels, overlap=0.940) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1103 voxels, peak = 76), gca=76.1 gca peak = 0.10629 (62) mri peak = 0.04558 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (24260 voxels, overlap=0.977) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (24260 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.04530 (64) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24982 voxels, overlap=0.972) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (24982 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.18628 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5565 voxels, overlap=0.252) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5565 voxels, peak = 94), gca=93.7 gca peak = 0.16819 (86) mri peak = 0.17900 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5635 voxels, overlap=0.277) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5635 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.13816 (68) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (456 voxels, overlap=0.150) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (456 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.12848 (68) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (419 voxels, overlap=1.026) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (419 voxels, peak = 69), gca=68.5 gca peak = 0.10041 (96) mri peak = 0.07521 (95) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5357 voxels, overlap=0.863) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5357 voxels, peak = 99), gca=99.4 gca peak = 0.13978 (88) mri peak = 0.08127 (90) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4829 voxels, overlap=0.972) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4829 voxels, peak = 89), gca=89.3 gca peak = 0.08514 (81) mri peak = 0.09864 (83) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2165 voxels, overlap=0.884) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2165 voxels, peak = 82), gca=82.2 gca peak = 0.09624 (82) mri peak = 0.10607 (82) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2787 voxels, overlap=0.889) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2787 voxels, peak = 85), gca=84.9 gca peak = 0.07543 (88) mri peak = 0.08791 (92) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11965 voxels, overlap=0.658) Brain_Stem (16): linear fit = 1.05 x + 0.0 (11965 voxels, peak = 93), gca=92.8 gca peak = 0.12757 (95) mri peak = 0.12624 (102) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1253 voxels, overlap=0.280) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1253 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.16227 (103) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1310 voxels, overlap=0.247) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1310 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.10826 (18) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (112 voxels, overlap=0.328) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (112 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) 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 1.05 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14539 (23) mri peak = 0.14762 (22) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (421 voxels, overlap=0.929) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (421 voxels, peak = 22), gca=22.4 gca peak = 0.21680 (18) mri peak = 0.13913 (20) Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (343 voxels, overlap=0.789) Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (343 voxels, peak = 18), gca=17.7 gca peak = 0.25294 (101) mri peak = 0.20812 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (394 voxels, peak = 101), gca=101.0 gca peak = 0.20055 (92) mri peak = 0.11388 (98) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (137 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (137 voxels, peak = 93), gca=93.4 gca peak = 0.26261 (67) mri peak = 0.12446 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (787 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (787 voxels, peak = 67), gca=67.0 gca peak = 0.28946 (67) mri peak = 0.16222 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (968 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (968 voxels, peak = 67), gca=67.0 gca peak = 0.08557 (106) mri peak = 0.15822 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52014 voxels, overlap=0.588) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52014 voxels, peak = 107), gca=106.5 gca peak = 0.08752 (107) mri peak = 0.14047 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44298 voxels, overlap=0.573) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (44298 voxels, peak = 108), gca=107.5 gca peak = 0.07876 (62) mri peak = 0.04857 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (52774 voxels, overlap=0.973) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (52774 voxels, peak = 64), gca=63.5 gca peak = 0.09132 (62) mri peak = 0.04695 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (48344 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (48344 voxels, peak = 64), gca=63.5 gca peak = 0.28607 (76) mri peak = 0.17433 (75) Right_Caudate (50): linear fit = 1.00 x + 0.0 (631 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (631 voxels, peak = 76), gca=76.0 gca peak = 0.18153 (76) mri peak = 0.13846 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1103 voxels, overlap=0.852) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1103 voxels, peak = 76), gca=76.0 gca peak = 0.10430 (63) mri peak = 0.04558 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (24260 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (24260 voxels, peak = 65), gca=64.6 gca peak = 0.12169 (64) mri peak = 0.04530 (64) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (24982 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (24982 voxels, peak = 63), gca=63.0 gca peak = 0.17927 (93) mri peak = 0.18628 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5565 voxels, overlap=0.896) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5565 voxels, peak = 93), gca=92.5 gca peak = 0.16064 (92) mri peak = 0.17900 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5635 voxels, overlap=0.905) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5635 voxels, peak = 92), gca=91.5 gca peak = 0.30598 (70) mri peak = 0.13816 (68) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (456 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (456 voxels, peak = 70), gca=70.0 gca peak = 0.32761 (68) mri peak = 0.12848 (68) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (419 voxels, overlap=1.005) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (419 voxels, peak = 67), gca=67.0 gca peak = 0.10678 (99) mri peak = 0.07521 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5357 voxels, overlap=0.984) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5357 voxels, peak = 99), gca=99.5 gca peak = 0.11452 (89) mri peak = 0.08127 (90) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4829 voxels, overlap=0.940) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4829 voxels, peak = 89), gca=88.6 gca peak = 0.07944 (82) mri peak = 0.09864 (83) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2165 voxels, overlap=0.941) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2165 voxels, peak = 82), gca=82.0 gca peak = 0.09612 (85) mri peak = 0.10607 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2787 voxels, overlap=0.857) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2787 voxels, peak = 85), gca=85.0 gca peak = 0.06954 (93) mri peak = 0.08791 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11965 voxels, overlap=0.800) Brain_Stem (16): linear fit = 1.00 x + 0.0 (11965 voxels, peak = 93), gca=93.5 gca peak = 0.13181 (98) mri peak = 0.12624 (102) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1253 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1253 voxels, peak = 98), gca=98.0 gca peak = 0.15766 (99) mri peak = 0.16227 (103) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1310 voxels, overlap=0.828) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1310 voxels, peak = 100), gca=100.5 gca peak = 0.21697 (31) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.22371 (20) mri peak = 0.10826 (18) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (112 voxels, overlap=0.484) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (112 voxels, peak = 16), gca=15.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.20906 (38) gca peak Third_Ventricle = 0.21697 (31) gca peak CSF = 0.26436 (33) gca peak Left_Accumbens_area = 0.56798 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65267 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.35686 (74) gca peak Right_vessel = 0.83490 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (36) gca peak WM_hypointensities = 0.15881 (82) gca peak non_WM_hypointensities = 0.09425 (53) gca peak Optic_Chiasm = 0.34488 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.92 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 18919 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 319 hippocampal voxels changed. 3 amygdala voxels changed. pass 1: 97385 changed. image ll: -2.241, PF=1.000 pass 2: 17267 changed. image ll: -2.237, PF=1.000 pass 3: 5569 changed. pass 4: 2238 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 34 minutes and 53 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/transforms/cc_up.lta S8861CSO1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/transforms/cc_up.lta reading aseg from /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/aseg.auto_noCCseg.mgz reading norm from /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/norm.mgz 32379 voxels in left wm, 51045 in right wm, xrange [123, 130] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 global minimum found at slice 127.0, rotations (-0.10, -0.55) final transformation (x=127.0, yr=-0.104, zr=-0.546): 1.000 0.010 -0.002 0.059; -0.010 1.000 0.000 11.214; 0.002 0.000 1.000 29.770; 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 128 155 118 eigenvectors: -0.002 0.005 1.000; -0.302 -0.953 0.005; 0.953 -0.302 0.004; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.3 minutes #-------------------------------------- #@# Merge ASeg Tue Feb 25 23:24:42 EST 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Feb 25 23:24:42 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_normalize -mprage -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 805 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 24 (24) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 71 (71), valley at 25 (25) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 6 minutes and 20 seconds. #-------------------------------------------- #@# Mask BFS Tue Feb 25 23:31:13 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2010971 voxels in mask (pct= 11.99) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Feb 25 23:31:21 EST 2014 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute11 machine x86_64 user Skhadka2 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 0 values in range Counting number of voxels Found 0 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute11 machine x86_64 user Skhadka2 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 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep -mprage 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 (105.0): 104.8 +- 6.6 [79.0 --> 125.0] GM (73.0) : 71.6 +- 9.9 [30.0 --> 95.0] setting bottom of white matter range to 81.5 setting top of gray matter range to 91.4 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... 7998 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4597 filled 5364 bright non-wm voxels segmented. 3757 diagonally connected voxels added... white matter segmentation took 3.1 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE 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 1.34 minutes reading wm segmentation from wm.seg.mgz... 113 voxels added to wm to prevent paths from MTL structures to cortex 1536 additional wm voxels added 0 additional wm voxels added SEG EDIT: 31197 voxels turned on, 44295 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 25 found - 25 modified | TOTAL: 25 pass 2 (xy+): 0 found - 25 modified | TOTAL: 25 pass 1 (xy-): 33 found - 33 modified | TOTAL: 58 pass 2 (xy-): 0 found - 33 modified | TOTAL: 58 pass 1 (yz+): 50 found - 50 modified | TOTAL: 108 pass 2 (yz+): 0 found - 50 modified | TOTAL: 108 pass 1 (yz-): 32 found - 32 modified | TOTAL: 140 pass 2 (yz-): 0 found - 32 modified | TOTAL: 140 pass 1 (xz+): 29 found - 29 modified | TOTAL: 169 pass 2 (xz+): 0 found - 29 modified | TOTAL: 169 pass 1 (xz-): 27 found - 27 modified | TOTAL: 196 pass 2 (xz-): 0 found - 27 modified | TOTAL: 196 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 32 found - 32 modified | TOTAL: 52 pass 2 (+++): 0 found - 32 modified | TOTAL: 52 pass 1 (+++): 25 found - 25 modified | TOTAL: 77 pass 2 (+++): 0 found - 25 modified | TOTAL: 77 pass 1 (+++): 17 found - 17 modified | TOTAL: 94 pass 2 (+++): 0 found - 17 modified | TOTAL: 94 Iteration Number : 1 pass 1 (++): 137 found - 137 modified | TOTAL: 137 pass 2 (++): 0 found - 137 modified | TOTAL: 137 pass 1 (+-): 187 found - 187 modified | TOTAL: 324 pass 2 (+-): 0 found - 187 modified | TOTAL: 324 pass 1 (--): 161 found - 161 modified | TOTAL: 485 pass 2 (--): 0 found - 161 modified | TOTAL: 485 pass 1 (-+): 127 found - 127 modified | TOTAL: 612 pass 2 (-+): 0 found - 127 modified | TOTAL: 612 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 5 found - 5 modified | TOTAL: 10 pass 2 (xy-): 0 found - 5 modified | TOTAL: 10 pass 1 (yz+): 2 found - 2 modified | TOTAL: 12 pass 2 (yz+): 0 found - 2 modified | TOTAL: 12 pass 1 (yz-): 5 found - 5 modified | TOTAL: 17 pass 2 (yz-): 0 found - 5 modified | TOTAL: 17 pass 1 (xz+): 2 found - 2 modified | TOTAL: 19 pass 2 (xz+): 0 found - 2 modified | TOTAL: 19 pass 1 (xz-): 5 found - 5 modified | TOTAL: 24 pass 2 (xz-): 0 found - 5 modified | TOTAL: 24 Iteration Number : 2 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 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 0 found - 0 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 1 found - 1 modified | TOTAL: 6 pass 2 (-+): 0 found - 1 modified | TOTAL: 6 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 = 936 (out of 643245: 0.145512) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue Feb 25 23:36:32 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/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 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.017 0.024 0.010 -8.633; -0.026 1.020 0.443 -61.428; 0.001 -0.444 0.810 83.306; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 900 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max = 0.75) no need to search using seed (125, 119, 147), TAL = (3.0, 19.0, 9.0) talairach voxel to voxel transform 0.983 -0.023 0.001 7.012; 0.021 0.791 -0.434 84.903; 0.010 0.434 0.998 -56.370; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 119, 147) --> (3.0, 19.0, 9.0) done. writing output to filled.mgz... filling took 1.7 minutes talairach cc position changed to (3.00, 19.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 19.00, 9.00) SRC: (109.59, 117.55, 143.00) search lh wm seed point around talairach space (-15.00, 19.00, 9.00), SRC: (144.98, 118.30, 143.38) 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 ... #-------------------------------------------- #@# Tessellate lh Tue Feb 25 23:38:13 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 4 found - 4 modified | TOTAL: 4 pass 2 (xy-): 0 found - 4 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 2 found - 2 modified | TOTAL: 13 pass 2 (xz-): 0 found - 2 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 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 0 found - 0 modified | TOTAL: 4 pass 1 (--): 0 found - 0 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 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 = 20 (out of 309415: 0.006464) 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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 2172 vertices, 2369 faces slice 40: 11309 vertices, 11730 faces slice 50: 24780 vertices, 25293 faces slice 60: 39881 vertices, 40388 faces slice 70: 54227 vertices, 54726 faces slice 80: 67935 vertices, 68361 faces slice 90: 80905 vertices, 81364 faces slice 100: 93523 vertices, 93989 faces slice 110: 105415 vertices, 105872 faces slice 120: 116266 vertices, 116682 faces slice 130: 127154 vertices, 127627 faces slice 140: 137732 vertices, 138128 faces slice 150: 147736 vertices, 148179 faces slice 160: 156025 vertices, 156358 faces slice 170: 162380 vertices, 162674 faces slice 180: 167051 vertices, 167266 faces slice 190: 169658 vertices, 169801 faces slice 200: 169824 vertices, 169926 faces slice 210: 169824 vertices, 169926 faces slice 220: 169824 vertices, 169926 faces slice 230: 169824 vertices, 169926 faces slice 240: 169824 vertices, 169926 faces slice 250: 169824 vertices, 169926 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... 169824 voxel in cpt #1: X=-102 [v=169824,e=509778,f=339852] located at (-26.469328, -32.001602, -2.578258) For the whole surface: X=-102 [v=169824,e=509778,f=339852] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Feb 25 23:38:36 EST 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Feb 25 23:38:47 EST 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts avg radius = 51.4 mm, total surface area = 89232 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 2.0 minutes Not saving sulc step 000: RMS=0.104 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.051 (target=0.015) step 020: RMS=0.045 (target=0.015) step 025: RMS=0.041 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Feb 25 23:40:48 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.55 (0.00-->6.61) (max @ vno 131249 --> 132334) face area 0.02 +- 0.03 (-0.11-->0.78) scaling brain by 0.294... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.455, avgs=0 005/300: dt: 0.9000, rms radial error=175.200, avgs=0 010/300: dt: 0.9000, rms radial error=174.653, avgs=0 015/300: dt: 0.9000, rms radial error=173.935, avgs=0 020/300: dt: 0.9000, rms radial error=173.118, avgs=0 025/300: dt: 0.9000, rms radial error=172.243, avgs=0 030/300: dt: 0.9000, rms radial error=171.336, avgs=0 035/300: dt: 0.9000, rms radial error=170.411, avgs=0 040/300: dt: 0.9000, rms radial error=169.478, avgs=0 045/300: dt: 0.9000, rms radial error=168.540, avgs=0 050/300: dt: 0.9000, rms radial error=167.602, avgs=0 055/300: dt: 0.9000, rms radial error=166.666, avgs=0 060/300: dt: 0.9000, rms radial error=165.733, avgs=0 065/300: dt: 0.9000, rms radial error=164.803, avgs=0 070/300: dt: 0.9000, rms radial error=163.877, avgs=0 075/300: dt: 0.9000, rms radial error=162.955, avgs=0 080/300: dt: 0.9000, rms radial error=162.038, avgs=0 085/300: dt: 0.9000, rms radial error=161.126, avgs=0 090/300: dt: 0.9000, rms radial error=160.217, avgs=0 095/300: dt: 0.9000, rms radial error=159.313, avgs=0 100/300: dt: 0.9000, rms radial error=158.413, avgs=0 105/300: dt: 0.9000, rms radial error=157.518, avgs=0 110/300: dt: 0.9000, rms radial error=156.628, avgs=0 115/300: dt: 0.9000, rms radial error=155.742, avgs=0 120/300: dt: 0.9000, rms radial error=154.860, avgs=0 125/300: dt: 0.9000, rms radial error=153.983, avgs=0 130/300: dt: 0.9000, rms radial error=153.111, avgs=0 135/300: dt: 0.9000, rms radial error=152.243, avgs=0 140/300: dt: 0.9000, rms radial error=151.381, avgs=0 145/300: dt: 0.9000, rms radial error=150.526, avgs=0 150/300: dt: 0.9000, rms radial error=149.677, avgs=0 155/300: dt: 0.9000, rms radial error=148.832, avgs=0 160/300: dt: 0.9000, rms radial error=147.992, avgs=0 165/300: dt: 0.9000, rms radial error=147.157, avgs=0 170/300: dt: 0.9000, rms radial error=146.326, avgs=0 175/300: dt: 0.9000, rms radial error=145.500, avgs=0 180/300: dt: 0.9000, rms radial error=144.679, avgs=0 185/300: dt: 0.9000, rms radial error=143.862, avgs=0 190/300: dt: 0.9000, rms radial error=143.051, avgs=0 195/300: dt: 0.9000, rms radial error=142.243, avgs=0 200/300: dt: 0.9000, rms radial error=141.441, avgs=0 205/300: dt: 0.9000, rms radial error=140.643, avgs=0 210/300: dt: 0.9000, rms radial error=139.849, avgs=0 215/300: dt: 0.9000, rms radial error=139.060, avgs=0 220/300: dt: 0.9000, rms radial error=138.276, avgs=0 225/300: dt: 0.9000, rms radial error=137.496, avgs=0 230/300: dt: 0.9000, rms radial error=136.721, avgs=0 235/300: dt: 0.9000, rms radial error=135.950, avgs=0 240/300: dt: 0.9000, rms radial error=135.183, avgs=0 245/300: dt: 0.9000, rms radial error=134.421, avgs=0 250/300: dt: 0.9000, rms radial error=133.663, avgs=0 255/300: dt: 0.9000, rms radial error=132.910, avgs=0 260/300: dt: 0.9000, rms radial error=132.161, avgs=0 265/300: dt: 0.9000, rms radial error=131.416, avgs=0 270/300: dt: 0.9000, rms radial error=130.675, avgs=0 275/300: dt: 0.9000, rms radial error=129.939, avgs=0 280/300: dt: 0.9000, rms radial error=129.206, avgs=0 285/300: dt: 0.9000, rms radial error=128.478, avgs=0 290/300: dt: 0.9000, rms radial error=127.754, avgs=0 295/300: dt: 0.9000, rms radial error=127.033, avgs=0 300/300: dt: 0.9000, rms radial error=126.318, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20268.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 3561.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 414.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00507 epoch 4 (K=640.0), pass 1, starting sse = 33.28 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00988 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.23 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Feb 25 23:54:46 EST 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 S8861CSO1 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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-102 (nv=169824, nf=339852, ne=509778, g=52) 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... 5901 ambiguous faces found in tessellation segmenting defects... 63 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 2 -merging segment 9 into 8 -merging segment 11 into 8 -merging segment 22 into 17 -merging segment 40 into 38 58 defects to be corrected 0 vertices coincident reading input surface /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3837 (-4.6918) -vertex loglikelihood: -6.3365 (-3.1683) -normal dot loglikelihood: -3.5389 (-3.5389) -quad curv loglikelihood: -6.4856 (-3.2428) Total Loglikelihood : -25.7447 CORRECTING DEFECT 0 (vertices=25, convex hull=66) After retessellation of defect 0, euler #=-58 (166152,496809,330599) : difference with theory (-55) = 3 CORRECTING DEFECT 1 (vertices=21, convex hull=41) After retessellation of defect 1, euler #=-57 (166156,496839,330626) : difference with theory (-54) = 3 CORRECTING DEFECT 2 (vertices=81, convex hull=97) After retessellation of defect 2, euler #=-55 (166169,496921,330697) : difference with theory (-53) = 2 CORRECTING DEFECT 3 (vertices=25, convex hull=55) After retessellation of defect 3, euler #=-54 (166180,496976,330742) : difference with theory (-52) = 2 CORRECTING DEFECT 4 (vertices=6, convex hull=30) After retessellation of defect 4, euler #=-53 (166180,496986,330753) : difference with theory (-51) = 2 CORRECTING DEFECT 5 (vertices=28, convex hull=62) After retessellation of defect 5, euler #=-52 (166190,497040,330798) : difference with theory (-50) = 2 CORRECTING DEFECT 6 (vertices=23, convex hull=63) After retessellation of defect 6, euler #=-51 (166198,497089,330840) : difference with theory (-49) = 2 CORRECTING DEFECT 7 (vertices=121, convex hull=168) After retessellation of defect 7, euler #=-48 (166237,497290,331005) : difference with theory (-48) = 0 CORRECTING DEFECT 8 (vertices=30, convex hull=67) After retessellation of defect 8, euler #=-47 (166257,497377,331073) : difference with theory (-47) = 0 CORRECTING DEFECT 9 (vertices=40, convex hull=46) After retessellation of defect 9, euler #=-46 (166278,497462,331138) : difference with theory (-46) = 0 CORRECTING DEFECT 10 (vertices=34, convex hull=55) After retessellation of defect 10, euler #=-45 (166298,497543,331200) : difference with theory (-45) = 0 CORRECTING DEFECT 11 (vertices=7, convex hull=35) After retessellation of defect 11, euler #=-44 (166300,497560,331216) : difference with theory (-44) = 0 CORRECTING DEFECT 12 (vertices=37, convex hull=57) After retessellation of defect 12, euler #=-43 (166310,497608,331255) : difference with theory (-43) = 0 CORRECTING DEFECT 13 (vertices=99, convex hull=73) After retessellation of defect 13, euler #=-42 (166345,497746,331359) : difference with theory (-42) = 0 CORRECTING DEFECT 14 (vertices=65, convex hull=111) After retessellation of defect 14, euler #=-40 (166366,497857,331451) : difference with theory (-41) = -1 CORRECTING DEFECT 15 (vertices=87, convex hull=34) After retessellation of defect 15, euler #=-39 (166373,497889,331477) : difference with theory (-40) = -1 CORRECTING DEFECT 16 (vertices=10, convex hull=24) After retessellation of defect 16, euler #=-38 (166376,497904,331490) : difference with theory (-39) = -1 CORRECTING DEFECT 17 (vertices=40, convex hull=87) After retessellation of defect 17, euler #=-37 (166406,498029,331586) : difference with theory (-38) = -1 CORRECTING DEFECT 18 (vertices=81, convex hull=37) After retessellation of defect 18, euler #=-36 (166416,498074,331622) : difference with theory (-37) = -1 CORRECTING DEFECT 19 (vertices=37, convex hull=23) After retessellation of defect 19, euler #=-35 (166422,498100,331643) : difference with theory (-36) = -1 CORRECTING DEFECT 20 (vertices=57, convex hull=90) After retessellation of defect 20, euler #=-34 (166439,498187,331714) : difference with theory (-35) = -1 CORRECTING DEFECT 21 (vertices=21, convex hull=52) After retessellation of defect 21, euler #=-33 (166451,498242,331758) : difference with theory (-34) = -1 CORRECTING DEFECT 22 (vertices=20, convex hull=61) After retessellation of defect 22, euler #=-32 (166463,498298,331803) : difference with theory (-33) = -1 CORRECTING DEFECT 23 (vertices=30, convex hull=44) After retessellation of defect 23, euler #=-31 (166472,498343,331840) : difference with theory (-32) = -1 CORRECTING DEFECT 24 (vertices=79, convex hull=71) After retessellation of defect 24, euler #=-30 (166492,498433,331911) : difference with theory (-31) = -1 CORRECTING DEFECT 25 (vertices=49, convex hull=69) After retessellation of defect 25, euler #=-29 (166514,498528,331985) : difference with theory (-30) = -1 CORRECTING DEFECT 26 (vertices=35, convex hull=64) After retessellation of defect 26, euler #=-28 (166532,498609,332049) : difference with theory (-29) = -1 CORRECTING DEFECT 27 (vertices=22, convex hull=30) After retessellation of defect 27, euler #=-27 (166538,498636,332071) : difference with theory (-28) = -1 CORRECTING DEFECT 28 (vertices=72, convex hull=32) After retessellation of defect 28, euler #=-26 (166546,498669,332097) : difference with theory (-27) = -1 CORRECTING DEFECT 29 (vertices=6, convex hull=16) After retessellation of defect 29, euler #=-25 (166546,498673,332102) : difference with theory (-26) = -1 CORRECTING DEFECT 30 (vertices=7, convex hull=24) After retessellation of defect 30, euler #=-24 (166548,498686,332114) : difference with theory (-25) = -1 CORRECTING DEFECT 31 (vertices=7, convex hull=27) After retessellation of defect 31, euler #=-23 (166551,498705,332131) : difference with theory (-24) = -1 CORRECTING DEFECT 32 (vertices=39, convex hull=63) After retessellation of defect 32, euler #=-22 (166570,498787,332195) : difference with theory (-23) = -1 CORRECTING DEFECT 33 (vertices=431, convex hull=226) After retessellation of defect 33, euler #=-22 (166698,499283,332563) : difference with theory (-22) = 0 CORRECTING DEFECT 34 (vertices=257, convex hull=194) After retessellation of defect 34, euler #=-20 (166786,499629,332823) : difference with theory (-21) = -1 CORRECTING DEFECT 35 (vertices=81, convex hull=96) After retessellation of defect 35, euler #=-19 (166808,499740,332913) : difference with theory (-20) = -1 CORRECTING DEFECT 36 (vertices=26, convex hull=34) After retessellation of defect 36, euler #=-18 (166814,499774,332942) : difference with theory (-19) = -1 CORRECTING DEFECT 37 (vertices=30, convex hull=41) After retessellation of defect 37, euler #=-17 (166820,499803,332966) : difference with theory (-18) = -1 CORRECTING DEFECT 38 (vertices=28, convex hull=28) After retessellation of defect 38, euler #=-16 (166825,499829,332988) : difference with theory (-17) = -1 CORRECTING DEFECT 39 (vertices=477, convex hull=196) After retessellation of defect 39, euler #=-16 (166898,500142,333228) : difference with theory (-16) = 0 CORRECTING DEFECT 40 (vertices=27, convex hull=49) After retessellation of defect 40, euler #=-15 (166902,500172,333255) : difference with theory (-15) = 0 CORRECTING DEFECT 41 (vertices=7, convex hull=17) After retessellation of defect 41, euler #=-14 (166903,500180,333263) : difference with theory (-14) = 0 CORRECTING DEFECT 42 (vertices=35, convex hull=85) After retessellation of defect 42, euler #=-13 (166920,500265,333332) : difference with theory (-13) = 0 CORRECTING DEFECT 43 (vertices=36, convex hull=27) After retessellation of defect 43, euler #=-12 (166925,500287,333350) : difference with theory (-12) = 0 CORRECTING DEFECT 44 (vertices=64, convex hull=56) After retessellation of defect 44, euler #=-11 (166939,500352,333402) : difference with theory (-11) = 0 CORRECTING DEFECT 45 (vertices=28, convex hull=57) After retessellation of defect 45, euler #=-10 (166948,500403,333445) : difference with theory (-10) = 0 CORRECTING DEFECT 46 (vertices=47, convex hull=88) After retessellation of defect 46, euler #=-9 (166972,500515,333534) : difference with theory (-9) = 0 CORRECTING DEFECT 47 (vertices=38, convex hull=19) After retessellation of defect 47, euler #=-8 (166974,500527,333545) : difference with theory (-8) = 0 CORRECTING DEFECT 48 (vertices=23, convex hull=50) After retessellation of defect 48, euler #=-7 (166987,500583,333589) : difference with theory (-7) = 0 CORRECTING DEFECT 49 (vertices=74, convex hull=94) After retessellation of defect 49, euler #=-6 (167026,500742,333710) : difference with theory (-6) = 0 CORRECTING DEFECT 50 (vertices=10, convex hull=26) After retessellation of defect 50, euler #=-5 (167029,500758,333724) : difference with theory (-5) = 0 CORRECTING DEFECT 51 (vertices=308, convex hull=277) After retessellation of defect 51, euler #=-4 (167139,501240,334097) : difference with theory (-4) = 0 CORRECTING DEFECT 52 (vertices=72, convex hull=83) After retessellation of defect 52, euler #=-3 (167158,501334,334173) : difference with theory (-3) = 0 CORRECTING DEFECT 53 (vertices=18, convex hull=43) After retessellation of defect 53, euler #=-2 (167165,501370,334203) : difference with theory (-2) = 0 CORRECTING DEFECT 54 (vertices=92, convex hull=88) After retessellation of defect 54, euler #=-1 (167189,501478,334288) : difference with theory (-1) = 0 CORRECTING DEFECT 55 (vertices=7, convex hull=23) After retessellation of defect 55, euler #=0 (167191,501491,334300) : difference with theory (0) = 0 CORRECTING DEFECT 56 (vertices=88, convex hull=125) After retessellation of defect 56, euler #=1 (167232,501675,334444) : difference with theory (1) = 0 CORRECTING DEFECT 57 (vertices=33, convex hull=35) After retessellation of defect 57, euler #=2 (167235,501699,334466) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.06-->6.28) (max @ vno 62092 --> 71004) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.06-->6.28) (max @ vno 62092 --> 71004) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 160 mutations (32.0%), 340 crossovers (68.0%), 140 vertices were eliminated building final representation... 2589 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=167235, nf=334466, ne=501699, g=0) writing corrected surface to /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 74.9 minutes 0 defective edges removing intersecting faces 000: 410 intersecting 001: 20 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 167235 - 501699 + 334466 = 2 --> 0 holes F =2V-4: 334466 = 334470-4 (0) 2E=3F: 1003398 = 1003398 (0) total defect index = 0 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Feb 26 01:09:50 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs S8861CSO1 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/filled.mgz... reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/brain.finalsurfs.mgz... reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/wm.mgz... 17593 bright wm thresholded. 5393 bright non-wm voxels segmented. reading original surface position from /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.orig... computing class statistics... border white: 302203 voxels (1.80%) border gray 354948 voxels (2.12%) WM (96.0): 96.9 +- 8.3 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 49.4 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.37) (max @ vno 166648 --> 166651) face area 0.28 +- 0.13 (0.00-->3.13) mean absolute distance = 0.66 +- 0.84 5157 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=72 mean inside = 96.5, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group 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 removing 4 vertex label from ripped group mean border=82.9, 131 (131) missing vertices, mean dist 0.3 [0.5 (%36.1)->0.7 (%63.9))] %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.06-->5.27) (max @ vno 166648 --> 166651) face area 0.28 +- 0.14 (0.00-->2.74) mean absolute distance = 0.36 +- 0.55 4891 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5871674.0, rms=9.37 001: dt: 0.5000, sse=7544144.0, rms=6.577 (0.000%) 002: dt: 0.5000, sse=8299027.0, rms=5.188 (0.000%) 003: dt: 0.5000, sse=8718289.0, rms=4.455 (0.000%) 004: dt: 0.5000, sse=8949160.0, rms=4.003 (0.000%) 005: dt: 0.5000, sse=9106287.0, rms=3.795 (0.000%) 006: dt: 0.5000, sse=9160480.0, rms=3.632 (0.000%) 007: dt: 0.5000, sse=9206359.0, rms=3.580 (0.000%) 008: dt: 0.5000, sse=9206592.0, rms=3.496 (0.000%) rms = 3.49, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9200472.0, rms=3.486 (0.000%) 010: dt: 0.2500, sse=5786066.5, rms=2.468 (0.000%) 011: dt: 0.2500, sse=5438278.0, rms=2.138 (0.000%) 012: dt: 0.2500, sse=5160809.0, rms=2.055 (0.000%) 013: dt: 0.2500, sse=5105026.0, rms=1.996 (0.000%) rms = 1.97, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5044638.5, rms=1.968 (0.000%) 015: dt: 0.1250, sse=4936587.5, rms=1.905 (0.000%) rms = 1.90, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4901089.0, rms=1.901 (0.000%) positioning took 3.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 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 removing 3 vertex label from ripped group mean border=86.3, 156 (57) missing vertices, mean dist -0.2 [0.4 (%76.8)->0.3 (%23.2))] %85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 0.89 +- 0.26 (0.07-->5.28) (max @ vno 166608 --> 128910) face area 0.34 +- 0.17 (0.00-->3.45) mean absolute distance = 0.24 +- 0.39 4454 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5626672.0, rms=4.75 017: dt: 0.5000, sse=6011840.0, rms=3.230 (0.000%) rms = 3.42, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5625391.5, rms=2.549 (0.000%) 019: dt: 0.2500, sse=5557362.5, rms=2.097 (0.000%) 020: dt: 0.2500, sse=5456214.5, rms=1.852 (0.000%) 021: dt: 0.2500, sse=5413238.0, rms=1.749 (0.000%) 022: dt: 0.2500, sse=5368158.5, rms=1.692 (0.000%) rms = 1.65, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5361051.5, rms=1.652 (0.000%) 024: dt: 0.1250, sse=5272042.5, rms=1.596 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5243888.5, rms=1.591 (0.000%) positioning took 2.0 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 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 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 removing 3 vertex label from ripped group mean border=88.1, 113 (31) missing vertices, mean dist -0.1 [0.2 (%68.6)->0.2 (%31.4))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.89 +- 0.25 (0.05-->5.79) (max @ vno 166608 --> 128910) face area 0.33 +- 0.16 (0.00-->3.39) mean absolute distance = 0.20 +- 0.33 3787 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5386206.5, rms=2.79 026: dt: 0.5000, sse=5941471.5, rms=2.646 (0.000%) rms = 3.14, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5565576.5, rms=1.869 (0.000%) 028: dt: 0.2500, sse=5593785.0, rms=1.568 (0.000%) 029: dt: 0.2500, sse=5499307.5, rms=1.494 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5506002.0, rms=1.485 (0.000%) 031: dt: 0.1250, sse=5401705.0, rms=1.425 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5401705.0, rms=1.425 (0.003%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 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 removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.7, 114 (19) missing vertices, mean dist -0.0 [0.2 (%54.7)->0.2 (%45.3))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5403773.5, rms=1.56 rms = 1.69, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5571483.5, rms=1.214 (0.000%) 034: dt: 0.2500, sse=5849293.5, rms=1.075 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5847404.0, rms=1.071 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 26 non-cortical segments detected only using segment with 2464 vertices erasing segment 1 (vno[0] = 83888) erasing segment 2 (vno[0] = 104139) erasing segment 3 (vno[0] = 105439) erasing segment 4 (vno[0] = 110699) erasing segment 5 (vno[0] = 110766) erasing segment 6 (vno[0] = 113815) erasing segment 7 (vno[0] = 114821) erasing segment 8 (vno[0] = 122402) erasing segment 9 (vno[0] = 122456) erasing segment 10 (vno[0] = 125493) erasing segment 11 (vno[0] = 126651) erasing segment 12 (vno[0] = 129990) erasing segment 13 (vno[0] = 130816) erasing segment 14 (vno[0] = 130845) erasing segment 15 (vno[0] = 130868) erasing segment 16 (vno[0] = 130879) erasing segment 17 (vno[0] = 130937) erasing segment 18 (vno[0] = 131795) erasing segment 19 (vno[0] = 131892) erasing segment 20 (vno[0] = 132812) erasing segment 21 (vno[0] = 134609) erasing segment 22 (vno[0] = 134630) erasing segment 23 (vno[0] = 135507) erasing segment 24 (vno[0] = 136328) erasing segment 25 (vno[0] = 166551) writing cortex label to /prod3/allegra/barcs_fs/tmp/S8861CSO1/label/lh.cortex.label... writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.curv writing smoothed area to lh.area writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->5.85) (max @ vno 166608 --> 128910) face area 0.33 +- 0.16 (0.00-->3.36) 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=62.4, 158 (158) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.9 (%100.0))] %16 local maxima, %44 large gradients and %37 min vals, 3995 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=25083184.0, rms=26.06 001: dt: 0.5000, sse=18871620.0, rms=22.041 (0.000%) 002: dt: 0.5000, sse=14615098.0, rms=18.816 (0.000%) 003: dt: 0.5000, sse=11826515.0, rms=16.298 (0.000%) 004: dt: 0.5000, sse=10116772.0, rms=14.354 (0.000%) 005: dt: 0.5000, sse=9052821.0, rms=12.846 (0.000%) 006: dt: 0.5000, sse=8426154.0, rms=11.671 (0.000%) 007: dt: 0.5000, sse=8045832.0, rms=10.683 (0.000%) 008: dt: 0.5000, sse=7798439.5, rms=9.775 (0.000%) 009: dt: 0.5000, sse=7662893.5, rms=8.936 (0.000%) 010: dt: 0.5000, sse=7555238.5, rms=8.155 (0.000%) 011: dt: 0.5000, sse=7605816.5, rms=7.458 (0.000%) 012: dt: 0.5000, sse=7608608.5, rms=6.836 (0.000%) 013: dt: 0.5000, sse=7754584.5, rms=6.290 (0.000%) 014: dt: 0.5000, sse=7813569.5, rms=5.803 (0.000%) 015: dt: 0.5000, sse=7991458.5, rms=5.383 (0.000%) 016: dt: 0.5000, sse=8077194.0, rms=5.025 (0.000%) 017: dt: 0.5000, sse=8195939.5, rms=4.724 (0.000%) 018: dt: 0.5000, sse=8252907.0, rms=4.490 (0.000%) 019: dt: 0.5000, sse=8355375.5, rms=4.301 (0.000%) 020: dt: 0.5000, sse=8344243.0, rms=4.174 (0.000%) 021: dt: 0.5000, sse=8468710.0, rms=4.056 (0.000%) 022: dt: 0.5000, sse=8435954.0, rms=3.975 (0.000%) 023: dt: 0.5000, sse=8535092.0, rms=3.905 (0.000%) rms = 3.86, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=8485677.0, rms=3.859 (0.000%) 025: dt: 0.2500, sse=6411709.0, rms=3.353 (0.000%) 026: dt: 0.2500, sse=6264373.5, rms=3.203 (0.000%) rms = 3.19, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=6121109.0, rms=3.194 (0.000%) 028: dt: 0.1250, sse=5868120.5, rms=3.094 (0.000%) rms = 3.08, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5828247.5, rms=3.077 (0.000%) positioning took 6.3 minutes mean border=60.3, 2005 (45) missing vertices, mean dist 0.2 [0.2 (%42.1)->0.6 (%57.9))] %40 local maxima, %26 large gradients and %29 min vals, 1931 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=6619688.5, rms=4.84 030: dt: 0.5000, sse=6860730.5, rms=4.254 (0.000%) 031: dt: 0.5000, sse=8688587.0, rms=4.071 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=7403671.0, rms=3.565 (0.000%) 033: dt: 0.2500, sse=6820354.0, rms=3.376 (0.000%) 034: dt: 0.2500, sse=6828952.5, rms=3.322 (0.000%) rms = 3.29, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=6812493.5, rms=3.294 (0.000%) 036: dt: 0.1250, sse=6581402.5, rms=3.165 (0.000%) rms = 3.13, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=6582023.0, rms=3.131 (0.000%) positioning took 1.8 minutes mean border=59.0, 2456 (37) missing vertices, mean dist 0.1 [0.2 (%38.1)->0.4 (%61.9))] %53 local maxima, %14 large gradients and %29 min vals, 2072 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=6735872.5, rms=3.70 rms = 3.90, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=6539870.0, rms=3.390 (0.000%) 039: dt: 0.2500, sse=6648533.0, rms=3.223 (0.000%) 040: dt: 0.2500, sse=6879945.5, rms=3.172 (0.000%) rms = 3.13, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=7057834.5, rms=3.134 (0.000%) 042: dt: 0.1250, sse=6840428.5, rms=3.020 (0.000%) rms = 2.99, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=6878190.5, rms=2.987 (0.000%) positioning took 1.4 minutes mean border=58.4, 5093 (35) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))] %54 local maxima, %11 large gradients and %28 min vals, 1739 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6908102.5, rms=3.13 rms = 3.49, time step reduction 1 of 3 to 0.250... 044: dt: 0.2500, sse=6840987.5, rms=2.997 (0.000%) 045: dt: 0.2500, sse=7145132.0, rms=2.941 (0.000%) rms = 2.93, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=7272772.5, rms=2.934 (0.000%) 047: dt: 0.1250, sse=7151607.5, rms=2.817 (0.000%) rms = 2.79, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=7191846.5, rms=2.793 (0.000%) positioning took 1.2 minutes writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.area.pial vertex spacing 1.03 +- 0.47 (0.06-->9.32) (max @ vno 123510 --> 123511) face area 0.42 +- 0.35 (0.00-->9.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 167235 vertices processed 25000 of 167235 vertices processed 50000 of 167235 vertices processed 75000 of 167235 vertices processed 100000 of 167235 vertices processed 125000 of 167235 vertices processed 150000 of 167235 vertices processed 0 of 167235 vertices processed 25000 of 167235 vertices processed 50000 of 167235 vertices processed 75000 of 167235 vertices processed 100000 of 167235 vertices processed 125000 of 167235 vertices processed 150000 of 167235 vertices processed thickness calculation complete, 2159:7141 truncations. 28515 vertices at 0 distance 88574 vertices at 1 distance 100536 vertices at 2 distance 62007 vertices at 3 distance 27188 vertices at 4 distance 9661 vertices at 5 distance 3536 vertices at 6 distance 1298 vertices at 7 distance 536 vertices at 8 distance 253 vertices at 9 distance 147 vertices at 10 distance 96 vertices at 11 distance 77 vertices at 12 distance 78 vertices at 13 distance 50 vertices at 14 distance 43 vertices at 15 distance 39 vertices at 16 distance 28 vertices at 17 distance 24 vertices at 18 distance 20 vertices at 19 distance 26 vertices at 20 distance writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/lh.thickness positioning took 28.8 minutes #-------------------------------------------- #@# Smooth2 lh Wed Feb 26 01:38:36 EST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /prod3/allegra/barcs_fs/tmp/S8861CSO1/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... #-------------------------------------------- #@# Inflation2 lh Wed Feb 26 01:38:46 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.7 mm, total surface area = 100384 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 1.8 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 233 vertices thresholded to be in k1 ~ [-0.27 0.32], k2 ~ [-0.11 0.06] total integrated curvature = 0.485*4pi (6.100) --> 1 handles ICI = 1.7, FI = 13.7, variation=220.596 159 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 182 vertices thresholded to be in [-0.15 0.11] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Feb 26 01:43:33 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm S8861CSO1 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ S8861CSO1/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 316 ] Gb_filter = 0 WARN: S lookup min: -0.434227 WARN: S explicit min: 0.000000 vertex = 1935 #-------------------------------------------- #@# Tessellate rh Wed Feb 26 01:43:43 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 3 found - 3 modified | TOTAL: 6 pass 2 (xz-): 0 found - 3 modified | TOTAL: 6 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 (++): 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 : 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 = 8 (out of 309271: 0.002587) 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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 30: 1581 vertices, 1737 faces slice 40: 9579 vertices, 9923 faces slice 50: 21922 vertices, 22419 faces slice 60: 36748 vertices, 37297 faces slice 70: 51576 vertices, 52091 faces slice 80: 65265 vertices, 65719 faces slice 90: 78277 vertices, 78752 faces slice 100: 91092 vertices, 91554 faces slice 110: 103057 vertices, 103524 faces slice 120: 114491 vertices, 114970 faces slice 130: 125101 vertices, 125553 faces slice 140: 135766 vertices, 136172 faces slice 150: 145182 vertices, 145626 faces slice 160: 154346 vertices, 154730 faces slice 170: 160439 vertices, 160727 faces slice 180: 165501 vertices, 165756 faces slice 190: 168426 vertices, 168590 faces slice 200: 168752 vertices, 168860 faces slice 210: 168752 vertices, 168860 faces slice 220: 168752 vertices, 168860 faces slice 230: 168752 vertices, 168860 faces slice 240: 168752 vertices, 168860 faces slice 250: 168752 vertices, 168860 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... 168752 voxel in cpt #1: X=-108 [v=168752,e=506580,f=337720] located at (29.218166, -30.497446, -0.799368) For the whole surface: X=-108 [v=168752,e=506580,f=337720] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Feb 26 01:44:05 EST 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Feb 26 01:44:16 EST 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts avg radius = 50.7 mm, total surface area = 87312 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.8 minutes Not saving sulc step 000: RMS=0.107 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.062 (target=0.015) step 015: RMS=0.053 (target=0.015) step 020: RMS=0.047 (target=0.015) step 025: RMS=0.043 (target=0.015) step 030: RMS=0.039 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.033 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Feb 26 01:46:07 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.56 (0.00-->6.60) (max @ vno 106263 --> 106295) face area 0.02 +- 0.03 (-0.34-->0.52) scaling brain by 0.296... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.633, avgs=0 005/300: dt: 0.9000, rms radial error=175.378, avgs=0 010/300: dt: 0.9000, rms radial error=174.831, avgs=0 015/300: dt: 0.9000, rms radial error=174.111, avgs=0 020/300: dt: 0.9000, rms radial error=173.290, avgs=0 025/300: dt: 0.9000, rms radial error=172.412, avgs=0 030/300: dt: 0.9000, rms radial error=171.502, avgs=0 035/300: dt: 0.9000, rms radial error=170.573, avgs=0 040/300: dt: 0.9000, rms radial error=169.636, avgs=0 045/300: dt: 0.9000, rms radial error=168.697, avgs=0 050/300: dt: 0.9000, rms radial error=167.757, avgs=0 055/300: dt: 0.9000, rms radial error=166.821, avgs=0 060/300: dt: 0.9000, rms radial error=165.887, avgs=0 065/300: dt: 0.9000, rms radial error=164.957, avgs=0 070/300: dt: 0.9000, rms radial error=164.032, avgs=0 075/300: dt: 0.9000, rms radial error=163.110, avgs=0 080/300: dt: 0.9000, rms radial error=162.193, avgs=0 085/300: dt: 0.9000, rms radial error=161.281, avgs=0 090/300: dt: 0.9000, rms radial error=160.373, avgs=0 095/300: dt: 0.9000, rms radial error=159.470, avgs=0 100/300: dt: 0.9000, rms radial error=158.570, avgs=0 105/300: dt: 0.9000, rms radial error=157.675, avgs=0 110/300: dt: 0.9000, rms radial error=156.784, avgs=0 115/300: dt: 0.9000, rms radial error=155.900, avgs=0 120/300: dt: 0.9000, rms radial error=155.023, avgs=0 125/300: dt: 0.9000, rms radial error=154.151, avgs=0 130/300: dt: 0.9000, rms radial error=153.283, avgs=0 135/300: dt: 0.9000, rms radial error=152.420, avgs=0 140/300: dt: 0.9000, rms radial error=151.561, avgs=0 145/300: dt: 0.9000, rms radial error=150.708, avgs=0 150/300: dt: 0.9000, rms radial error=149.859, avgs=0 155/300: dt: 0.9000, rms radial error=149.015, avgs=0 160/300: dt: 0.9000, rms radial error=148.176, avgs=0 165/300: dt: 0.9000, rms radial error=147.343, avgs=0 170/300: dt: 0.9000, rms radial error=146.514, avgs=0 175/300: dt: 0.9000, rms radial error=145.690, avgs=0 180/300: dt: 0.9000, rms radial error=144.871, avgs=0 185/300: dt: 0.9000, rms radial error=144.056, avgs=0 190/300: dt: 0.9000, rms radial error=143.245, avgs=0 195/300: dt: 0.9000, rms radial error=142.439, avgs=0 200/300: dt: 0.9000, rms radial error=141.637, avgs=0 205/300: dt: 0.9000, rms radial error=140.840, avgs=0 210/300: dt: 0.9000, rms radial error=140.048, avgs=0 215/300: dt: 0.9000, rms radial error=139.259, avgs=0 220/300: dt: 0.9000, rms radial error=138.475, avgs=0 225/300: dt: 0.9000, rms radial error=137.697, avgs=0 230/300: dt: 0.9000, rms radial error=136.923, avgs=0 235/300: dt: 0.9000, rms radial error=136.153, avgs=0 240/300: dt: 0.9000, rms radial error=135.387, avgs=0 245/300: dt: 0.9000, rms radial error=134.626, avgs=0 250/300: dt: 0.9000, rms radial error=133.869, avgs=0 255/300: dt: 0.9000, rms radial error=133.117, avgs=0 260/300: dt: 0.9000, rms radial error=132.368, avgs=0 265/300: dt: 0.9000, rms radial error=131.624, avgs=0 270/300: dt: 0.9000, rms radial error=130.884, avgs=0 275/300: dt: 0.9000, rms radial error=130.148, avgs=0 280/300: dt: 0.9000, rms radial error=129.416, avgs=0 285/300: dt: 0.9000, rms radial error=128.688, avgs=0 290/300: dt: 0.9000, rms radial error=127.965, avgs=0 295/300: dt: 0.9000, rms radial error=127.245, avgs=0 300/300: dt: 0.9000, rms radial error=126.530, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20146.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3555.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 421.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00453 epoch 4 (K=640.0), pass 1, starting sse = 35.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00764 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.22 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Feb 26 01:59:25 EST 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 S8861CSO1 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 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-108 (nv=168752, nf=337720, ne=506580, g=55) 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... 9779 ambiguous faces found in tessellation segmenting defects... 58 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 23 into 21 -merging segment 42 into 40 -merging segment 45 into 40 -merging segment 50 into 46 54 defects to be corrected 0 vertices coincident reading input surface /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4819 (-4.7410) -vertex loglikelihood: -6.3924 (-3.1962) -normal dot loglikelihood: -3.6478 (-3.6478) -quad curv loglikelihood: -6.5059 (-3.2530) Total Loglikelihood : -26.0280 CORRECTING DEFECT 0 (vertices=6, convex hull=13) Warning - incorrect dp selected!!!!(-102.322464 >= -102.322468 ) After retessellation of defect 0, euler #=-52 (162930,486695,323713) : difference with theory (-51) = 1 CORRECTING DEFECT 1 (vertices=42, convex hull=96) After retessellation of defect 1, euler #=-51 (162945,486779,323783) : difference with theory (-50) = 1 CORRECTING DEFECT 2 (vertices=59, convex hull=112) After retessellation of defect 2, euler #=-50 (162987,486952,323915) : difference with theory (-49) = 1 CORRECTING DEFECT 3 (vertices=51, convex hull=81) After retessellation of defect 3, euler #=-49 (163012,487061,324000) : difference with theory (-48) = 1 CORRECTING DEFECT 4 (vertices=22, convex hull=28) After retessellation of defect 4, euler #=-48 (163013,487072,324011) : difference with theory (-47) = 1 CORRECTING DEFECT 5 (vertices=19, convex hull=44) After retessellation of defect 5, euler #=-47 (163014,487093,324032) : difference with theory (-46) = 1 CORRECTING DEFECT 6 (vertices=27, convex hull=57) After retessellation of defect 6, euler #=-46 (163029,487158,324083) : difference with theory (-45) = 1 CORRECTING DEFECT 7 (vertices=453, convex hull=209) After retessellation of defect 7, euler #=-45 (163124,487541,324372) : difference with theory (-44) = 1 CORRECTING DEFECT 8 (vertices=37, convex hull=55) After retessellation of defect 8, euler #=-44 (163132,487586,324410) : difference with theory (-43) = 1 CORRECTING DEFECT 9 (vertices=22, convex hull=48) After retessellation of defect 9, euler #=-43 (163145,487644,324456) : difference with theory (-42) = 1 CORRECTING DEFECT 10 (vertices=46, convex hull=50) After retessellation of defect 10, euler #=-42 (163155,487694,324497) : difference with theory (-41) = 1 CORRECTING DEFECT 11 (vertices=51, convex hull=75) After retessellation of defect 11, euler #=-41 (163188,487820,324591) : difference with theory (-40) = 1 CORRECTING DEFECT 12 (vertices=19, convex hull=30) After retessellation of defect 12, euler #=-40 (163189,487835,324606) : difference with theory (-39) = 1 CORRECTING DEFECT 13 (vertices=54, convex hull=95) After retessellation of defect 13, euler #=-39 (163219,487968,324710) : difference with theory (-38) = 1 CORRECTING DEFECT 14 (vertices=7, convex hull=34) After retessellation of defect 14, euler #=-38 (163220,487983,324725) : difference with theory (-37) = 1 CORRECTING DEFECT 15 (vertices=31, convex hull=93) After retessellation of defect 15, euler #=-37 (163234,488060,324789) : difference with theory (-36) = 1 CORRECTING DEFECT 16 (vertices=42, convex hull=82) After retessellation of defect 16, euler #=-36 (163242,488119,324841) : difference with theory (-35) = 1 CORRECTING DEFECT 17 (vertices=51, convex hull=115) After retessellation of defect 17, euler #=-35 (163269,488247,324943) : difference with theory (-34) = 1 CORRECTING DEFECT 18 (vertices=50, convex hull=87) After retessellation of defect 18, euler #=-35 (163301,488383,325047) : difference with theory (-33) = 2 CORRECTING DEFECT 19 (vertices=49, convex hull=88) After retessellation of defect 19, euler #=-34 (163334,488516,325148) : difference with theory (-32) = 2 CORRECTING DEFECT 20 (vertices=21, convex hull=56) After retessellation of defect 20, euler #=-33 (163343,488564,325188) : difference with theory (-31) = 2 CORRECTING DEFECT 21 (vertices=970, convex hull=572) After retessellation of defect 21, euler #=-31 (163620,489681,326030) : difference with theory (-30) = 1 CORRECTING DEFECT 22 (vertices=147, convex hull=146) After retessellation of defect 22, euler #=-30 (163647,489831,326154) : difference with theory (-29) = 1 CORRECTING DEFECT 23 (vertices=6, convex hull=27) After retessellation of defect 23, euler #=-29 (163649,489844,326166) : difference with theory (-28) = 1 CORRECTING DEFECT 24 (vertices=112, convex hull=43) After retessellation of defect 24, euler #=-28 (163658,489891,326205) : difference with theory (-27) = 1 CORRECTING DEFECT 25 (vertices=27, convex hull=59) After retessellation of defect 25, euler #=-27 (163667,489940,326246) : difference with theory (-26) = 1 CORRECTING DEFECT 26 (vertices=30, convex hull=44) After retessellation of defect 26, euler #=-26 (163676,489987,326285) : difference with theory (-25) = 1 CORRECTING DEFECT 27 (vertices=32, convex hull=48) After retessellation of defect 27, euler #=-25 (163691,490054,326338) : difference with theory (-24) = 1 CORRECTING DEFECT 28 (vertices=273, convex hull=84) After retessellation of defect 28, euler #=-24 (163729,490208,326455) : difference with theory (-23) = 1 CORRECTING DEFECT 29 (vertices=23, convex hull=68) After retessellation of defect 29, euler #=-23 (163739,490264,326502) : difference with theory (-22) = 1 CORRECTING DEFECT 30 (vertices=69, convex hull=84) After retessellation of defect 30, euler #=-22 (163762,490368,326584) : difference with theory (-21) = 1 CORRECTING DEFECT 31 (vertices=44, convex hull=90) After retessellation of defect 31, euler #=-21 (163779,490456,326656) : difference with theory (-20) = 1 CORRECTING DEFECT 32 (vertices=329, convex hull=121) After retessellation of defect 32, euler #=-20 (163840,490692,326832) : difference with theory (-19) = 1 CORRECTING DEFECT 33 (vertices=42, convex hull=90) After retessellation of defect 33, euler #=-19 (163855,490772,326898) : difference with theory (-18) = 1 CORRECTING DEFECT 34 (vertices=34, convex hull=27) After retessellation of defect 34, euler #=-18 (163862,490803,326923) : difference with theory (-17) = 1 CORRECTING DEFECT 35 (vertices=81, convex hull=102) After retessellation of defect 35, euler #=-17 (163902,490964,327045) : difference with theory (-16) = 1 CORRECTING DEFECT 36 (vertices=23, convex hull=51) After retessellation of defect 36, euler #=-16 (163911,491010,327083) : difference with theory (-15) = 1 CORRECTING DEFECT 37 (vertices=27, convex hull=37) Warning - incorrect dp selected!!!!(-100.898652 >= -100.898661 ) After retessellation of defect 37, euler #=-15 (163914,491030,327101) : difference with theory (-14) = 1 CORRECTING DEFECT 38 (vertices=29, convex hull=32) After retessellation of defect 38, euler #=-14 (163921,491061,327126) : difference with theory (-13) = 1 CORRECTING DEFECT 39 (vertices=790, convex hull=440) After retessellation of defect 39, euler #=-11 (164059,491709,327639) : difference with theory (-12) = -1 CORRECTING DEFECT 40 (vertices=62, convex hull=79) After retessellation of defect 40, euler #=-10 (164077,491798,327711) : difference with theory (-11) = -1 CORRECTING DEFECT 41 (vertices=536, convex hull=173) After retessellation of defect 41, euler #=-9 (164146,492083,327928) : difference with theory (-10) = -1 CORRECTING DEFECT 42 (vertices=304, convex hull=46) After retessellation of defect 42, euler #=-8 (164156,492129,327965) : difference with theory (-9) = -1 CORRECTING DEFECT 43 (vertices=215, convex hull=123) After retessellation of defect 43, euler #=-7 (164189,492286,328090) : difference with theory (-8) = -1 CORRECTING DEFECT 44 (vertices=75, convex hull=127) After retessellation of defect 44, euler #=-6 (164249,492525,328270) : difference with theory (-7) = -1 CORRECTING DEFECT 45 (vertices=28, convex hull=22) After retessellation of defect 45, euler #=-5 (164250,492537,328282) : difference with theory (-6) = -1 CORRECTING DEFECT 46 (vertices=40, convex hull=21) After retessellation of defect 46, euler #=-4 (164251,492544,328289) : difference with theory (-5) = -1 CORRECTING DEFECT 47 (vertices=23, convex hull=60) After retessellation of defect 47, euler #=-3 (164260,492597,328334) : difference with theory (-4) = -1 CORRECTING DEFECT 48 (vertices=139, convex hull=98) After retessellation of defect 48, euler #=-3 (164280,492714,328431) : difference with theory (-3) = 0 CORRECTING DEFECT 49 (vertices=26, convex hull=46) After retessellation of defect 49, euler #=-2 (164288,492756,328466) : difference with theory (-2) = 0 CORRECTING DEFECT 50 (vertices=30, convex hull=65) After retessellation of defect 50, euler #=-1 (164301,492824,328522) : difference with theory (-1) = 0 CORRECTING DEFECT 51 (vertices=40, convex hull=61) After retessellation of defect 51, euler #=0 (164318,492897,328579) : difference with theory (0) = 0 CORRECTING DEFECT 52 (vertices=23, convex hull=61) After retessellation of defect 52, euler #=1 (164331,492958,328628) : difference with theory (1) = 0 CORRECTING DEFECT 53 (vertices=32, convex hull=65) After retessellation of defect 53, euler #=2 (164343,493023,328682) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.04-->19.46) (max @ vno 146362 --> 167243) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.04-->19.46) (max @ vno 146362 --> 167243) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 173 mutations (32.8%), 354 crossovers (67.2%), 317 vertices were eliminated building final representation... 4409 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=164343, nf=328682, ne=493023, g=0) writing corrected surface to /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 86.7 minutes 0 defective edges removing intersecting faces 000: 561 intersecting 001: 17 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 164343 - 493023 + 328682 = 2 --> 0 holes F =2V-4: 328682 = 328686-4 (0) 2E=3F: 986046 = 986046 (0) total defect index = 0 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 106 intersecting 001: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Feb 26 03:26:20 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs S8861CSO1 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/filled.mgz... reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/brain.finalsurfs.mgz... reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/wm.mgz... 17194 bright wm thresholded. 5407 bright non-wm voxels segmented. reading original surface position from /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.orig... computing class statistics... border white: 302203 voxels (1.80%) border gray 354948 voxels (2.12%) WM (96.0): 96.8 +- 8.1 [70.0 --> 110.0] GM (83.0) : 81.3 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.4 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 72.0 (was 85) setting MAX_CSF to 48.8 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->7.51) (max @ vno 18459 --> 38557) face area 0.28 +- 0.14 (0.00-->9.73) mean absolute distance = 0.65 +- 0.82 4821 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=72 mean inside = 96.0, mean outside = 78.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.1, 131 (131) missing vertices, mean dist 0.3 [0.5 (%38.6)->0.7 (%61.4))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.10-->10.30) (max @ vno 18459 --> 38557) face area 0.28 +- 0.15 (0.00-->9.75) mean absolute distance = 0.34 +- 0.56 4727 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5746982.0, rms=9.23 001: dt: 0.5000, sse=7570237.0, rms=6.597 (0.000%) 002: dt: 0.5000, sse=8445005.0, rms=5.302 (0.000%) 003: dt: 0.5000, sse=8760650.0, rms=4.587 (0.000%) 004: dt: 0.5000, sse=9103029.0, rms=4.124 (0.000%) 005: dt: 0.5000, sse=9140494.0, rms=3.865 (0.000%) 006: dt: 0.5000, sse=9326939.0, rms=3.677 (0.000%) 007: dt: 0.5000, sse=9229213.0, rms=3.604 (0.000%) 008: dt: 0.5000, sse=9362083.0, rms=3.523 (0.000%) rms = 3.52, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9227902.0, rms=3.519 (0.000%) 010: dt: 0.2500, sse=5937253.5, rms=2.462 (0.000%) 011: dt: 0.2500, sse=5541497.5, rms=2.131 (0.000%) 012: dt: 0.2500, sse=5273315.5, rms=2.054 (0.000%) 013: dt: 0.2500, sse=5219613.5, rms=1.998 (0.000%) rms = 1.98, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=5152132.0, rms=1.984 (0.000%) 015: dt: 0.1250, sse=5038365.5, rms=1.913 (0.000%) rms = 1.91, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=5007978.5, rms=1.906 (0.000%) positioning took 3.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.9, 104 (35) missing vertices, mean dist -0.2 [0.4 (%73.4)->0.3 (%26.6))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 0.89 +- 0.26 (0.10-->10.47) (max @ vno 18459 --> 38557) face area 0.34 +- 0.18 (0.00-->12.88) mean absolute distance = 0.25 +- 0.41 4542 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5576686.0, rms=4.19 017: dt: 0.5000, sse=6158734.0, rms=3.041 (0.000%) rms = 3.34, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5760623.0, rms=2.349 (0.000%) 019: dt: 0.2500, sse=5726199.5, rms=1.983 (0.000%) 020: dt: 0.2500, sse=5604849.5, rms=1.809 (0.000%) 021: dt: 0.2500, sse=5593931.5, rms=1.746 (0.000%) rms = 1.71, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5540592.0, rms=1.715 (0.000%) 023: dt: 0.1250, sse=5470777.0, rms=1.648 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5436761.5, rms=1.644 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.6, 122 (25) missing vertices, mean dist -0.1 [0.3 (%66.8)->0.2 (%33.2))] %90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.89 +- 0.26 (0.01-->10.55) (max @ vno 18459 --> 38557) face area 0.33 +- 0.18 (0.00-->13.36) mean absolute distance = 0.21 +- 0.35 4297 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5564846.0, rms=2.72 025: dt: 0.5000, sse=6141359.0, rms=2.615 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5787725.5, rms=1.911 (0.000%) 027: dt: 0.2500, sse=5816681.5, rms=1.636 (0.000%) 028: dt: 0.2500, sse=5704068.5, rms=1.567 (0.000%) rms = 1.55, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5723215.0, rms=1.549 (0.000%) 030: dt: 0.1250, sse=5613397.0, rms=1.488 (0.000%) rms = 1.49, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5613397.0, rms=1.488 (0.002%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.2, 140 (13) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5614010.5, rms=1.63 rms = 1.73, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5801416.5, rms=1.286 (0.000%) 033: dt: 0.2500, sse=6113581.0, rms=1.137 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.13, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=6111641.0, rms=1.130 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 20 non-cortical segments detected only using segment with 2376 vertices erasing segment 1 (vno[0] = 122852) erasing segment 2 (vno[0] = 122865) erasing segment 3 (vno[0] = 123878) erasing segment 4 (vno[0] = 123890) erasing segment 5 (vno[0] = 124916) erasing segment 6 (vno[0] = 125936) erasing segment 7 (vno[0] = 127070) erasing segment 8 (vno[0] = 127096) erasing segment 9 (vno[0] = 128094) erasing segment 10 (vno[0] = 128133) erasing segment 11 (vno[0] = 128397) erasing segment 12 (vno[0] = 129157) erasing segment 13 (vno[0] = 130112) erasing segment 14 (vno[0] = 130193) erasing segment 15 (vno[0] = 131129) erasing segment 16 (vno[0] = 131309) erasing segment 17 (vno[0] = 131324) erasing segment 18 (vno[0] = 132860) erasing segment 19 (vno[0] = 133837) writing cortex label to /prod3/allegra/barcs_fs/tmp/S8861CSO1/label/rh.cortex.label... writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.curv writing smoothed area to rh.area writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.area vertex spacing 0.89 +- 0.26 (0.07-->10.54) (max @ vno 18459 --> 38557) face area 0.33 +- 0.17 (0.00-->13.30) 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=62.2, 165 (165) missing vertices, mean dist 1.7 [0.1 (%0.0)->3.1 (%100.0))] %16 local maxima, %38 large gradients and %42 min vals, 4908 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=24236340.0, rms=25.76 001: dt: 0.5000, sse=18418604.0, rms=21.881 (0.000%) 002: dt: 0.5000, sse=14426870.0, rms=18.778 (0.000%) 003: dt: 0.5000, sse=11782090.0, rms=16.338 (0.000%) 004: dt: 0.5000, sse=10134384.0, rms=14.431 (0.000%) 005: dt: 0.5000, sse=9086527.0, rms=12.915 (0.000%) 006: dt: 0.5000, sse=8391538.0, rms=11.718 (0.000%) 007: dt: 0.5000, sse=7938396.0, rms=10.687 (0.000%) 008: dt: 0.5000, sse=7663590.0, rms=9.755 (0.000%) 009: dt: 0.5000, sse=7464308.0, rms=8.896 (0.000%) 010: dt: 0.5000, sse=7424436.0, rms=8.132 (0.000%) 011: dt: 0.5000, sse=7380886.0, rms=7.444 (0.000%) 012: dt: 0.5000, sse=7467982.0, rms=6.832 (0.000%) 013: dt: 0.5000, sse=7557565.5, rms=6.277 (0.000%) 014: dt: 0.5000, sse=7638137.0, rms=5.784 (0.000%) 015: dt: 0.5000, sse=7766528.5, rms=5.357 (0.000%) 016: dt: 0.5000, sse=7889043.5, rms=4.990 (0.000%) 017: dt: 0.5000, sse=7999432.5, rms=4.714 (0.000%) 018: dt: 0.5000, sse=8092968.0, rms=4.485 (0.000%) 019: dt: 0.5000, sse=8135855.5, rms=4.309 (0.000%) 020: dt: 0.5000, sse=8220658.5, rms=4.159 (0.000%) 021: dt: 0.5000, sse=8278782.0, rms=4.057 (0.000%) 022: dt: 0.5000, sse=8301141.0, rms=3.965 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=8347528.5, rms=3.915 (0.000%) 024: dt: 0.2500, sse=6483307.5, rms=3.478 (0.000%) 025: dt: 0.2500, sse=6346956.0, rms=3.354 (0.000%) rms = 3.34, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=6242910.5, rms=3.340 (0.000%) 027: dt: 0.1250, sse=5998753.0, rms=3.254 (0.000%) rms = 3.24, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5975430.5, rms=3.238 (0.000%) positioning took 5.7 minutes mean border=60.3, 2303 (78) missing vertices, mean dist 0.2 [0.2 (%43.1)->0.7 (%56.9))] %36 local maxima, %25 large gradients and %34 min vals, 2108 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=6685249.0, rms=4.74 029: dt: 0.5000, sse=6924326.0, rms=4.261 (0.000%) 030: dt: 0.5000, sse=8590337.0, rms=4.060 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 031: dt: 0.5000, sse=8247226.5, rms=4.050 (0.000%) 032: dt: 0.2500, sse=7135452.5, rms=3.514 (0.000%) 033: dt: 0.2500, sse=7069346.5, rms=3.352 (0.000%) rms = 3.34, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=6998659.5, rms=3.339 (0.000%) 035: dt: 0.1250, sse=6779483.0, rms=3.221 (0.000%) rms = 3.19, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=6756775.0, rms=3.193 (0.000%) positioning took 1.6 minutes mean border=59.3, 2856 (74) missing vertices, mean dist 0.1 [0.2 (%40.1)->0.5 (%59.9))] %48 local maxima, %13 large gradients and %33 min vals, 2202 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=6877629.0, rms=3.61 rms = 3.77, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=6689480.5, rms=3.374 (0.000%) 038: dt: 0.2500, sse=6780643.5, rms=3.257 (0.000%) rms = 3.21, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=6986955.0, rms=3.211 (0.000%) 040: dt: 0.1250, sse=6844930.5, rms=3.105 (0.000%) rms = 3.07, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=6889635.5, rms=3.074 (0.000%) positioning took 1.2 minutes mean border=58.7, 5799 (71) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.4 (%54.4))] %49 local maxima, %11 large gradients and %32 min vals, 1911 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6918061.5, rms=3.21 rms = 3.43, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=6869461.0, rms=3.095 (0.000%) 043: dt: 0.2500, sse=7200923.0, rms=3.020 (0.000%) rms = 2.99, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=7340101.0, rms=2.994 (0.000%) 045: dt: 0.1250, sse=7225115.5, rms=2.889 (0.000%) rms = 2.86, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=7263662.0, rms=2.857 (0.000%) positioning took 1.2 minutes writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.area.pial vertex spacing 1.03 +- 0.48 (0.05-->10.85) (max @ vno 18459 --> 38557) face area 0.42 +- 0.36 (0.00-->13.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 164343 vertices processed 25000 of 164343 vertices processed 50000 of 164343 vertices processed 75000 of 164343 vertices processed 100000 of 164343 vertices processed 125000 of 164343 vertices processed 150000 of 164343 vertices processed 0 of 164343 vertices processed 25000 of 164343 vertices processed 50000 of 164343 vertices processed 75000 of 164343 vertices processed 100000 of 164343 vertices processed 125000 of 164343 vertices processed 150000 of 164343 vertices processed thickness calculation complete, 2925:7037 truncations. 24003 vertices at 0 distance 81511 vertices at 1 distance 100246 vertices at 2 distance 65224 vertices at 3 distance 28483 vertices at 4 distance 10063 vertices at 5 distance 3490 vertices at 6 distance 1318 vertices at 7 distance 644 vertices at 8 distance 321 vertices at 9 distance 206 vertices at 10 distance 130 vertices at 11 distance 89 vertices at 12 distance 71 vertices at 13 distance 58 vertices at 14 distance 56 vertices at 15 distance 50 vertices at 16 distance 46 vertices at 17 distance 28 vertices at 18 distance 33 vertices at 19 distance 50 vertices at 20 distance writing curvature file /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf/rh.thickness positioning took 26.1 minutes #-------------------------------------------- #@# Smooth2 rh Wed Feb 26 03:52:24 EST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /prod3/allegra/barcs_fs/tmp/S8861CSO1/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... #-------------------------------------------- #@# Inflation2 rh Wed Feb 26 03:52:32 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 98714 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.083 (target=0.015) step 010: RMS=0.062 (target=0.015) step 015: RMS=0.051 (target=0.015) step 020: RMS=0.042 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.4 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 235 vertices thresholded to be in k1 ~ [-0.26 0.27], k2 ~ [-0.13 0.06] total integrated curvature = 0.501*4pi (6.290) --> 0 handles ICI = 1.6, FI = 12.7, variation=205.928 148 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 160 vertices thresholded to be in [-0.15 0.12] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Wed Feb 26 03:56:43 EST 2014 /prod3/allegra/barcs_fs/tmp/S8861CSO1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm S8861CSO1 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ S8861CSO1/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 325 ] Gb_filter = 0 WARN: S lookup min: -0.568836 WARN: S explicit min: 0.000000 vertex = 278 #-------------------------------------------- #@# ASeg Stats Wed Feb 26 03:56:53 EST 2014 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /prod3/allegra/barcs_fs/tmp/S8861CSO1 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject S8861CSO1 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject S8861CSO1 sysname Linux hostname compute11 machine x86_64 user Skhadka2 UseRobust 0 atlas_icv (eTIV) = 1840397 mm^3 (det: 1.058524 ) mghRead(/prod3/allegra/barcs_fs/tmp/S8861CSO1/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -102, rheno = -108 orig.nofix lhholes = 52, rhholes = 55 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux compute11 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s S8861CSO1 exited with ERRORS at Wed Feb 26 03:57:18 EST 2014 For more details, see the log file /prod3/allegra/barcs_fs/tmp/S8861CSO1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting