INFO: SUBJECTS_DIR is /home/xonobo/FSRFsubjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-rw- 1 xonobo xonobo 673432 Apr 10 02:33 /home/xonobo/FSRFsubjects/bert/scripts/recon-all.log
Linux telenetPC 2.6.19-1.2911.fc6 #1 SMP Sat Feb 10 15:16:31 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
#-------------------------------------
#@# EM Registration Tue Apr 10 02:35:07 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta 

using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
average std = 7.4   using min determinant for regularization = 5.5
0 singular and 1662 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
total sample mean = 87.9 (483 zeros)
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2242, passno 0, spacing 8
************************************************
First Search limited to translation only.
************************************************
Found translation: (-1.7, 0.6, -6.3): log p = -18047.0
Result so far: scale 1.000: max_log_p=-14274.6, old_max_log_p =-18047.0 (thresh=-18028.9)
 1.125   0.000   0.000  -17.751;
 0.000   1.114   0.122  -26.437;
 0.000  -0.166   0.921   22.203;
 0.000   0.000   0.000   1.000;
Result so far: scale 1.000: max_log_p=-14274.6, old_max_log_p =-14274.6 (thresh=-14260.4)
 1.125   0.000   0.000  -17.751;
 0.000   1.114   0.122  -26.437;
 0.000  -0.166   0.921   22.203;
 0.000   0.000   0.000   1.000;
freeing gibbs priors...done.
bounding unknown intensity as < 16.0 or > 799.3 
************************************************
spacing=8, using 2242 sample points, tol=1.00e-05...
************************************************
resetting wm mean[0]: 109 --> 116
resetting gm mean[0]: 68 --> 68
input volume #1 is the most T1-like
using real data threshold=31.0
using (108, 99, 116) as brain centroid...
mean wm in atlas = 116, using box (93,85,94) --> (123, 113,138) to find MRI wm
before smoothing, mri peak at 149
after smoothing, mri peak at 151, scaling input intensities by 0.768
scaling channel 0 by 0.768212
initial log_p = -41786.7

****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
****************************************
Nine parameter search.  iteration 1 nscales = 1 ...
****************************************
reducing scale to 0.2500
***********************************************
Computing MAP estimate using 2242 samplesdt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.12500   0.00000   0.00000  -17.75125;
 0.00000   1.11405   0.12178  -26.43692;
 0.00000  -0.16636   0.92064   22.20286;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2242
Quasinewton: input matrix
 1.12500   0.00000   0.00000  -17.75125;
 0.00000   1.11405   0.12178  -26.43692;
 0.00000  -0.16636   0.92064   22.20286;
 0.00000   0.00000   0.00000   1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
...
***********************************************
dfp_em_step_func: 002: -log(p) = 14274.6
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.11, 0.12, -26.44)
                      ( 0.00, -0.17, 0.92, 22.20)
dfp_em_step_func: 003: -log(p) = 14072.6
after pass:transform: ( 1.13, 0.01, 0.01, -17.75)
                      ( 0.00, 1.11, 0.12, -26.44)
                      ( 0.01, -0.16, 0.93, 22.20)
dfp_em_step_func: 004: -log(p) = 13091.0
after pass:transform: ( 1.12, -0.00, -0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 005: -log(p) = 13038.3
after pass:transform: ( 1.12, -0.00, -0.00, -17.75)
                      ( 0.00, 1.11, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 006: -log(p) = 12882.0
after pass:transform: ( 1.12, -0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.12500   0.00000   0.00000  -17.75125;
 0.00000   1.11405   0.12178  -26.43692;
 0.00000  -0.16636   0.92064   22.20286;
 0.00000   0.00000   0.00000   1.00000;
nsamples 242283
Quasinewton: input matrix
 1.12500   0.00000   0.00000  -17.75125;
 0.00000   1.11405   0.12178  -26.43692;
 0.00000  -0.16636   0.92064   22.20286;
 0.00000   0.00000   0.00000   1.00000;
pass 2 through quasi-newton minimization...
func: 007: -log(p) = 12876.2
after pass:transform: ( 1.12, -0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
outof QuasiNewtonEMA: 009: -log(p) = 12739.8  tol 0.000010
Resulting transform:
 1.125   0.000   0.000  -17.751;
 0.000   1.114   0.122  -26.437;
 0.000  -0.166   0.921   22.203;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -14274.6 (old=-41786.7)
transform before final EM align:
 1.125   0.000   0.000  -17.751;
 0.000   1.114   0.122  -26.437;
 0.000  -0.166   0.921   22.203;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 242283 samples. 
**************************************************
dfp_em_step_func: 008: -log(p) = 1699531.0
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.11, 0.12, -26.44)
                      ( 0.00, -0.17, 0.92, 22.20)
dfp_em_step_func: 009: -log(p) = 1596138.pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
2
after pass:transform: ( 1.13, 0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 010: -log(p) = 1579318.9
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 011: -log(p) = 1579209.6
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 012: -log(p) = 1579203.8
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 013: -log(p) = 1579162.4
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.12, 0.13, -26.44)
                      ( 0.01, -0.15, 0.93, 22.20)
outof QuasiNewtonEMA: 015: -log(p) = 1579161.9  tol 0.000000
final transform:
 1.123   0.004   0.001  -17.751;
 0.003   1.117   0.128  -26.437;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 5 minutes and 21 seconds.
#--------------------------------------
#@# CA Normalize Tue Apr 10 02:40:28 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_ca_normalize -f /home/xonobo/FSRFsubjects/bert/tmp/control.dat -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz 

reading manually defined control points from /home/xonobo/FSRFsubjects/bert/tmp/control.dat
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
reading transform from 'transforms/talairach.lta'...
INFO: compute sample coordinates transform
 1.123   0.004   0.001  -17.751;
 0.003   1.117   0.128  -26.437;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;
INFO: transform used
reading input volume from nu.mgz...
resetting wm mean[0]: 109 --> 116
resetting gm mean[0]: 68 --> 68
input volume #1 is the most T1-like
using real data threshold=36.0
using (107, 99, 116) as brain centroid...
mean wm in atlas = 116, using box (92,85,94) --> (122, 113,138) to find MRI wm
before smoothing, mri peak at 149
after smoothing, mri peak at 151, scaling input intensities by 0.768
scaling channel 0 by 0.768212
using 242283 sample points...
finding control points in Left_Cerebral_White_Matter....
found 38929 control points for structure...
bounding box (127, 60, 24) --> (186, 160, 201)
Left_Cerebral_White_Matter: limiting intensities to 106.0 --> 117.0
1707 of 5027 (34.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 38531 control points for structure...
bounding box (70, 60, 24) --> (128, 160, 202)
Right_Cerebral_White_Matter: limiting intensities to 105.0 --> 119.0
1574 of 5330 (29.5%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
foundReading 0 control points...
 3087 control points for structure...
bounding box (129, 138, 53) --> (170, 175, 110)
Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 114.0
84 of 231 (36.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2900 control points for structure...
bounding box (86, 140, 50) --> (127, 175, 111)
Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 113.0
39 of 129 (30.2%) samples deleted
finding control points in Brain_Stem....
found 3414 control points for structure...
bounding box (111, 126, 90) --> (142, 189, 122)
Brain_Stem: limiting intensities to 96.0 --> 109.0
149 of 507 (29.4%) samples deleted
using 11224 total control points for intensity normalization...
bias field = 1.006 +- 0.056
40 of 7671 control points discarded
writing normalized volume to norm.mgz...
freeing GCA...done.
normalization took 1 minutes and 7 seconds.
#--------------------------------------
#@# CA Reg Tue Apr 10 02:41:35 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.m3z 

renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-regularize_mean 0.500
	-regularize 0.500
not handling expanded ventricles...
using MR volume brainmask.mgz to mask input volume...
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
renormalizing by structure alignment....
renormalizing input #0
aligning Left_Pallidum...
gca peak = 0.11705 (100)
mri peak = 0.20477 (107)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (648 voxels, overlap=0.666)
aligning Right_Pallidum...
gca peak = 0.13501 (106)
mri peak = 0.15604 (106)
Right_Pallidum (52): linear fit = 0.98 x + 0.0 (847 voxels, overlap=0.870)
aligning Right_Cerebral_White_Matter...
gca peak = 0.05652 (116)
mri peak = 0.12066 (114)
Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (108347 voxels, overlap=0.419)
aligning Left_Cerebral_White_Matter...
gca peak = 0.05682 (116)
mri peak = 0.07704 (112)
Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (121964 voxels, overlap=0.432)
aligning Left_Lateral_Ventricle...
gca peak = 0.05153 (25)
mri peak = 0.11297 (32)
Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (4890 voxels, overlap=0.258)
aligning Right_Lateral_Ventricle...
gca peak = 0.07557 (30)
mri peak = 0.06740 (35)
unreasonable value (41.2), not in range [ 0, 40] - rejecting
aligning Right_Hippocampus...
gca peak = 0.14805 (66)
mri peak = 0.07413 (80)
Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (1427 voxels, overlap=0.037)
aligning Left_Hippocampus...
gca peak = 0.17297 (66)
mri peak = 0.06677 (83)
Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1549 voxels, overlap=0.057)
aligning Left_Cerebral_Cortex...
gca peak = 0.05671 (68)
mri peak = 0.02876 (82)
uniform distribution in MR - rejecting arbitrary fit
aligning Right_Cerebral_Cortex...
gca peak = 0.06581 (70)
mri peak = 0.03025 (85)
Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (141369 voxels, overlap=0.015)
aligning Right_Caudate...
gca peak = 0.07786 (81)
mri peak = 0.13116 (88)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (1509 voxels, overlap=0.223)
aligning Left_Caudate...
gca peak = 0.07814 (81)
mri peak = 0.15456 (85)
Left_Caudate (11): linear fit = 1.05 x + 0.0 (1363 voxels, overlap=0.452)
aligning Left_Cerebellum_Cortex...
gca peak = 0.06033 (63)
mri peak = 0.06196 (88)
overlap = 0.00017735, overlap_threshold = 0.001
insufficient overlap 0.0002 in histograms - rejecting
aligning Right_Cerebellum_Cortex...
gca peak = 0.05990 (64)
mri peak = 0.05336 (88)
Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (30391 voxels, overlap=0.002)
aligning Left_Cerebellum_White_Matter...
gca peak = 0.09299 (92)
mri peak = 0.08935 (102)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (13062 voxels, overlap=0.452)
aligning Right_Cerebellum_White_Matter...
gca peak = 0.08899 (93)
mri peak = 0.10421 (102)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (8607 voxels, overlap=0.142)
aligning Left_Amygdala...
gca peak = 0.13911 (71)
mri peak = 0.10396 (86)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (761 voxels, overlap=0.004)
aligning Right_Amygdala...
gca peak = 0.15703 (65)
mri peak = 0.14403 (89)
overlap = 0.000345209, overlap_threshold = 0.001
insufficient overlap 0.0003 in histograms - rejecting
aligning Left_Thalamus_Proper...
gca peak = 0.06537 (100)
mri peak = 0.09828 (98)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (5399 voxels, overlap=0.486)
aligning Right_Thalamus_Proper...
gca peak = 0.07019 (99)
mri peak = 0.10195 (102)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5158 voxels, overlap=0.429)
aligning Left_Putamen...
gca peak = 0.09468 (90)
mri peak = 0.10125 (97)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (3084 voxels, overlap=0.331)
aligning Right_Putamen...
gca peak = 0.07184 (82)
mri peak = 0.09596 (94)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (3377 voxels, overlap=0.569)
aligning Brain_Stem...
gca peak = 0.05597 (80)
mri peak = 0.10630 (98)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12922 voxels, overlap=0.364)
aligning Right_VentralDC...
gca peak = 0.05879 (97)
mri peak = 0.10276 (105)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2703 voxels, overlap=0.411)
aligning Left_VentralDC...
gca peak = 0.06932 (98)
mri peak = 0.09825 (106)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (3060 voxels, overlap=0.500)
aligning Third_Ventricle...
gca peak = 0.10105 (38)
mri peak = 0.04095 (25)
unreasonable value (60.8), not in range [ 0, 40] - rejecting
aligning Fourth_Ventricle...
gca peak = 0.10426 (32)
mri peak = 0.08541 (30)
not using caudate to estimate GM means
setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 1.25 x +  0
setting label Left_Lateral_Ventricle based on Right_Lateral_Ventricle = 1.48 x +  0
setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.42 x +  0
setting label Left_Amygdala based on Right_Amygdala = 1.23 x +  0
Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (841 voxels, overlap=0.230)
estimating mean gm scale to be 1.24 x + 0.0
estimating mean wm scale to be 0.98 x + 0.0
estimating mean csf scale to be 1.29 x + 0.0
21 transforms computed
0000: dt=0.000000, rms=0.758 (0.137%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0001: dt=0.000000, rms=0.757 (-0.126%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0003: dt=0.000000, rms=0.757 (-0.172%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0005: dt=0.000000, rms=0.757 (-0.261%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0007: dt=0.000000, rms=0.757 (-0.266%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0009: dt=0.000000, rms=0.755 (-0.281%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0011: dt=0.000000, rms=0.755 (-0.283%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0013: dt=0.000000, rms=0.755 (-0.291%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0015: dt=0.000000, rms=0.755 (-0.291%), neg=0, invalid=1511, LIN
rms increased - undoing step...
0017: dt=0.000000, rms=0.754 (-0.293%), neg=0, invalid=1511, LIN
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.752, neg=0, invalid=1511
0020: dt=255.336521, rms=0.683 (9.117%), neg=0, invalid=1511
0021: dt=123.625382, rms=0.659 (3.523%), neg=0, invalid=1511
0022: dt=228.611502, rms=0.650 (1.407%), neg=0, invalid=1511
0023: dt=139.342923, rms=0.644 (0.923%), neg=0, invalid=1511
0024: dt=175.551579, rms=0.640 (0.558%), neg=0, invalid=1511
0025: dt=179.293990, rms=0.637 (0.570%), neg=0, invalid=1511
0026: dt=131.752219, rms=0.634 (0.389%), neg=0, invalid=1511
0027: dt=295.936004, rms=0.631 (0.511%), neg=0, invalid=1511
0028: dt=107.748866, rms=0.629 (0.383%), neg=0, invalid=1511
0029: dt=517.888008, rms=0.625 (0.589%), neg=0, invalid=1511
0030: dt=89.234238, rms=0.623 (0.366%), neg=0, invalid=1511
0031: dt=2071.552031, rms=0.614 (1.364%), neg=0, invalid=1511
0032: dt=129.472002, rms=0.613 (0.230%), neg=0, invalid=1511
0033: dt=295.936004, rms=0.612 (0.163%), neg=0, invalid=1511
0034: dt=92.480001, rms=0.611 (0.061%), neg=0, invalid=1511
0035: dt=1775.616026, rms=0.609 (0.403%), neg=0, invalid=1511
0036: dt=75.954099, rms=0.608 (0.175%), neg=0, invalid=1511
0037: dt=110.976002, rms=0.608 (0.016%), neg=0, invalid=1511
0038: dt=110.976002, rms=0.607 (0.043%), neg=0, invalid=1511
0039: dt=110.976002, rms=0.607 (0.061%), neg=0, invalid=1511
0040: dt=110.976002, rms=0.607 (0.070%), neg=0, invalid=1511
0041: dt=110.976002, rms=0.606 (0.091%), neg=0, invalid=1511
0042: dt=110.976002, rms=0.605 (0.115%), neg=0, invalid=1511
0043: dt=110.976002, rms=0.605 (0.120%), neg=0, invalid=1511
0044: dt=110.976002, rms=0.604 (0.125%), neg=0, invalid=1511
0045: dt=110.976002, rms=0.603 (0.127%), neg=0, invalid=1511
0046: dt=110.976002, rms=0.602 (0.116%), neg=0, invalid=1511
0047: dt=110.976002, rms=0.602 (0.114%), neg=0, invalid=1511
0048: dt=110.976002, rms=0.601 (0.120%), neg=0, invalid=1511
0049: dt=110.976002, rms=0.600 (0.135%), neg=0, invalid=1511
0050: dt=110.976002, rms=0.600 (0.117%), neg=0, invalid=1511
0051: dt=110.976002, rms=0.599 (0.103%), neg=0, invalid=1511
0052: dt=110.976002, rms=0.598 (0.109%), neg=0, invalid=1511
0053: dt=110.976002, rms=0.597 (0.138%), neg=0, invalid=1511
0054: dt=110.976002, rms=0.597 (0.128%), neg=0, invalid=1511
0055: dt=110.976002, rms=0.596 (0.121%), neg=0, invalid=1511
0056: dt=110.976002, rms=0.595 (0.106%), neg=0, invalid=1511
0057: dt=110.976002, rms=0.595 (0.099%), neg=0, invalid=1511
0058: dt=110.976002, rms=0.594 (0.116%), neg=0, invalid=1511
0059: dt=110.976002, rms=0.593 (0.111%), neg=0, invalid=1511
0060: dt=110.976002, rms=0.593 (0.099%), neg=0, invalid=1511
0061: dt=110.976002, rms=0.592 (0.082%), neg=0, invalid=1511
0062: dt=110.976002, rms=0.592 (0.078%), neg=0, invalid=1511
0063: dt=110.976002, rms=0.591 (0.111%), neg=0, invalid=1511
0064: dt=110.976002, rms=0.591 (0.105%), neg=0, invalid=1511
0065: dt=110.976002, rms=0.590 (0.079%), neg=0, invalid=1511
0066: dt=110.976002, rms=0.590 (0.062%), neg=0, invalid=1511
0067: dt=110.976002, rms=0.589 (0.069%), neg=0, invalid=1511
0068: dt=110.976002, rms=0.589 (0.085%), neg=0, invalid=1511
0069: dt=110.976002, rms=0.588 (0.084%), neg=0, invalid=1511
0070: dt=110.976002, rms=0.588 (0.086%), neg=0, invalid=1511
0071: dt=110.976002, rms=0.587 (0.078%), neg=0, invalid=1511
0072: dt=110.976002, rms=0.587 (0.060%), neg=0, invalid=1511
0073: dt=110.976002, rms=0.587 (0.054%), neg=0, invalid=1511
0074: dt=110.976002, rms=0.586 (0.066%), neg=0, invalid=1511
0075: dt=110.976002, rms=0.586 (0.061%), neg=0, invalid=1511
0076: dt=110.976002, rms=0.586 (0.059%), neg=0, invalid=1511
0077: dt=110.976002, rms=0.585 (0.058%), neg=0, invalid=1511
0078: dt=110.976002, rms=0.585 (0.060%), neg=0, invalid=1511
0079: dt=110.976002, rms=0.585 (0.052%), neg=0, invalid=1511
0080: dt=110.976002, rms=0.584 (0.046%), neg=0, invalid=1511
0081: dt=110.976002, rms=0.584 (0.058%), neg=0, invalid=1511
0082: dt=110.976002, rms=0.584 (0.060%), neg=0, invalid=1511
0083: dt=110.976002, rms=0.583 (0.063%), neg=0, invalid=1511
0084: dt=110.976002, rms=0.583 (0.060%), neg=0, invalid=1511
0085: dt=110.976002, rms=0.583 (0.059%), neg=0, invalid=1511
0086: dt=110.976002, rms=0.582 (0.044%), neg=0, invalid=1511
0087: dt=110.976002, rms=0.582 (0.040%), neg=0, invalid=1511
0088: dt=110.976002, rms=0.582 (0.055%), neg=0, invalid=1511
0089: dt=110.976002, rms=0.581 (0.060%), neg=0, invalid=1511
0090: dt=110.976002, rms=0.581 (0.044%), neg=0, invalid=1511
0091: dt=110.976002, rms=0.581 (0.042%), neg=0, invalid=1511
0092: dt=110.976002, rms=0.581 (0.040%), neg=0, invalid=1511
0093: dt=110.976002, rms=0.580 (0.049%), neg=0, invalid=1511
0094: dt=110.976002, rms=0.580 (0.051%), neg=0, invalid=1511
0095: dt=110.976002, rms=0.580 (0.045%), neg=0, invalid=1511
0096: dt=110.976002, rms=0.580 (0.047%), neg=0, invalid=1511
0097: dt=110.976002, rms=0.579 (0.055%), neg=0, invalid=1511
0098: dt=110.976002, rms=0.579 (0.046%), neg=0, invalid=1511
0099: dt=110.976002, rms=0.579 (0.037%), neg=0, invalid=1511
0100: dt=110.976002, rms=0.579 (0.036%), neg=0, invalid=1511
0101: dt=110.976002, rms=0.578 (0.045%), neg=0, invalid=1511
0102: dt=110.976002, rms=0.578 (0.039%), neg=0, invalid=1511
0103: dt=110.976002, rms=0.578 (0.040%), neg=0, invalid=1511
0104: dt=110.976002, rms=0.578 (0.044%), neg=0, invalid=1511
0105: dt=110.976002, rms=0.577 (0.042%), neg=0, invalid=1511
0106: dt=110.976002, rms=0.577 (0.035%), neg=0, invalid=1511
0107: dt=110.976002, rms=0.577 (0.032%), neg=0, invalid=1511
0108: dt=110.976002, rms=0.577 (0.024%), neg=0, invalid=1511
0109: dt=110.976002, rms=0.577 (0.031%), neg=0, invalid=1511
0110: dt=110.976002, rms=0.576 (0.054%), neg=0, invalid=1511
0111: dt=110.976002, rms=0.576 (0.032%), neg=0, invalid=1511
0112: dt=110.976002, rms=0.576 (0.026%), neg=0, invalid=1511
0113: dt=110.976002, rms=0.576 (0.021%), neg=0, invalid=1511
0114: dt=110.976002, rms=0.576 (0.031%), neg=0, invalid=1511
0115: dt=110.976002, rms=0.576 (0.039%), neg=0, invalid=1511
0116: dt=110.976002, rms=0.575 (0.038%), neg=0, invalid=1511
0117: dt=110.976002, rms=0.575 (0.025%), neg=0, invalid=1511
0118: dt=110.976002, rms=0.575 (0.029%), neg=0, invalid=1511
0119: dt=110.976002, rms=0.575 (0.040%), neg=0, invalid=1511
0120: dt=110.976002, rms=0.575 (0.028%), neg=0, invalid=1511
0121: dt=110.976002, rms=0.574 (0.025%), neg=0, invalid=1511
0122: dt=110.976002, rms=0.574 (0.019%), neg=0, invalid=1511
0123: dt=110.976002, rms=0.574 (0.022%), neg=0, invalid=1511
0124: dt=110.976002, rms=0.574 (0.028%), neg=0, invalid=1511
0125: dt=110.976002, rms=0.574 (0.026%), neg=0, invalid=1511
0126: dt=110.976002, rms=0.574 (0.026%), neg=0, invalid=1511
0127: dt=110.976002, rms=0.574 (0.026%), neg=0, invalid=1511
0128: dt=110.976002, rms=0.573 (0.027%), neg=0, invalid=1511
0129: dt=110.976002, rms=0.573 (0.026%), neg=0, invalid=1511
0130: dt=110.976002, rms=0.573 (0.022%), neg=0, invalid=1511
0131: dt=110.976002, rms=0.573 (0.021%), neg=0, invalid=1511
0132: dt=517.888008, rms=0.573 (0.022%), neg=0, invalid=1511
0133: dt=1.734000, rms=0.573 (-0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.573, neg=0, invalid=1511
0134: dt=369.920006, rms=0.572 (0.219%), neg=0, invalid=1511
0135: dt=129.472002, rms=0.571 (0.046%), neg=0, invalid=1511
0136: dt=129.472002, rms=0.571 (0.024%), neg=0, invalid=1511
0137: dt=129.472002, rms=0.571 (0.036%), neg=0, invalid=1511
0138: dt=129.472002, rms=0.571 (0.047%), neg=0, invalid=1511
0139: dt=129.472002, rms=0.571 (0.048%), neg=0, invalid=1511
0140: dt=129.472002, rms=0.570 (0.055%), neg=0, invalid=1511
0141: dt=129.472002, rms=0.570 (0.050%), neg=0, invalid=1511
0142: dt=129.472002, rms=0.570 (0.054%), neg=0, invalid=1511
0143: dt=129.472002, rms=0.569 (0.048%), neg=0, invalid=1511
0144: dt=129.472002, rms=0.569 (0.037%), neg=0, invalid=1511
0145: dt=129.472002, rms=0.569 (0.033%), neg=0, invalid=1511
0146: dt=129.472002, rms=0.569 (0.036%), neg=0, invalid=1511
0147: dt=129.472002, rms=0.569 (0.033%), neg=0, invalid=1511
0148: dt=129.472002, rms=0.568 (0.023%), neg=0, invalid=1511
0149: dt=129.472002, rms=0.568 (0.020%), neg=0, invalid=1511
0150: dt=221.952003, rms=0.568 (0.023%), neg=0, invalid=1511
0151: dt=32.368000, rms=0.568 (0.002%), neg=0, invalid=1511
0152: dt=32.368000, rms=0.568 (0.001%), neg=0, invalid=1511
0153: dt=32.368000, rms=0.568 (-0.001%), neg=0, invalid=1511
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.571, neg=0, invalid=1511
0154: dt=64.984013, rms=0.570 (0.184%), neg=0, invalid=1511
0155: dt=248.832004, rms=0.566 (0.689%), neg=0, invalid=1511
0156: dt=54.443849, rms=0.565 (0.237%), neg=0, invalid=1511
0157: dt=248.832004, rms=0.560 (0.767%), neg=0, invalid=1511
0158: dt=40.864614, rms=0.558 (0.364%), neg=0, invalid=1511
0159: dt=145.152002, rms=0.557 (0.177%), neg=0, invalid=1511
0160: dt=116.851832, rms=0.555 (0.322%), neg=0, invalid=1511
0161: dt=36.288001, rms=0.555 (0.109%), neg=0, invalid=1511
0162: dt=414.720006, rms=0.552 (0.506%), neg=0, invalid=1511
0163: dt=34.303267, rms=0.551 (0.229%), neg=0, invalid=1511
0164: dt=103.680002, rms=0.550 (0.118%), neg=0, invalid=1511
0165: dt=145.152002, rms=0.549 (0.272%), neg=0, invalid=1511
0166: dt=42.805696, rms=0.548 (0.046%), neg=0, invalid=1511
0167: dt=42.805696, rms=0.548 (0.052%), neg=0, invalid=1511
0168: dt=42.805696, rms=0.548 (0.093%), neg=0, invalid=1511
0169: dt=42.805696, rms=0.547 (0.127%), neg=0, invalid=1511
0170: dt=42.805696, rms=0.546 (0.152%), neg=0, invalid=1511
0171: dt=42.805696, rms=0.545 (0.174%), neg=0, invalid=1511
0172: dt=42.805696, rms=0.544 (0.193%), neg=0, invalid=1511
0173: dt=42.805696, rms=0.543 (0.212%), neg=0, invalid=1511
0174: dt=42.805696, rms=0.542 (0.213%), neg=0, invalid=1511
0175: dt=42.805696, rms=0.541 (0.219%), neg=0, invalid=1511
0176: dt=42.805696, rms=0.539 (0.198%), neg=0, invalid=1511
0177: dt=42.805696, rms=0.538 (0.185%), neg=0, invalid=1511
0178: dt=42.805696, rms=0.537 (0.189%), neg=0, invalid=1511
0179: dt=42.805696, rms=0.536 (0.203%), neg=0, invalid=1511
0180: dt=42.805696, rms=0.535 (0.194%), neg=0, invalid=1511
0181: dt=42.805696, rms=0.534 (0.184%), neg=0, invalid=1511
0182: dt=42.805696, rms=0.533 (0.167%), neg=0, invalid=1511
0183: dt=42.805696, rms=0.533 (0.158%), neg=0, invalid=1511
0184: dt=42.805696, rms=0.532 (0.177%), neg=0, invalid=1511
0185: dt=42.805696, rms=0.531 (0.162%), neg=0, invalid=1511
0186: dt=42.805696, rms=0.530 (0.138%), neg=0, invalid=1511
0187: dt=42.805696, rms=0.529 (0.126%), neg=0, invalid=1511
0188: dt=42.805696, rms=0.529 (0.131%), neg=0, invalid=1511
0189: dt=42.805696, rms=0.528 (0.138%), neg=0, invalid=1511
0190: dt=42.805696, rms=0.527 (0.131%), neg=0, invalid=1511
0191: dt=42.805696, rms=0.527 (0.106%), neg=0, invalid=1511
0192: dt=42.805696, rms=0.526 (0.089%), neg=0, invalid=1511
0193: dt=42.805696, rms=0.526 (0.101%), neg=0, invalid=1511
0194: dt=42.805696, rms=0.525 (0.107%), neg=0, invalid=1511
0195: dt=42.805696, rms=0.525 (0.084%), neg=0, invalid=1511
0196: dt=42.805696, rms=0.524 (0.075%), neg=0, invalid=1511
0197: dt=42.805696, rms=0.524 (0.075%), neg=0, invalid=1511
0198: dt=42.805696, rms=0.523 (0.092%), neg=0, invalid=1511
0199: dt=42.805696, rms=0.523 (0.093%), neg=0, invalid=1511
0200: dt=42.805696, rms=0.523 (0.072%), neg=0, invalid=1511
0201: dt=42.805696, rms=0.522 (0.050%), neg=0, invalid=1511
0202: dt=42.805696, rms=0.522 (0.047%), neg=0, invalid=1511
0203: dt=42.805696, rms=0.522 (0.058%), neg=0, invalid=1511
0204: dt=42.805696, rms=0.521 (0.075%), neg=0, invalid=1511
0205: dt=42.805696, rms=0.521 (0.074%), neg=0, invalid=1511
0206: dt=42.805696, rms=0.521 (0.053%), neg=0, invalid=1511
0207: dt=42.805696, rms=0.520 (0.041%), neg=0, invalid=1511
0208: dt=42.805696, rms=0.520 (0.049%), neg=0, invalid=1511
0209: dt=42.805696, rms=0.520 (0.051%), neg=0, invalid=1511
0210: dt=42.805696, rms=0.520 (0.052%), neg=0, invalid=1511
0211: dt=42.805696, rms=0.520 (0.034%), neg=0, invalid=1511
0212: dt=42.805696, rms=0.519 (0.032%), neg=0, invalid=1511
0213: dt=42.805696, rms=0.519 (0.034%), neg=0, invalid=1511
0214: dt=42.805696, rms=0.519 (0.040%), neg=0, invalid=1511
0215: dt=42.805696, rms=0.519 (0.031%), neg=0, invalid=1511
0216: dt=42.805696, rms=0.519 (0.028%), neg=0, invalid=1511
0217: dt=42.805696, rms=0.519 (0.030%), neg=0, invalid=1511
0218: dt=42.805696, rms=0.518 (0.052%), neg=0, invalid=1511
0219: dt=42.805696, rms=0.518 (0.053%), neg=0, invalid=1511
0220: dt=42.805696, rms=0.518 (0.026%), neg=0, invalid=1511
0221: dt=42.805696, rms=0.518 (0.005%), neg=0, invalid=1511
0222: dt=42.805696, rms=0.518 (0.005%), neg=0, invalid=1511
0223: dt=42.805696, rms=0.518 (0.030%), neg=0, invalid=1511
0224: dt=42.805696, rms=0.517 (0.056%), neg=0, invalid=1511
0225: dt=42.805696, rms=0.517 (0.027%), neg=0, invalid=1511
0226: dt=42.805696, rms=0.517 (0.014%), neg=0, invalid=1511
0227: dt=42.805696, rms=0.517 (0.021%), neg=0, invalid=1511
0228: dt=42.805696, rms=0.517 (0.027%), neg=0, invalid=1511
0229: dt=42.805696, rms=0.517 (0.027%), neg=0, invalid=1511
0230: dt=42.805696, rms=0.517 (0.024%), neg=0, invalid=1511
0231: dt=42.805696, rms=0.517 (0.019%), neg=0, invalid=1511
0232: dt=145.152002, rms=0.516 (0.021%), neg=0, invalid=1511
0233: dt=25.920000, rms=0.516 (0.002%), neg=0, invalid=1511
0234: dt=25.920000, rms=0.516 (-0.002%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.516, neg=0, invalid=1511
0235: dt=150.317002, rms=0.514 (0.458%), neg=0, invalid=1511
0236: dt=44.443913, rms=0.514 (0.098%), neg=0, invalid=1511
0237: dt=103.680002, rms=0.513 (0.085%), neg=0, invalid=1511
0238: dt=36.288001, rms=0.513 (0.059%), neg=0, invalid=1511
0239: dt=124.416002, rms=0.512 (0.073%), neg=0, invalid=1511
0240: dt=29.138128, rms=0.512 (0.046%), neg=0, invalid=1511
0241: dt=29.138128, rms=0.512 (0.016%), neg=0, invalid=1511
0242: dt=29.138128, rms=0.512 (0.028%), neg=0, invalid=1511
0243: dt=29.138128, rms=0.512 (0.039%), neg=0, invalid=1511
0244: dt=29.138128, rms=0.511 (0.052%), neg=0, invalid=1511
0245: dt=29.138128, rms=0.511 (0.053%), neg=0, invalid=1511
0246: dt=29.138128, rms=0.511 (0.057%), neg=0, invalid=1511
0247: dt=29.138128, rms=0.511 (0.055%), neg=0, invalid=1511
0248: dt=29.138128, rms=0.510 (0.050%), neg=0, invalid=1511
0249: dt=29.138128, rms=0.510 (0.047%), neg=0, invalid=1511
0250: dt=29.138128, rms=0.510 (0.049%), neg=0, invalid=1511
0251: dt=29.138128, rms=0.510 (0.041%), neg=0, invalid=1511
0252: dt=29.138128, rms=0.510 (0.033%), neg=0, invalid=1511
0253: dt=29.138128, rms=0.509 (0.037%), neg=0, invalid=1511
0254: dt=29.138128, rms=0.509 (0.036%), neg=0, invalid=1511
0255: dt=29.138128, rms=0.509 (0.034%), neg=0, invalid=1511
0256: dt=29.138128, rms=0.509 (0.030%), neg=0, invalid=1511
0257: dt=29.138128, rms=0.509 (0.030%), neg=0, invalid=1511
0258: dt=29.138128, rms=0.508 (0.035%), neg=0, invalid=1511
0259: dt=29.138128, rms=0.508 (0.038%), neg=0, invalid=1511
0260: dt=29.138128, rms=0.508 (0.035%), neg=0, invalid=1511
0261: dt=29.138128, rms=0.508 (0.025%), neg=0, invalid=1511
0262: dt=29.138128, rms=0.508 (0.030%), neg=0, invalid=1511
0263: dt=29.138128, rms=0.508 (0.031%), neg=0, invalid=1511
0264: dt=29.138128, rms=0.507 (0.039%), neg=0, invalid=1511
0265: dt=29.138128, rms=0.507 (0.032%), neg=0, invalid=1511
0266: dt=29.138128, rms=0.507 (0.021%), neg=0, invalid=1511
0267: dt=29.138128, rms=0.507 (0.024%), neg=0, invalid=1511
0268: dt=29.138128, rms=0.507 (0.023%), neg=0, invalid=1511
0269: dt=248.832004, rms=0.507 (0.036%), neg=0, invalid=1511
0270: dt=15.552000, rms=0.507 (0.002%), neg=0, invalid=1511
0271: dt=15.552000, rms=0.507 (-0.000%), neg=0, invalid=1511
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.518, neg=0, invalid=1511
0272: dt=9.259877, rms=0.518 (0.047%), neg=0, invalid=1511
0273: dt=6.400000, rms=0.518 (0.013%), neg=0, invalid=1511
0274: dt=6.400000, rms=0.518 (0.014%), neg=0, invalid=1511
0275: dt=6.400000, rms=0.518 (0.002%), neg=0, invalid=1511
0276: dt=6.400000, rms=0.518 (-0.016%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.518, neg=0, invalid=1511
0277: dt=67.035808, rms=0.514 (0.862%), neg=0, invalid=1511
0278: dt=27.394065, rms=0.512 (0.294%), neg=0, invalid=1511
0279: dt=58.199566, rms=0.510 (0.485%), neg=0, invalid=1511
0280: dt=22.040275, rms=0.508 (0.252%), neg=0, invalid=1511
0281: dt=147.826525, rms=0.505 (0.580%), neg=0, invalid=1511
0282: dt=35.561090, rms=0.503 (0.420%), neg=0, invalid=1511
0283: dt=36.007362, rms=0.502 (0.174%), neg=0, invalid=1511
0284: dt=44.663816, rms=0.501 (0.218%), neg=0, invalid=1511
0285: dt=23.742773, rms=0.501 (0.124%), neg=0, invalid=1511
0286: dt=38.618073, rms=0.500 (0.114%), neg=0, invalid=1511
0287: dt=14.608586, rms=0.500 (0.083%), neg=0, invalid=1511
0288: dt=51.926132, rms=0.499 (0.107%), neg=0, invalid=1511
0289: dt=14.789239, rms=0.499 (0.093%), neg=0, invalid=1511
0290: dt=37.828531, rms=0.498 (0.100%), neg=0, invalid=1511
0291: dt=13.543923, rms=0.498 (0.074%), neg=0, invalid=1511
0292: dt=38.400001, rms=0.497 (0.078%), neg=0, invalid=1511
0293: dt=12.447732, rms=0.497 (0.066%), neg=0, invalid=1511
0294: dt=76.800001, rms=0.496 (0.136%), neg=0, invalid=1511
0295: dt=13.135309, rms=0.496 (0.095%), neg=0, invalid=1511
0296: dt=44.800001, rms=0.496 (0.073%), neg=0, invalid=1511
0297: dt=21.275035, rms=0.495 (0.071%), neg=0, invalid=1511
0298: dt=20.759334, rms=0.495 (0.046%), neg=0, invalid=1511
0299: dt=20.759334, rms=0.495 (0.057%), neg=0, invalid=1511
0300: dt=20.759334, rms=0.494 (0.075%), neg=0, invalid=1511
0301: dt=20.759334, rms=0.494 (0.107%), neg=0, invalid=1511
0302: dt=20.759334, rms=0.493 (0.129%), neg=0, invalid=1511
0303: dt=20.759334, rms=0.492 (0.147%), neg=0, invalid=1511
0304: dt=20.759334, rms=0.492 (0.154%), neg=0, invalid=1511
0305: dt=20.759334, rms=0.491 (0.166%), neg=0, invalid=1511
0306: dt=20.759334, rms=0.490 (0.154%), neg=0, invalid=1511
0307: dt=20.759334, rms=0.489 (0.207%), neg=0, invalid=1511
0308: dt=20.759334, rms=0.488 (0.181%), neg=0, invalid=1511
0309: dt=20.759334, rms=0.487 (0.168%), neg=0, invalid=1511
0310: dt=20.759334, rms=0.487 (0.147%), neg=0, invalid=1511
0311: dt=20.759334, rms=0.486 (0.156%), neg=0, invalid=1511
0312: dt=20.759334, rms=0.485 (0.135%), neg=0, invalid=1511
0313: dt=20.759334, rms=0.485 (0.123%), neg=0, invalid=1511
0314: dt=20.759334, rms=0.484 (0.104%), neg=0, invalid=1511
0315: dt=20.759334, rms=0.484 (0.113%), neg=0, invalid=1511
0316: dt=20.759334, rms=0.483 (0.103%), neg=0, invalid=1511
0317: dt=20.759334, rms=0.483 (0.092%), neg=0, invalid=1511
0318: dt=20.759334, rms=0.482 (0.079%), neg=0, invalid=1511
0319: dt=20.759334, rms=0.482 (0.084%), neg=0, invalid=1511
0320: dt=20.759334, rms=0.482 (0.071%), neg=0, invalid=1511
0321: dt=20.759334, rms=0.481 (0.059%), neg=0, invalid=1511
0322: dt=20.759334, rms=0.481 (0.056%), neg=0, invalid=1511
0323: dt=20.759334, rms=0.481 (0.051%), neg=0, invalid=1511
0324: dt=20.759334, rms=0.481 (0.047%), neg=0, invalid=1511
0325: dt=20.759334, rms=0.480 (0.037%), neg=0, invalid=1511
0326: dt=20.759334, rms=0.480 (0.042%), neg=0, invalid=1511
0327: dt=20.759334, rms=0.480 (0.037%), neg=0, invalid=1511
0328: dt=20.759334, rms=0.480 (0.035%), neg=0, invalid=1511
0329: dt=20.759334, rms=0.480 (0.042%), neg=0, invalid=1511
0330: dt=20.759334, rms=0.479 (0.042%), neg=0, invalid=1511
0331: dt=20.759334, rms=0.479 (0.043%), neg=0, invalid=1511
0332: dt=20.759334, rms=0.479 (0.038%), neg=0, invalid=1511
0333: dt=20.759334, rms=0.479 (0.043%), neg=0, invalid=1511
0334: dt=20.759334, rms=0.479 (0.033%), neg=0, invalid=1511
0335: dt=20.759334, rms=0.479 (0.027%), neg=0, invalid=1511
0336: dt=20.759334, rms=0.478 (0.037%), neg=0, invalid=1511
0337: dt=20.759334, rms=0.478 (0.031%), neg=0, invalid=1511
0338: dt=20.759334, rms=0.478 (0.027%), neg=0, invalid=1511
0339: dt=20.759334, rms=0.478 (0.020%), neg=0, invalid=1511
0340: dt=20.759334, rms=0.478 (0.021%), neg=0, invalid=1511
0341: dt=20.759334, rms=0.478 (0.024%), neg=0, invalid=1511
0342: dt=20.759334, rms=0.478 (0.026%), neg=0, invalid=1511
0343: dt=20.759334, rms=0.478 (0.008%), neg=0, invalid=1511
0344: dt=20.759334, rms=0.477 (0.041%), neg=0, invalid=1511
0345: dt=20.759334, rms=0.477 (0.022%), neg=0, invalid=1511
0346: dt=20.759334, rms=0.477 (0.025%), neg=0, invalid=1511
0347: dt=20.759334, rms=0.477 (0.013%), neg=0, invalid=1511
0348: dt=20.759334, rms=0.477 (0.034%), neg=0, invalid=1511
0349: dt=20.759334, rms=0.477 (0.017%), neg=0, invalid=1511
0350: dt=20.759334, rms=0.477 (0.008%), neg=0, invalid=1511
0351: dt=11.200000, rms=0.477 (0.016%), neg=0, invalid=1511
0352: dt=6.400000, rms=0.477 (0.001%), neg=0, invalid=1511
0353: dt=6.400000, rms=0.477 (0.001%), neg=0, invalid=1511
0354: dt=6.400000, rms=0.477 (0.001%), neg=0, invalid=1511
0355: dt=6.400000, rms=0.477 (0.003%), neg=0, invalid=1511
0356: dt=6.400000, rms=0.477 (0.002%), neg=0, invalid=1511
0357: dt=6.400000, rms=0.477 (0.000%), neg=0, invalid=1511
setting smoothness coefficient to 0.40
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.499, neg=0, invalid=1511
0358: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=1511
0359: dt=0.000000, rms=0.499 (-0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.499, neg=0, invalid=1511
0360: dt=0.000000, rms=0.499 (-0.000%), neg=0, invalid=1511
setting smoothness coefficient to 1.00
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.545, neg=0, invalid=1511
0361: dt=1.234491, rms=0.541 (0.625%), neg=0, invalid=1511
0362: dt=0.256000, rms=0.541 (0.013%), neg=0, invalid=1511
0363: dt=0.256000, rms=0.541 (-0.007%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.541, neg=0, invalid=1511
0364: dt=0.719563, rms=0.541 (0.082%), neg=0, invalid=1511
0365: dt=0.112000, rms=0.541 (0.004%), neg=0, invalid=1511
0366: dt=0.112000, rms=0.541 (-0.001%), neg=0, invalid=1511
resetting metric properties...
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.486, neg=0, invalid=1511
0367: dt=0.448000, rms=0.472 (2.788%), neg=0, invalid=1511
0368: dt=0.448000, rms=0.470 (0.410%), neg=0, invalid=1511
0369: dt=0.448000, rms=0.469 (0.314%), neg=0, invalid=1511
0370: dt=0.448000, rms=0.468 (0.185%), neg=0, invalid=1511
0371: dt=0.028000, rms=0.468 (0.008%), neg=0, invalid=1511
0372: dt=0.028000, rms=0.468 (0.009%), neg=0, invalid=1511
0373: dt=0.028000, rms=0.468 (0.017%), neg=0, invalid=1511
0374: dt=0.028000, rms=0.467 (0.024%), neg=0, invalid=1511
0375: dt=0.028000, rms=0.467 (0.028%), neg=0, invalid=1511
0376: dt=0.028000, rms=0.467 (0.034%), neg=0, invalid=1511
0377: dt=0.028000, rms=0.467 (0.035%), neg=0, invalid=1511
0378: dt=0.028000, rms=0.467 (0.038%), neg=0, invalid=1511
0379: dt=0.028000, rms=0.467 (0.038%), neg=0, invalid=1511
0380: dt=0.028000, rms=0.466 (0.041%), neg=0, invalid=1511
0381: dt=0.028000, rms=0.466 (0.040%), neg=0, invalid=1511
0382: dt=0.028000, rms=0.466 (0.039%), neg=0, invalid=1511
0383: dt=0.028000, rms=0.466 (0.039%), neg=0, invalid=1511
0384: dt=0.028000, rms=0.466 (0.037%), neg=0, invalid=1511
0385: dt=0.028000, rms=0.466 (0.035%), neg=0, invalid=1511
0386: dt=0.028000, rms=0.465 (0.036%), neg=0, invalid=1511
0387: dt=0.028000, rms=0.465 (0.032%), neg=0, invalid=1511
0388: dt=0.028000, rms=0.465 (0.002%), neg=0, invalid=1511
0389: dt=0.028000, rms=0.465 (0.003%), neg=0, invalid=1511
0390: dt=0.028000, rms=0.465 (0.002%), neg=0, invalid=1511
0391: dt=0.384000, rms=0.465 (0.018%), neg=0, invalid=1511
0392: dt=0.028000, rms=0.465 (0.002%), neg=0, invalid=1511
0393: dt=0.028000, rms=0.465 (0.003%), neg=0, invalid=1511
0394: dt=0.028000, rms=0.465 (0.003%), neg=0, invalid=1511
0395: dt=0.028000, rms=0.465 (0.004%), neg=0, invalid=1511
0396: dt=0.028000, rms=0.465 (0.004%), neg=0, invalid=1511
0397: dt=0.028000, rms=0.465 (0.006%), neg=0, invalid=1511
0398: dt=0.028000, rms=0.465 (0.006%), neg=0, invalid=1511
0399: dt=0.028000, rms=0.465 (0.007%), neg=0, invalid=1511
0400: dt=0.028000, rms=0.465 (0.008%), neg=0, invalid=1511
0401: dt=0.028000, rms=0.465 (0.007%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.465, neg=0, invalid=1511
0402: dt=0.112000, rms=0.464 (0.242%), neg=0, invalid=1511
0403: dt=0.384000, rms=0.461 (0.598%), neg=0, invalid=1511
0404: dt=0.112000, rms=0.461 (0.036%), neg=0, invalid=1511
0405: dt=0.112000, rms=0.461 (0.028%), neg=0, invalid=1511
0406: dt=0.112000, rms=0.460 (0.053%), neg=0, invalid=1511
0407: dt=0.056000, rms=0.460 (0.010%), neg=0, invalid=1511
0408: dt=0.056000, rms=0.460 (0.015%), neg=0, invalid=1511
0409: dt=0.028000, rms=0.460 (0.004%), neg=0, invalid=1511
0410: dt=0.112000, rms=0.460 (0.014%), neg=0, invalid=1511
0411: dt=0.384000, rms=0.460 (0.043%), neg=0, invalid=1511
0412: dt=0.101112, rms=0.460 (0.005%), neg=0, invalid=1511
0413: dt=0.050556, rms=0.460 (0.004%), neg=0, invalid=1511
0414: dt=0.050556, rms=0.460 (0.004%), neg=0, invalid=1511
0415: dt=0.050556, rms=0.460 (0.004%), neg=0, invalid=1511
0416: dt=0.050556, rms=0.460 (0.006%), neg=0, invalid=1511
0417: dt=0.050556, rms=0.460 (0.009%), neg=0, invalid=1511
0418: dt=0.050556, rms=0.460 (0.011%), neg=0, invalid=1511
0419: dt=0.050556, rms=0.460 (0.014%), neg=0, invalid=1511
0420: dt=0.050556, rms=0.460 (0.002%), neg=0, invalid=1511
0421: dt=0.050556, rms=0.460 (0.004%), neg=0, invalid=1511
0422: dt=0.050556, rms=0.460 (0.006%), neg=0, invalid=1511
0423: dt=0.050556, rms=0.460 (0.009%), neg=0, invalid=1511
0424: dt=0.050556, rms=0.460 (0.009%), neg=0, invalid=1511
0425: dt=0.050556, rms=0.460 (0.011%), neg=0, invalid=1511
0426: dt=0.050556, rms=0.460 (0.011%), neg=0, invalid=1511
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
label assignment complete, 0 changed (0.00%)
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.01
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.458, neg=0, invalid=1511
0427: dt=23.120000, rms=0.458 (-0.061%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.458, neg=0, invalid=1511
0428: dt=129.472002, rms=0.457 (0.139%), neg=0, invalid=1511
0429: dt=295.936004, rms=0.457 (0.071%), neg=0, invalid=1511
0430: dt=129.472002, rms=0.457 (0.059%), neg=0, invalid=1511
0431: dt=73.984001, rms=0.457 (0.011%), neg=0, invalid=1511
0432: dt=73.984001, rms=0.457 (0.010%), neg=0, invalid=1511
0433: dt=73.984001, rms=0.457 (0.018%), neg=0, invalid=1511
0434: dt=73.984001, rms=0.457 (0.024%), neg=0, invalid=1511
0435: dt=73.984001, rms=0.456 (0.027%), neg=0, invalid=1511
0436: dt=73.984001, rms=0.456 (0.027%), neg=0, invalid=1511
0437: dt=73.984001, rms=0.456 (0.025%), neg=0, invalid=1511
0438: dt=73.984001, rms=0.456 (0.023%), neg=0, invalid=1511
0439: dt=73.984001, rms=0.456 (0.021%), neg=0, invalid=1511
0440: dt=2071.552031, rms=0.456 (0.067%), neg=0, invalid=1511
0441: dt=32.368000, rms=0.456 (0.008%), neg=0, invalid=1511
0442: dt=32.368000, rms=0.456 (0.002%), neg=0, invalid=1511
0443: dt=32.368000, rms=0.456 (0.000%), neg=0, invalid=1511
0444: dt=32.368000, rms=0.456 (-0.001%), neg=0, invalid=1511
setting smoothness coefficient to 0.03
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.456, neg=0, invalid=1511
0445: dt=6.480000, rms=0.456 (0.003%), neg=0, invalid=1511
0446: dt=1.296000, rms=0.456 (0.000%), neg=0, invalid=1511
0447: dt=1.296000, rms=0.456 (-0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=1511
0448: dt=145.152002, rms=0.454 (0.395%), neg=0, invalid=1511
0449: dt=36.288001, rms=0.454 (0.060%), neg=0, invalid=1511
0450: dt=36.288001, rms=0.453 (0.044%), neg=0, invalid=1511
0451: dt=4.536000, rms=0.453 (0.006%), neg=0, invalid=1511
0452: dt=2.268000, rms=0.453 (0.003%), neg=0, invalid=1511
0453: dt=0.567000, rms=0.453 (0.001%), neg=0, invalid=1511
0454: dt=0.141750, rms=0.453 (0.000%), neg=0, invalid=1511
setting smoothness coefficient to 0.12
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.453, neg=0, invalid=1511
0455: dt=0.001953, rms=0.453 (0.000%), neg=0, invalid=1511
0456: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.453, neg=0, invalid=1511
0457: dt=0.000684, rms=0.453 (0.000%), neg=0, invalid=1511
0458: dt=0.000488, rms=0.453 (0.000%), neg=0, invalid=1511
0459: dt=0.000122, rms=0.453 (0.000%), neg=0, invalid=1511
0460: dt=0.000015, rms=0.453 (0.000%), neg=0, invalid=1511
0461: dt=0.000001, rms=0.453 (0.000%), neg=0, invalid=1511
setting smoothness coefficient to 0.40
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.454, neg=0, invalid=1511
0462: dt=4.032000, rms=0.450 (0.845%), neg=0, invalid=1511
0463: dt=4.032000, rms=0.448 (0.545%), neg=0, invalid=1511
0464: dt=4.032000, rms=0.446 (0.370%), neg=0, invalid=1511
0465: dt=3.456000, rms=0.445 (0.235%), neg=0, invalid=1511
0466: dt=4.032000, rms=0.444 (0.210%), neg=0, invalid=1511
0467: dt=4.032000, rms=0.443 (0.160%), neg=0, invalid=1511
0468: dt=3.456000, rms=0.443 (0.114%), neg=0, invalid=1511
0469: dt=4.032000, rms=0.442 (0.107%), neg=0, invalid=1511
0470: dt=4.032000, rms=0.442 (0.077%), neg=0, invalid=1511
0471: dt=4.032000, rms=0.442 (0.075%), neg=0, invalid=1511
0472: dt=4.032000, rms=0.441 (0.062%), neg=0, invalid=1511
0473: dt=4.032000, rms=0.441 (0.049%), neg=0, invalid=1511
0474: dt=4.032000, rms=0.441 (0.042%), neg=0, invalid=1511
0475: dt=4.032000, rms=0.441 (0.070%), neg=0, invalid=1511
0476: dt=4.032000, rms=0.440 (0.083%), neg=0, invalid=1511
0477: dt=4.032000, rms=0.440 (0.090%), neg=0, invalid=1511
0478: dt=4.032000, rms=0.440 (0.084%), neg=0, invalid=1511
0479: dt=4.032000, rms=0.439 (0.067%), neg=0, invalid=1511
0480: dt=4.032000, rms=0.439 (0.055%), neg=0, invalid=1511
0481: dt=4.032000, rms=0.439 (0.039%), neg=0, invalid=1511
0482: dt=4.032000, rms=0.439 (0.018%), neg=0, invalid=1511
0483: dt=4.032000, rms=0.439 (-0.001%), neg=0, invalid=1511
0484: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.439, neg=0, invalid=1511
0485: dt=4.032000, rms=0.437 (0.402%), neg=0, invalid=1511
0486: dt=4.032000, rms=0.436 (0.276%), neg=0, invalid=1511
0487: dt=4.032000, rms=0.435 (0.195%), neg=0, invalid=1511
0488: dt=16.128000, rms=0.433 (0.471%), neg=0, invalid=1511
0489: dt=4.032000, rms=0.433 (0.055%), neg=0, invalid=1511
0490: dt=16.128000, rms=0.432 (0.154%), neg=0, invalid=1511
0491: dt=4.032000, rms=0.432 (0.031%), neg=0, invalid=1511
0492: dt=4.032000, rms=0.432 (0.031%), neg=0, invalid=1511
0493: dt=4.032000, rms=0.432 (0.028%), neg=0, invalid=1511
0494: dt=4.032000, rms=0.431 (0.048%), neg=0, invalid=1511
0495: dt=4.032000, rms=0.431 (0.061%), neg=0, invalid=1511
0496: dt=4.032000, rms=0.431 (0.063%), neg=0, invalid=1511
0497: dt=4.032000, rms=0.431 (0.059%), neg=0, invalid=1511
0498: dt=4.032000, rms=0.430 (0.056%), neg=0, invalid=1511
0499: dt=4.032000, rms=0.430 (0.052%), neg=0, invalid=1511
0500: dt=4.032000, rms=0.430 (0.055%), neg=0, invalid=1511
0501: dt=4.032000, rms=0.430 (0.061%), neg=0, invalid=1511
0502: dt=4.032000, rms=0.429 (0.062%), neg=0, invalid=1511
0503: dt=4.032000, rms=0.429 (0.067%), neg=0, invalid=1511
0504: dt=4.032000, rms=0.429 (0.068%), neg=0, invalid=1511
0505: dt=4.032000, rms=0.429 (0.066%), neg=0, invalid=1511
0506: dt=4.032000, rms=0.428 (0.055%), neg=0, invalid=1511
0507: dt=4.032000, rms=0.428 (0.051%), neg=0, invalid=1511
0508: dt=2.016000, rms=0.428 (0.003%), neg=0, invalid=1511
0509: dt=0.252000, rms=0.428 (0.000%), neg=0, invalid=1511
0510: dt=0.063000, rms=0.428 (0.000%), neg=0, invalid=1511
0511: dt=0.000492, rms=0.428 (0.000%), neg=0, invalid=1511
0512: dt=0.000246, rms=0.428 (0.000%), neg=0, invalid=1511
0513: dt=0.000062, rms=0.428 (0.000%), neg=0, invalid=1511
0514: dt=0.000031, rms=0.428 (-0.000%), neg=0, invalid=1511
setting smoothness coefficient to 1.00
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.433, neg=0, invalid=1511
0515: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=1511
0516: dt=0.100000, rms=0.433 (-0.069%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=1511
0517: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=1511
0518: dt=0.100000, rms=0.433 (-0.057%), neg=0, invalid=1511
resetting metric properties...
setting smoothness coefficient to 2.00
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.425, neg=0, invalid=1511
0519: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=1511
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.425, neg=0, invalid=1511
0520: dt=0.000000, rms=0.425 (0.000%), neg=0, invalid=1511
writing output transformation to transforms/talairach.m3z...

CA registration took 5 hours, 49 minutes and 51 seconds.
#--------------------------------------
#@# CA Reg Inv Tue Apr 10 08:31:27 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z 

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
gcam->type = vox
reading labels out of gcam file...
Inverting GCAM
Saving inverse 
#--------------------------------------
#@# Remove Neck Tue Apr 10 08:33:04 CEST 2007

 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz 

erasing everything more than 25 mm from possible brain
reading atlas '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
gcam->type = vox
reading labels out of gcam file...
removing structures at least 25 mm from brain...
11088539 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 2 minutes and 9 seconds.
#--------------------------------------
#@# SkullLTA Tue Apr 10 08:35:13 CEST 2007

 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2006-02-15.gca'...
setting gca type = Normal gca type
average std = 23.5   using min determinant for regularization = 55.2
0 singular and 6473 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
total sample mean = 91.1 (1456 zeros)
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3516, passno 0, spacing 8
Result so far: scale 1.000: max_log_p=-15683.2, old_max_log_p =-22479.6 (thresh=-22457.1)
 1.123   0.004   0.001  -17.751;
 0.003   1.178   0.135  -34.553;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;
Result so far: scale 1.000: max_log_p=-15683.2, old_max_log_p =-15683.2 (thresh=-15667.5)
 1.123   0.004   0.001  -17.751;
 0.003   1.178   0.135  -34.553;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;
freeing gibbs priors...done.
bounding unknown intensity as < 20.7 or > 1320.6 
************************************************
spacing=8, using 3516 sample points, tol=1.00e-05...
************************************************
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 73 --> 73
input volume #1 is the most T1-like
using real data threshold=9.0
using (100, 103, 108) as brain centroid...
mean wm in atlas = 126, using box (80,82,84) --> (119, 123,132) to find MRI wm
before smoothing, mri peak at 149
after smoothing, mri peak at 151, scaling input intensities by 0.834
scaling channel 0 by 0.834437
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
****************************************
Nine parameter search.  iteration 1 nscales = 1 ...
****************************************
reducing scale to 0.2500
***********************************************
Computing MAP estimate using 3516 samples...
*********************dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.12347   0.00357   0.00143  -17.75125;
 0.00314   1.17836   0.13489  -34.55275;
 0.00980  -0.15394   0.92859   22.20286;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3516
Quasinewton: input matrix
 1.12347   0.00357   0.00143  -17.75125;
 0.00314   1.17836   0.13489  -34.55275;
 0.00980  -0.15394   0.92859   22.20286;
 0.00000   0.00000   0.00000   1.00000;
pass 2 through quasi-newton minimization...
pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
pass 5 through quasi-newton minimization...
pass 6 through quasi-newton minimization...
**************************
dfp_em_step_func: 002: -log(p) = 15683.2
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.18, 0.13, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 003: -log(p) = 15630.5
after pass:transform: ( 1.12, -0.00, -0.00, -17.75)
                      ( 0.01, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 004: -log(p) = 15564.4
after pass:transform: ( 1.12, -0.00, -0.00, -17.75)
                      ( 0.01, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 005: -log(p) = 15543.5
after pass:transform: ( 1.12, 0.00, -0.00, -17.75)
                      ( 0.01, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 006: -log(p) = 15539.7
after pass:transform: ( 1.12, 0.00, -0.00, -17.75)
                      ( 0.00, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 007: -log(p) = 155dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.12347   0.00357   0.00143  -17.75125;
 0.00314   1.17836   0.13489  -34.55275;
 0.00980  -0.15394   0.92859   22.20286;
 0.00000   0.00000   0.00000   1.00000;
nsamples 385836
Quasinewton: input matrix
 1.12347   0.00357   0.00143  -17.75125;
 0.00314   1.17836   0.13489  -34.55275;
 0.00980  -0.15394   0.92859   22.20286;
 0.00000   0.00000   0.00000   1.00000;
pass 2 through quasi-newton minimization...
29.5
after pass:transform: ( 1.12, 0.01, -0.00, -17.75)
                      ( 0.00, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.92, 22.20)
outof QuasiNewtonEMA: 009: -log(p) = 15464.4  tol 0.000010
Resulting transform:
 1.123   0.004   0.001  -17.751;
 0.003   1.178   0.135  -34.553;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -15683.2 (old=-22479.6)
transform before final EM align:
 1.123   0.004   0.001  -17.751;
 0.003   1.178   0.135  -34.553;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 385836 samples. 
**************************************************
dfp_em_step_func: 008: -log(p) = 1899932.9
after pass:transform: ( 1.12, 0.00, 0.00, -17.75)
                      ( 0.00, 1.18, 0.13, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 009: -log(p) = 1896187.5
after pass:transform: pass 3 through quasi-newton minimization...
pass 4 through quasi-newton minimization...
fp = 1893629.000000, fret = 1893630.000000, ftol = 0.000000, EPS = 0.000000
( 1.12, 0.00, -0.00, -17.75)
                      ( 0.00, 1.18, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 010: -log(p) = 1893794.9
after pass:transform: ( 1.12, 0.00, -0.00, -17.75)
                      ( 0.00, 1.17, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
dfp_em_step_func: 011: -log(p) = 1893629.0
after pass:transform: ( 1.12, 0.00, -0.00, -17.75)
                      ( 0.00, 1.17, 0.14, -34.55)
                      ( 0.01, -0.15, 0.93, 22.20)
outof QuasiNewtonEMA: 013: -log(p) = 1893629.0  tol 0.000000
final transform:
 1.119   0.003  -0.001  -17.751;
 0.003   1.175   0.137  -34.553;
 0.011  -0.152   0.927   22.203;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 7 minutes and 56 seconds.
#--------------------------------------
#@# SubCort Seg Tue Apr 10 08:43:09 CEST 2007

 mri_diff aseg.auto.mgz aseg.mgz 

  Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm
  Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm
0

 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2006-02-15.gca aseg.auto.mgz 

renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes...
reading classifier array from /usr/local/freesurfer/average/RB_all_2006-02-15.gca...
setting gca type = Normal gca type
reading input volume from norm.mgz...
average std[0] = 7.4
reading transform from transforms/talairach.m3z...
gcam->type = vox
reading labels out of gcam file...
Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2006-02-15.gca
average std = 7.4   using min determinant for regularization = 5.5
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.13482 (104)
mri peak = 0.15919 (106)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (586 voxels, overlap=0.988)
gca peak = 0.19307 (105)
mri peak = 0.16748 (106)
Right_Pallidum (52): linear fit = 0.98 x + 0.0 (530 voxels, overlap=1.000)
gca peak = 0.07702 (114)
mri peak = 0.15729 (114)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (74150 voxels, overlap=0.553)
gca peak = 0.07016 (114)
mri peak = 0.12527 (114)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (71312 voxels, overlap=0.567)
gca peak = 0.10443 (32)
mri peak = 0.19213 (32)
Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2907 voxels, overlap=0.632)
gca peak = 0.11491 (25)
mri peak = 0.12378 (32)
Right_Lateral_Ventricle (43): linear fit = 1.35 x + 0.0 (2306 voxels, overlap=0.383)
gca peak = 0.27319 (66)
mri peak = 0.09850 (80)
Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1102 voxels, overlap=0.000)
gca peak = 0.29477 (66)
mri peak = 0.10750 (83)
Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1183 voxels, overlap=0.000)
gca peak = 0.06920 (68)
mri peak = 0.04782 (82)
Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (78649 voxels, overlap=0.035)
gca peak = 0.08287 (69)
mri peak = 0.04480 (85)
Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (74987 voxels, overlap=0.026)
gca peak = 0.22476 (80)
mri peak = 0.20474 (88)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (857 voxels, overlap=0.000)
gca peak = 0.18589 (81)
mri peak = 0.21317 (85)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (829 voxels, overlap=0.723)
gca peak = 0.08091 (61)
mri peak = 0.05977 (88)
Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (37652 voxels, overlap=0.000)
gca peak = 0.10638 (61)
mri peak = 0.05744 (84)
Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (40133 voxels, overlap=0.000)
gca peak = 0.15522 (88)
mri peak = 0.12230 (102)
Left_Cerebellum_White_Matter (7): linear fit = 1.15 x + 0.0 (8812 voxels, overlap=0.000)
gca peak = 0.12507 (87)
mri peak = 0.12881 (102)
Right_Cerebellum_White_Matter (46): linear fit = 1.15 x + 0.0 (6615 voxels, overlap=0.000)
gca peak = 0.25800 (69)
mri peak = 0.12011 (80)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (520 voxels, overlap=0.000)
gca peak = 0.29193 (67)
mri peak = 0.13985 (83)
Right_Amygdala (54): linear fit = 1.27 x + 0.0 (428 voxels, overlap=0.000)
gca peak = 0.11200 (101)
mri peak = 0.11013 (98)
Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4762 voxels, overlap=0.854)
gca peak = 0.10010 (92)
mri peak = 0.10184 (98)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4680 voxels, overlap=0.829)
gca peak = 0.07167 (89)
mri peak = 0.11231 (94)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (2542 voxels, overlap=0.696)
gca peak = 0.09514 (89)
mri peak = 0.09724 (94)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (2279 voxels, overlap=0.718)
gca peak = 0.07535 (89)
mri peak = 0.09317 (98)
Brain_Stem (16): linear fit = 1.08 x + 0.0 (16958 voxels, overlap=0.417)
gca peak = 0.11225 (101)
mri peak = 0.10782 (102)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (2032 voxels, overlap=0.517)
gca peak = 0.15721 (97)
mri peak = 0.11476 (102)
Left_VentralDC (28): linear fit = 1.05 x + 0.0 (2211 voxels, overlap=0.738)
gca peak = 0.13106 (39)
mri peak = 0.11492 (32)
Third_Ventricle (14): linear fit = 0.85 x + 0.0 (99 voxels, overlap=0.481)
gca peak = 0.19587 (25)
mri peak = 0.21588 (30)
not using caudate to estimate GM means
Fourth_Ventricle (15): linear fit = 1.20 x + 0.0 (269 voxels, overlap=0.506)
estimating mean gm scale to be 1.24 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.10 x + 0.0
53674 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
456 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 84897 changed. image ll: -2.249, PF=1.000
pass 2: 14011 changed. image ll: -2.247, PF=1.000
pass 3: 5599 changed.
pass 4: 2711 changed.
16907 border labels changed to MLE ...
writing labeled volume to aseg.auto.mgz...
auto-labeling took 30 minutes and 29 seconds.

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# ASeg Stats Tue Apr 10 09:13:46 CEST 2007
/home/xonobo/FSRFsubjects/bert

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject bert 

Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt
atlas_icv = 1.73126e+06
Loading mri/aseg.mgz
Loading mri/norm.mgz
Loading mri/norm.mgz
Loading mri/brainmask.mgz
# nbrainmaskvoxels 1730337
# brainmaskvolume  1730337.0
# nbrainsegvoxels 1299938
# brainsegvolume  1299938.0
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 686 segmentations
Computing statistics for each segmentation
  1     1  Left-Cerebral-Exterior  0
  2     2  Left-Cerebral-White-Matter 265452  265452
  3     3  Left-Cerebral-Cortex 252623  252623
  4     4  Left-Lateral-Ventricle 7313  7313
  5     5  Left-Inf-Lat-Vent  485  485
  6     6  Left-Cerebellum-Exterior  0
  7     7  Left-Cerebellum-White-Matter 16247  16247
  8     8  Left-Cerebellum-Cortex 60509  60509
  9     9  Left-Thalamus  0
 10    10  Left-Thalamus-Proper 8138  8138
 11    11  Left-Caudate 3267  3267
 12    12  Left-Putamen 5581  5581
 13    13  Left-Pallidum 1965  1965
 14    14  3rd-Ventricle  842  842
 15    15  4th-Ventricle 1950  1950
 16    16  Brain-Stem 24793  24793
 17    17  Left-Hippocampus 4359  4359
 18    18  Left-Amygdala 1646  1646
 19    19  Left-Insula  0
 20    20  Left-Operculum  0
 21    21  Line-1  0
 22    22  Line-2  0
 23    23  Line-3  0
 24    24  CSF 1462  1462
 25    25  Left-Lesion  0
 26    26  Left-Accumbens-area  548  548
 27    27  Left-Substancia-Nigra  0
 28    28  Left-VentralDC 4699  4699
 29    29  Left-undetermined  0
 30    30  Left-vessel   80  80
 31    31  Left-choroid-plexus  0
 32    32  Left-F3orb  0
 33    33  Left-lOg  0
 34    34  Left-aOg  0
 35    35  Left-mOg  0
 36    36  Left-pOg  0
 37    37  Left-Stellate  0
 38    38  Left-Porg  0
 39    39  Left-Aorg  0
 40    40  Right-Cerebral-Exterior  0
 41    41  Right-Cerebral-White-Matter 277847  277847
 42    42  Right-Cerebral-Cortex 250195  250195
 43    43  Right-Lateral-Ventricle 6907  6907
 44    44  Right-Inf-Lat-Vent  288  288
 45    45  Right-Cerebellum-Exterior  0
 46    46  Right-Cerebellum-White-Matter 15091  15091
 47    47  Right-Cerebellum-Cortex 62604  62604
 48    48  Right-Thalamus  0
 49    49  Right-Thalamus-Proper 8152  8152
 50    50  Right-Caudate 3238  3238
 51    51  Right-Putamen 5262  5262
 52    52  Right-Pallidum 1876  1876
 53    53  Right-Hippocampus 4407  4407
 54    54  Right-Amygdala 1434  1434
 55    55  Right-Insula  0
 56    56  Right-Operculum  0
 57    57  Right-Lesion  0
 58    58  Right-Accumbens-area  560  560
 59    59  Right-Substancia-Nigra  0
 60    60  Right-VentralDC 4515  4515
 61    61  Right-undetermined  0
 62    62  Right-vessel   45  45
 63    63  Right-choroid-plexus  0
 64    64  Right-F3orb  0
 65    65  Right-lOg  0
 66    66  Right-aOg  0
 67    67  Right-mOg  0
 68    68  Right-pOg  0
 69    69  Right-Stellate  0
 70    70  Right-Porg  0
 71    71  Right-Aorg  0
 72    72  5th-Ventricle  205  205
 73    73  Left-Interior  0
 74    74  Right-Interior  0
 75    75  Left-Lateral-Ventricles  0
 76    76  Right-Lateral-Ventricles  0
 77    77  WM-hypointensities  0
 78    78  Left-WM-hypointensities  883  883
 79    79  Right-WM-hypointensities  918  918
 80    80  non-WM-hypointensities  0
 81    81  Left-non-WM-hypointensities   12  12
 82    82  Right-non-WM-hypointensities  0
 83    83  Left-F1  0
 84    84  Right-F1  0
 85    85  Optic-Chiasm  312  312
 86    86  Corpus_Callosum  0
 87    96  Left-Amygdala-Anterior  0
 88    97  Right-Amygdala-Anterior  0
 89    98  Dura  0
 90   100  Left-wm-intensity-abnormality  0
 91   101  Left-caudate-intensity-abnormality  0
 92   102  Left-putamen-intensity-abnormality  0
 93   103  Left-accumbens-intensity-abnormality  0
 94   104  Left-pallidum-intensity-abnormality  0
 95   105  Left-amygdala-intensity-abnormality  0
 96   106  Left-hippocampus-intensity-abnormality  0
 97   107  Left-thalamus-intensity-abnormality  0
 98   108  Left-VDC-intensity-abnormality  0
 99   109  Right-wm-intensity-abnormality  0
100   110  Right-caudate-intensity-abnormality  0
101   111  Right-putamen-intensity-abnormality  0
102   112  Right-accumbens-intensity-abnormality  0
103   113  Right-pallidum-intensity-abnormality  0
104   114  Right-amygdala-intensity-abnormality  0
105   115  Right-hippocampus-intensity-abnormality  0
106   116  Right-thalamus-intensity-abnormality  0
107   117  Right-VDC-intensity-abnormality  0
108   118  Epidermis  0
109   119  Conn-Tissue  0
110   120  SC-Fat/Muscle  0
111   121  Cranium  0
112   122  CSF-SA  0
113   123  Muscle  0
114   124  Ear  0
115   125  Adipose  0
116   126  Spinal-Cord  0
117   127  Soft-Tissue  0
118   128  Nerve  0
119   129  Bone  0
120   130  Air  0
121   131  Orbital-Fat  0
122   132  Tongue  0
123   133  Nasal-Structures  0
124   134  Globe  0
125   135  Teeth  0
126   136  Left-Caudate/Putamen  0
127   137  Right-Caudate/Putamen  0
128   138  Left-Claustrum  0
129   139  Right-Claustrum  0
130   140  Cornea  0
131   142  Diploe  0
132   143  Vitreous-Humor  0
133   144  Lens  0
134   145  Aqueous-Humor  0
135   146  Outer-Table  0
136   147  Inner-Table  0
137   148  Periosteum  0
138   149  Endosteum  0
139   150  R/C/S  0
140   151  Iris  0
141   152  SC-Adipose/Muscle  0
142   153  SC-Tissue  0
143   154  Orbital-Adipose  0
144   193  Left-hippocampal_fissure  0
145   194  Left-CADG-head  0
146   195  Left-subiculum  0
147   196  Left-fimbria  0
148   197  Right-hippocampal_fissure  0
149   198  Right-CADG-head  0
150   199  Right-subiculum  0
151   200  Right-fimbria  0
152   201  alveus  0
153   202  perforant_pathway  0
154   203  parasubiculum  0
155   204  presubiculum  0
156   205  subiculum  0
157   206  CA1  0
158   207  CA2  0
159   208  CA3  0
160   209  CA4  0
161   210  GC-DG  0
162   211  HATA  0
163   212  fimbria  0
164   213  lateral_ventricle  0
165   214  molecular_layer_HP  0
166   215  hippocampal_fissure  0
167   216  entorhinal_cortex  0
168   217  molecular_layer_subiculum  0
169   218  Amygdala  0
170   219  Cerebral_White_Matter  0
171   220  Cerebral_Cortex  0
172   221  Inf_Lat_Vent  0
173   222  Ectorhinal  0
174   222  Perirhinal  0
175   223  Cerebral_White_Matter_Edge  0
176   224  fMRI_Background  0
177   331  Aorta  0
178   332  Left-Common-IliacA  0
179   333  Right-Common-IliacA  0
180   334  Left-External-IliacA  0
181   335  Right-External-IliacA  0
182   336  Left-Internal-IliacA  0
183   337  Right-Internal-IliacA  0
184   338  Left-Lateral-SacralA  0
185   339  Right-Lateral-SacralA  0
186   340  Left-ObturatorA  0
187   341  Right-ObturatorA  0
188   342  Left-Internal-PudendalA  0
189   343  Right-Internal-PudendalA  0
190   344  Left-UmbilicalA  0
191   345  Right-UmbilicalA  0
192   346  Left-Inf-RectalA  0
193   347  Right-Inf-RectalA  0
194   348  Left-Common-IliacV  0
195   349  Right-Common-IliacV  0
196   350  Left-External-IliacV  0
197   351  Right-External-IliacV  0
198   352  Left-Internal-IliacV  0
199   353  Right-Internal-IliacV  0
200   354  Left-ObturatorV  0
201   355  Right-ObturatorV  0
202   356  Left-Internal-PudendalV  0
203   357  Right-Internal-PudendalV  0
204   358  Pos-Lymph  0
205   359  Neg-Lymph  0
206   400  V1  0
207   401  V2  0
208   402  BA44  0
209   403  BA45  0
210   404  BA4a  0
211   405  BA4p  0
212   406  BA6  0
213   407  BA2  0
214   408  BAun1  0
215   409  BAun2  0
216   1000  ctx-lh-unknown  0
217   1001  ctx-lh-bankssts  0
218   1002  ctx-lh-caudalanteriorcingulate  0
219   1003  ctx-lh-caudalmiddlefrontal  0
220   1004  ctx-lh-corpuscallosum  0
221   1005  ctx-lh-cuneus  0
222   1006  ctx-lh-entorhinal  0
223   1007  ctx-lh-fusiform  0
224   1008  ctx-lh-inferiorparietal  0
225   1009  ctx-lh-inferiortemporal  0
226   1010  ctx-lh-isthmuscingulate  0
227   1011  ctx-lh-lateraloccipital  0
228   1012  ctx-lh-lateralorbitofrontal  0
229   1013  ctx-lh-lingual  0
230   1014  ctx-lh-medialorbitofrontal  0
231   1015  ctx-lh-middletemporal  0
232   1016  ctx-lh-parahippocampal  0
233   1017  ctx-lh-paracentral  0
234   1018  ctx-lh-parsopercularis  0
235   1019  ctx-lh-parsorbitalis  0
236   1020  ctx-lh-parstriangularis  0
237   1021  ctx-lh-pericalcarine  0
238   1022  ctx-lh-postcentral  0
239   1023  ctx-lh-posteriorcingulate  0
240   1024  ctx-lh-precentral  0
241   1025  ctx-lh-precuneus  0
242   1026  ctx-lh-rostralanteriorcingulate  0
243   1027  ctx-lh-rostralmiddlefrontal  0
244   1028  ctx-lh-superiorfrontal  0
245   1029  ctx-lh-superiorparietal  0
246   1030  ctx-lh-superiortemporal  0
247   1031  ctx-lh-supramarginal  0
248   1032  ctx-lh-frontalpole  0
249   1033  ctx-lh-temporalpole  0
250   1034  ctx-lh-transversetemporal  0
251   2000  ctx-rh-unknown  0
252   2001  ctx-rh-bankssts  0
253   2002  ctx-rh-caudalanteriorcingulate  0
254   2003  ctx-rh-caudalmiddlefrontal  0
255   2004  ctx-rh-corpuscallosum  0
256   2005  ctx-rh-cuneus  0
257   2006  ctx-rh-entorhinal  0
258   2007  ctx-rh-fusiform  0
259   2008  ctx-rh-inferiorparietal  0
260   2009  ctx-rh-inferiortemporal  0
261   2010  ctx-rh-isthmuscingulate  0
262   2011  ctx-rh-lateraloccipital  0
263   2012  ctx-rh-lateralorbitofrontal  0
264   2013  ctx-rh-lingual  0
265   2014  ctx-rh-medialorbitofrontal  0
266   2015  ctx-rh-middletemporal  0
267   2016  ctx-rh-parahippocampal  0
268   2017  ctx-rh-paracentral  0
269   2018  ctx-rh-parsopercularis  0
270   2019  ctx-rh-parsorbitalis  0
271   2020  ctx-rh-parstriangularis  0
272   2021  ctx-rh-pericalcarine  0
273   2022  ctx-rh-postcentral  0
274   2023  ctx-rh-posteriorcingulate  0
275   2024  ctx-rh-precentral  0
276   2025  ctx-rh-precuneus  0
277   2026  ctx-rh-rostralanteriorcingulate  0
278   2027  ctx-rh-rostralmiddlefrontal  0
279   2028  ctx-rh-superiorfrontal  0
280   2029  ctx-rh-superiorparietal  0
281   2030  ctx-rh-superiortemporal  0
282   2031  ctx-rh-supramarginal  0
283   2032  ctx-rh-frontalpole  0
284   2033  ctx-rh-temporalpole  0
285   2034  ctx-rh-transversetemporal  0
286   3000  wm-lh-unknown  0
287   3001  wm-lh-bankssts  0
288   3002  wm-lh-caudalanteriorcingulate  0
289   3003  wm-lh-caudalmiddlefrontal  0
290   3004  wm-lh-corpuscallosum  0
291   3005  wm-lh-cuneus  0
292   3006  wm-lh-entorhinal  0
293   3007  wm-lh-fusiform  0
294   3008  wm-lh-inferiorparietal  0
295   3009  wm-lh-inferiortemporal  0
296   3010  wm-lh-isthmuscingulate  0
297   3011  wm-lh-lateraloccipital  0
298   3012  wm-lh-lateralorbitofrontal  0
299   3013  wm-lh-lingual  0
300   3014  wm-lh-medialorbitofrontal  0
301   3015  wm-lh-middletemporal  0
302   3016  wm-lh-parahippocampal  0
303   3017  wm-lh-paracentral  0
304   3018  wm-lh-parsopercularis  0
305   3019  wm-lh-parsorbitalis  0
306   3020  wm-lh-parstriangularis  0
307   3021  wm-lh-pericalcarine  0
308   3022  wm-lh-postcentral  0
309   3023  wm-lh-posteriorcingulate  0
310   3024  wm-lh-precentral  0
311   3025  wm-lh-precuneus  0
312   3026  wm-lh-rostralanteriorcingulate  0
313   3027  wm-lh-rostralmiddlefrontal  0
314   3028  wm-lh-superiorfrontal  0
315   3029  wm-lh-superiorparietal  0
316   3030  wm-lh-superiortemporal  0
317   3031  wm-lh-supramarginal  0
318   3032  wm-lh-frontalpole  0
319   3033  wm-lh-temporalpole  0
320   3034  wm-lh-transversetemporal  0
321   4000  wm-rh-unknown  0
322   4001  wm-rh-bankssts  0
323   4002  wm-rh-caudalanteriorcingulate  0
324   4003  wm-rh-caudalmiddlefrontal  0
325   4004  wm-rh-corpuscallosum  0
326   4005  wm-rh-cuneus  0
327   4006  wm-rh-entorhinal  0
328   4007  wm-rh-fusiform  0
329   4008  wm-rh-inferiorparietal  0
330   4009  wm-rh-inferiortemporal  0
331   4010  wm-rh-isthmuscingulate  0
332   4011  wm-rh-lateraloccipital  0
333   4012  wm-rh-lateralorbitofrontal  0
334   4013  wm-rh-lingual  0
335   4014  wm-rh-medialorbitofrontal  0
336   4015  wm-rh-middletemporal  0
337   4016  wm-rh-parahippocampal  0
338   4017  wm-rh-paracentral  0
339   4018  wm-rh-parsopercularis  0
340   4019  wm-rh-parsorbitalis  0
341   4020  wm-rh-parstriangularis  0
342   4021  wm-rh-pericalcarine  0
343   4022  wm-rh-postcentral  0
344   4023  wm-rh-posteriorcingulate  0
345   4024  wm-rh-precentral  0
346   4025  wm-rh-precuneus  0
347   4026  wm-rh-rostralanteriorcingulate  0
348   4027  wm-rh-rostralmiddlefrontal  0
349   4028  wm-rh-superiorfrontal  0
350   4029  wm-rh-superiorparietal  0
351   4030  wm-rh-superiortemporal  0
352   4031  wm-rh-supramarginal  0
353   4032  wm-rh-frontalpole  0
354   4033  wm-rh-temporalpole  0
355   4034  wm-rh-transversetemporal  0
356   5001  wm-lh-centrum-semiovale  0
357   5002  wm-rh-centrum-semiovale  0
358   1100  ctx-lh-Unknown  0
359   1101  ctx-lh-Corpus_callosum  0
360   1102  ctx-lh-G_and_S_Insula_ONLY_AVERAGE  0
361   1103  ctx-lh-G_cingulate-Isthmus  0
362   1104  ctx-lh-G_cingulate-Main_part  0
363   1105  ctx-lh-G_cuneus  0
364   1106  ctx-lh-G_frontal_inf-Opercular_part  0
365   1107  ctx-lh-G_frontal_inf-Orbital_part  0
366   1108  ctx-lh-G_frontal_inf-Triangular_part  0
367   1109  ctx-lh-G_frontal_middle  0
368   1110  ctx-lh-G_frontal_superior  0
369   1111  ctx-lh-G_frontomarginal  0
370   1112  ctx-lh-G_insular_long  0
371   1113  ctx-lh-G_insular_short  0
372   1114  ctx-lh-G_and_S_occipital_inferior  0
373   1115  ctx-lh-G_occipital_middle  0
374   1116  ctx-lh-G_occipital_superior  0
375   1117  ctx-lh-G_occipit-temp_lat-Or_fusiform  0
376   1118  ctx-lh-G_occipit-temp_med-Lingual_part  0
377   1119  ctx-lh-G_occipit-temp_med-Parahippocampal_part  0
378   1120  ctx-lh-G_orbital  0
379   1121  ctx-lh-G_paracentral  0
380   1122  ctx-lh-G_parietal_inferior-Angular_part  0
381   1123  ctx-lh-G_parietal_inferior-Supramarginal_part  0
382   1124  ctx-lh-G_parietal_superior  0
383   1125  ctx-lh-G_postcentral  0
384   1126  ctx-lh-G_precentral  0
385   1127  ctx-lh-G_precuneus  0
386   1128  ctx-lh-G_rectus  0
387   1129  ctx-lh-G_subcallosal  0
388   1130  ctx-lh-G_subcentral  0
389   1131  ctx-lh-G_temporal_inferior  0
390   1132  ctx-lh-G_temporal_middle  0
391   1133  ctx-lh-G_temp_sup-G_temp_transv_and_interm_S  0
392   1134  ctx-lh-G_temp_sup-Lateral_aspect  0
393   1135  ctx-lh-G_temp_sup-Planum_polare  0
394   1136  ctx-lh-G_temp_sup-Planum_tempolare  0
395   1137  ctx-lh-G_and_S_transverse_frontopolar  0
396   1138  ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal  0
397   1139  ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical  0
398   1140  ctx-lh-Lat_Fissure-post_sgt  0
399   1141  ctx-lh-Medial_wall  0
400   1142  ctx-lh-Pole_occipital  0
401   1143  ctx-lh-Pole_temporal  0
402   1144  ctx-lh-S_calcarine  0
403   1145  ctx-lh-S_central  0
404   1146  ctx-lh-S_central_insula  0
405   1147  ctx-lh-S_cingulate-Main_part_and_Intracingulate  0
406   1148  ctx-lh-S_cingulate-Marginalis_part  0
407   1149  ctx-lh-S_circular_insula_anterior  0
408   1150  ctx-lh-S_circular_insula_inferior  0
409   1151  ctx-lh-S_circular_insula_superior  0
410   1152  ctx-lh-S_collateral_transverse_ant  0
411   1153  ctx-lh-S_collateral_transverse_post  0
412   1154  ctx-lh-S_frontal_inferior  0
413   1155  ctx-lh-S_frontal_middle  0
414   1156  ctx-lh-S_frontal_superior  0
415   1157  ctx-lh-S_frontomarginal  0
416   1158  ctx-lh-S_intermedius_primus-Jensen  0
417   1159  ctx-lh-S_intraparietal-and_Parietal_transverse  0
418   1160  ctx-lh-S_occipital_anterior  0
419   1161  ctx-lh-S_occipital_middle_and_Lunatus  0
420   1162  ctx-lh-S_occipital_superior_and_transversalis  0
421   1163  ctx-lh-S_occipito-temporal_lateral  0
422   1164  ctx-lh-S_occipito-temporal_medial_and_S_Lingual  0
423   1165  ctx-lh-S_orbital-H_shapped  0
424   1166  ctx-lh-S_orbital_lateral  0
425   1167  ctx-lh-S_orbital_medial-Or_olfactory  0
426   1168  ctx-lh-S_paracentral  0
427   1169  ctx-lh-S_parieto_occipital  0
428   1170  ctx-lh-S_pericallosal  0
429   1171  ctx-lh-S_postcentral  0
430   1172  ctx-lh-S_precentral-Inferior-part  0
431   1173  ctx-lh-S_precentral-Superior-part  0
432   1174  ctx-lh-S_subcentral_ant  0
433   1175  ctx-lh-S_subcentral_post  0
434   1176  ctx-lh-S_suborbital  0
435   1177  ctx-lh-S_subparietal  0
436   1178  ctx-lh-S_supracingulate  0
437   1179  ctx-lh-S_temporal_inferior  0
438   1180  ctx-lh-S_temporal_superior  0
439   1181  ctx-lh-S_temporal_transverse  0
440   2100  ctx-rh-Unknown  0
441   2101  ctx-rh-Corpus_callosum  0
442   2102  ctx-rh-G_and_S_Insula_ONLY_AVERAGE  0
443   2103  ctx-rh-G_cingulate-Isthmus  0
444   2104  ctx-rh-G_cingulate-Main_part  0
445   2105  ctx-rh-G_cuneus  0
446   2106  ctx-rh-G_frontal_inf-Opercular_part  0
447   2107  ctx-rh-G_frontal_inf-Orbital_part  0
448   2108  ctx-rh-G_frontal_inf-Triangular_part  0
449   2109  ctx-rh-G_frontal_middle  0
450   2110  ctx-rh-G_frontal_superior  0
451   2111  ctx-rh-G_frontomarginal  0
452   2112  ctx-rh-G_insular_long  0
453   2113  ctx-rh-G_insular_short  0
454   2114  ctx-rh-G_and_S_occipital_inferior  0
455   2115  ctx-rh-G_occipital_middle  0
456   2116  ctx-rh-G_occipital_superior  0
457   2117  ctx-rh-G_occipit-temp_lat-Or_fusiform  0
458   2118  ctx-rh-G_occipit-temp_med-Lingual_part  0
459   2119  ctx-rh-G_occipit-temp_med-Parahippocampal_part  0
460   2120  ctx-rh-G_orbital  0
461   2121  ctx-rh-G_paracentral  0
462   2122  ctx-rh-G_parietal_inferior-Angular_part  0
463   2123  ctx-rh-G_parietal_inferior-Supramarginal_part  0
464   2124  ctx-rh-G_parietal_superior  0
465   2125  ctx-rh-G_postcentral  0
466   2126  ctx-rh-G_precentral  0
467   2127  ctx-rh-G_precuneus  0
468   2128  ctx-rh-G_rectus  0
469   2129  ctx-rh-G_subcallosal  0
470   2130  ctx-rh-G_subcentral  0
471   2131  ctx-rh-G_temporal_inferior  0
472   2132  ctx-rh-G_temporal_middle  0
473   2133  ctx-rh-G_temp_sup-G_temp_transv_and_interm_S  0
474   2134  ctx-rh-G_temp_sup-Lateral_aspect  0
475   2135  ctx-rh-G_temp_sup-Planum_polare  0
476   2136  ctx-rh-G_temp_sup-Planum_tempolare  0
477   2137  ctx-rh-G_and_S_transverse_frontopolar  0
478   2138  ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal  0
479   2139  ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical  0
480   2140  ctx-rh-Lat_Fissure-post_sgt  0
481   2141  ctx-rh-Medial_wall  0
482   2142  ctx-rh-Pole_occipital  0
483   2143  ctx-rh-Pole_temporal  0
484   2144  ctx-rh-S_calcarine  0
485   2145  ctx-rh-S_central  0
486   2146  ctx-rh-S_central_insula  0
487   2147  ctx-rh-S_cingulate-Main_part_and_Intracingulate  0
488   2148  ctx-rh-S_cingulate-Marginalis_part  0
489   2149  ctx-rh-S_circular_insula_anterior  0
490   2150  ctx-rh-S_circular_insula_inferior  0
491   2151  ctx-rh-S_circular_insula_superior  0
492   2152  ctx-rh-S_collateral_transverse_ant  0
493   2153  ctx-rh-S_collateral_transverse_post  0
494   2154  ctx-rh-S_frontal_inferior  0
495   2155  ctx-rh-S_frontal_middle  0
496   2156  ctx-rh-S_frontal_superior  0
497   2157  ctx-rh-S_frontomarginal  0
498   2158  ctx-rh-S_intermedius_primus-Jensen  0
499   2159  ctx-rh-S_intraparietal-and_Parietal_transverse  0
500   2160  ctx-rh-S_occipital_anterior  0
501   2161  ctx-rh-S_occipital_middle_and_Lunatus  0
502   2162  ctx-rh-S_occipital_superior_and_transversalis  0
503   2163  ctx-rh-S_occipito-temporal_lateral  0
504   2164  ctx-rh-S_occipito-temporal_medial_and_S_Lingual  0
505   2165  ctx-rh-S_orbital-H_shapped  0
506   2166  ctx-rh-S_orbital_lateral  0
507   2167  ctx-rh-S_orbital_medial-Or_olfactory  0
508   2168  ctx-rh-S_paracentral  0
509   2169  ctx-rh-S_parieto_occipital  0
510   2170  ctx-rh-S_pericallosal  0
511   2171  ctx-rh-S_postcentral  0
512   2172  ctx-rh-S_precentral-Inferior-part  0
513   2173  ctx-rh-S_precentral-Superior-part  0
514   2174  ctx-rh-S_subcentral_ant  0
515   2175  ctx-rh-S_subcentral_post  0
516   2176  ctx-rh-S_suborbital  0
517   2177  ctx-rh-S_subparietal  0
518   2178  ctx-rh-S_supracingulate  0
519   2179  ctx-rh-S_temporal_inferior  0
520   2180  ctx-rh-S_temporal_superior  0
521   2181  ctx-rh-S_temporal_transverse  0
522   3100  wm-lh-Unknown  0
523   3101  wm-lh-Corpus_callosum  0
524   3102  wm-lh-G_and_S_Insula_ONLY_AVERAGE  0
525   3103  wm-lh-G_cingulate-Isthmus  0
526   3104  wm-lh-G_cingulate-Main_part  0
527   3105  wm-lh-G_cuneus  0
528   3106  wm-lh-G_frontal_inf-Opercular_part  0
529   3107  wm-lh-G_frontal_inf-Orbital_part  0
530   3108  wm-lh-G_frontal_inf-Triangular_part  0
531   3109  wm-lh-G_frontal_middle  0
532   3110  wm-lh-G_frontal_superior  0
533   3111  wm-lh-G_frontomarginal  0
534   3112  wm-lh-G_insular_long  0
535   3113  wm-lh-G_insular_short  0
536   3114  wm-lh-G_and_S_occipital_inferior  0
537   3115  wm-lh-G_occipital_middle  0
538   3116  wm-lh-G_occipital_superior  0
539   3117  wm-lh-G_occipit-temp_lat-Or_fusiform  0
540   3118  wm-lh-G_occipit-temp_med-Lingual_part  0
541   3119  wm-lh-G_occipit-temp_med-Parahippocampal_part  0
542   3120  wm-lh-G_orbital  0
543   3121  wm-lh-G_paracentral  0
544   3122  wm-lh-G_parietal_inferior-Angular_part  0
545   3123  wm-lh-G_parietal_inferior-Supramarginal_part  0
546   3124  wm-lh-G_parietal_superior  0
547   3125  wm-lh-G_postcentral  0
548   3126  wm-lh-G_precentral  0
549   3127  wm-lh-G_precuneus  0
550   3128  wm-lh-G_rectus  0
551   3129  wm-lh-G_subcallosal  0
552   3130  wm-lh-G_subcentral  0
553   3131  wm-lh-G_temporal_inferior  0
554   3132  wm-lh-G_temporal_middle  0
555   3133  wm-lh-G_temp_sup-G_temp_transv_and_interm_S  0
556   3134  wm-lh-G_temp_sup-Lateral_aspect  0
557   3135  wm-lh-G_temp_sup-Planum_polare  0
558   3136  wm-lh-G_temp_sup-Planum_tempolare  0
559   3137  wm-lh-G_and_S_transverse_frontopolar  0
560   3138  wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal  0
561   3139  wm-lh-Lat_Fissure-ant_sgt-ramus_vertical  0
562   3140  wm-lh-Lat_Fissure-post_sgt  0
563   3141  wm-lh-Medial_wall  0
564   3142  wm-lh-Pole_occipital  0
565   3143  wm-lh-Pole_temporal  0
566   3144  wm-lh-S_calcarine  0
567   3145  wm-lh-S_central  0
568   3146  wm-lh-S_central_insula  0
569   3147  wm-lh-S_cingulate-Main_part_and_Intracingulate  0
570   3148  wm-lh-S_cingulate-Marginalis_part  0
571   3149  wm-lh-S_circular_insula_anterior  0
572   3150  wm-lh-S_circular_insula_inferior  0
573   3151  wm-lh-S_circular_insula_superior  0
574   3152  wm-lh-S_collateral_transverse_ant  0
575   3153  wm-lh-S_collateral_transverse_post  0
576   3154  wm-lh-S_frontal_inferior  0
577   3155  wm-lh-S_frontal_middle  0
578   3156  wm-lh-S_frontal_superior  0
579   3157  wm-lh-S_frontomarginal  0
580   3158  wm-lh-S_intermedius_primus-Jensen  0
581   3159  wm-lh-S_intraparietal-and_Parietal_transverse  0
582   3160  wm-lh-S_occipital_anterior  0
583   3161  wm-lh-S_occipital_middle_and_Lunatus  0
584   3162  wm-lh-S_occipital_superior_and_transversalis  0
585   3163  wm-lh-S_occipito-temporal_lateral  0
586   3164  wm-lh-S_occipito-temporal_medial_and_S_Lingual  0
587   3165  wm-lh-S_orbital-H_shapped  0
588   3166  wm-lh-S_orbital_lateral  0
589   3167  wm-lh-S_orbital_medial-Or_olfactory  0
590   3168  wm-lh-S_paracentral  0
591   3169  wm-lh-S_parieto_occipital  0
592   3170  wm-lh-S_pericallosal  0
593   3171  wm-lh-S_postcentral  0
594   3172  wm-lh-S_precentral-Inferior-part  0
595   3173  wm-lh-S_precentral-Superior-part  0
596   3174  wm-lh-S_subcentral_ant  0
597   3175  wm-lh-S_subcentral_post  0
598   3176  wm-lh-S_suborbital  0
599   3177  wm-lh-S_subparietal  0
600   3178  wm-lh-S_supracingulate  0
601   3179  wm-lh-S_temporal_inferior  0
602   3180  wm-lh-S_temporal_superior  0
603   3181  wm-lh-S_temporal_transverse  0
604   4100  wm-rh-Unknown  0
605   4101  wm-rh-Corpus_callosum  0
606   4102  wm-rh-G_and_S_Insula_ONLY_AVERAGE  0
607   4103  wm-rh-G_cingulate-Isthmus  0
608   4104  wm-rh-G_cingulate-Main_part  0
609   4105  wm-rh-G_cuneus  0
610   4106  wm-rh-G_frontal_inf-Opercular_part  0
611   4107  wm-rh-G_frontal_inf-Orbital_part  0
612   4108  wm-rh-G_frontal_inf-Triangular_part  0
613   4109  wm-rh-G_frontal_middle  0
614   4110  wm-rh-G_frontal_superior  0
615   4111  wm-rh-G_frontomarginal  0
616   4112  wm-rh-G_insular_long  0
617   4113  wm-rh-G_insular_short  0
618   4114  wm-rh-G_and_S_occipital_inferior  0
619   4115  wm-rh-G_occipital_middle  0
620   4116  wm-rh-G_occipital_superior  0
621   4117  wm-rh-G_occipit-temp_lat-Or_fusiform  0
622   4118  wm-rh-G_occipit-temp_med-Lingual_part  0
623   4119  wm-rh-G_occipit-temp_med-Parahippocampal_part  0
624   4120  wm-rh-G_orbital  0
625   4121  wm-rh-G_paracentral  0
626   4122  wm-rh-G_parietal_inferior-Angular_part  0
627   4123  wm-rh-G_parietal_inferior-Supramarginal_part  0
628   4124  wm-rh-G_parietal_superior  0
629   4125  wm-rh-G_postcentral  0
630   4126  wm-rh-G_precentral  0
631   4127  wm-rh-G_precuneus  0
632   4128  wm-rh-G_rectus  0
633   4129  wm-rh-G_subcallosal  0
634   4130  wm-rh-G_subcentral  0
635   4131  wm-rh-G_temporal_inferior  0
636   4132  wm-rh-G_temporal_middle  0
637   4133  wm-rh-G_temp_sup-G_temp_transv_and_interm_S  0
638   4134  wm-rh-G_temp_sup-Lateral_aspect  0
639   4135  wm-rh-G_temp_sup-Planum_polare  0
640   4136  wm-rh-G_temp_sup-Planum_tempolare  0
641   4137  wm-rh-G_and_S_transverse_frontopolar  0
642   4138  wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal  0
643   4139  wm-rh-Lat_Fissure-ant_sgt-ramus_vertical  0
644   4140  wm-rh-Lat_Fissure-post_sgt  0
645   4141  wm-rh-Medial_wall  0
646   4142  wm-rh-Pole_occipital  0
647   4143  wm-rh-Pole_temporal  0
648   4144  wm-rh-S_calcarine  0
649   4145  wm-rh-S_central  0
650   4146  wm-rh-S_central_insula  0
651   4147  wm-rh-S_cingulate-Main_part_and_Intracingulate  0
652   4148  wm-rh-S_cingulate-Marginalis_part  0
653   4149  wm-rh-S_circular_insula_anterior  0
654   4150  wm-rh-S_circular_insula_inferior  0
655   4151  wm-rh-S_circular_insula_superior  0
656   4152  wm-rh-S_collateral_transverse_ant  0
657   4153  wm-rh-S_collateral_transverse_post  0
658   4154  wm-rh-S_frontal_inferior  0
659   4155  wm-rh-S_frontal_middle  0
660   4156  wm-rh-S_frontal_superior  0
661   4157  wm-rh-S_frontomarginal  0
662   4158  wm-rh-S_intermedius_primus-Jensen  0
663   4159  wm-rh-S_intraparietal-and_Parietal_transverse  0
664   4160  wm-rh-S_occipital_anterior  0
665   4161  wm-rh-S_occipital_middle_and_Lunatus  0
666   4162  wm-rh-S_occipital_superior_and_transversalis  0
667   4163  wm-rh-S_occipito-temporal_lateral  0
668   4164  wm-rh-S_occipito-temporal_medial_and_S_Lingual  0
669   4165  wm-rh-S_orbital-H_shapped  0
670   4166  wm-rh-S_orbital_lateral  0
671   4167  wm-rh-S_orbital_medial-Or_olfactory  0
672   4168  wm-rh-S_paracentral  0
673   4169  wm-rh-S_parieto_occipital  0
674   4170  wm-rh-S_pericallosal  0
675   4171  wm-rh-S_postcentral  0
676   4172  wm-rh-S_precentral-Inferior-part  0
677   4173  wm-rh-S_precentral-Superior-part  0
678   4174  wm-rh-S_subcentral_ant  0
679   4175  wm-rh-S_subcentral_post  0
680   4176  wm-rh-S_suborbital  0
681   4177  wm-rh-S_subparietal  0
682   4178  wm-rh-S_supracingulate  0
683   4179  wm-rh-S_temporal_inferior  0
684   4180  wm-rh-S_temporal_superior  0
685   4181  wm-rh-S_temporal_transverse  0

Reporting on 685 segmentations
#--------------------------------------------
#@# Intensity Normalization2 Tue Apr 10 09:25:26 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_normalize -f /home/xonobo/FSRFsubjects/bert/tmp/control.dat -mask brainmask.mgz -aseg aseg.mgz norm.mgz brain.mgz 

using control points from file /home/xonobo/FSRFsubjects/bert/tmp/control.dat...
using segmentation for initial intensity normalization
reading from norm.mgz...
normalizing image...
Reading 0 control points...
only using 0 control points from file...
building Voronoi diagram...
performing soap bubble smoothing...
removing outliers in the aseg WM...
41354 control points removed
building Voronoi diagram...
performing soap bubble smoothing...
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 1 of 2
building Voronoi diagram...
performing soap bubble smoothing...
3d normalization pass 2 of 2
building Voronoi diagram...
performing soap bubble smoothing...
writing output to brain.mgz
3D bias adjustment took 5 minutes and 12 seconds.
using MR volume brainmask.mgz to mask input volume...
using wm threshold 103.0 for removing exterior voxels
white matter peak found at 110
gm peak at 87 (87), valley at 25 (25)
csf peak at 44, setting threshold to 72
white matter peak found at 110
gm peak at 87 (87), valley at 25 (25)
csf peak at 44, setting threshold to 72
#--------------------------------------------
#@# Mask BFS Tue Apr 10 09:30:45 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
writing masked volume to brain.finalsurfs.mgz...
#--------------------------------------------
#@# WM Segmentation Tue Apr 10 09:30:51 CEST 2007

 cp wm.mgz wm.seg.mgz 


 mri_segment -keep brain.mgz wm.seg.mgz 

preserving editing changes in output volume...
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM: 104.3 +- 5.3 [80.0 --> 125.0]
GM: 80.6 +- 11.8 [30.0 --> 96.0]
setting bottom of white matter range to 92.4
setting top of gray matter range to 104.2
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...
4169 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4310 filled
2678 bright non-wm voxels segmented.
2587 diagonally connected voxels added...
white matter segmentation took 4.4 minutes
writing output to wm.seg.mgz...
  Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm

 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz 

preserving editing changes in input volume...
auto filling took 0.72 minutes
reading wm segmentation from wm.seg.mgz...
163 voxels added to wm to prevent paths from MTL structures to cortex
3306 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 51145 voxels turned on, 50100 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 108   new 108
115,126,128 old 108   new 108
writing edited volume to wm.asegedit.mgz....

 mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  26 found -  26 modified     |    TOTAL:  26
pass   2 (xy+):   0 found -  26 modified     |    TOTAL:  26
pass   1 (xy-):  32 found -  32 modified     |    TOTAL:  58
pass   2 (xy-):   0 found -  32 modified     |    TOTAL:  58
pass   1 (yz+):  30 found -  30 modified     |    TOTAL:  88
pass   2 (yz+):   0 found -  30 modified     |    TOTAL:  88
pass   1 (yz-):  46 found -  46 modified     |    TOTAL: 134
pass   2 (yz-):   0 found -  46 modified     |    TOTAL: 134
pass   1 (xz+):  20 found -  20 modified     |    TOTAL: 154
pass   2 (xz+):   0 found -  20 modified     |    TOTAL: 154
pass   1 (xz-):  25 found -  25 modified     |    TOTAL: 179
pass   2 (xz-):   0 found -  25 modified     |    TOTAL: 179
Iteration Number : 1
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  16
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  16
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  26
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  26
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  36
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  36
pass   1 (+++):  17 found -  17 modified     |    TOTAL:  53
pass   2 (+++):   0 found -  17 modified     |    TOTAL:  53
Iteration Number : 1
pass   1 (++):  53 found -  53 modified     |    TOTAL:  53
pass   2 (++):   0 found -  53 modified     |    TOTAL:  53
pass   1 (+-):  66 found -  66 modified     |    TOTAL: 119
pass   2 (+-):   0 found -  66 modified     |    TOTAL: 119
pass   1 (--):  63 found -  63 modified     |    TOTAL: 182
pass   2 (--):   0 found -  63 modified     |    TOTAL: 182
pass   1 (-+):  53 found -  53 modified     |    TOTAL: 235
pass   2 (-+):   0 found -  53 modified     |    TOTAL: 235
Iteration Number : 2
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   6
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   8
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  16
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  16
pass   1 (xz+):   5 found -   5 modified     |    TOTAL:  21
pass   2 (xz+):   0 found -   5 modified     |    TOTAL:  21
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  22
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  22
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 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (--):   3 found -   3 modified     |    TOTAL:   8
pass   2 (--):   0 found -   3 modified     |    TOTAL:   8
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   8
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+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   2
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 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 500 (out of 581140: 0.086038)
keeping edits
binarizing input wm segmentation...
Ambiguous edge configurations... 

Searching for edits to keep ...
  Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /home/xonobo/FSRFsubjects/bert/mri/transforms/talairach.xfm
  kept 0 WM ON voxels
  kept 0 WM OFF voxels

mri_pretess done

#--------------------------------------------
#@# Fill Tue Apr 10 09:36:15 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.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.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.123   0.004   0.001  -17.751;
 0.003   1.117   0.128  -26.437;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.123   0.004   0.001  -17.751;
 0.003   1.117   0.128  -26.437;
 0.010  -0.154   0.929   22.203;
 0.000   0.000   0.000   1.000;
Looking for area (min, max) = (350, 1400)
area[0] = 2772 (min = 350, max = 1400), aspect = 1.17 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 121, 153), TAL = (1.0, 25.0, 7.0)
talairach voxel to voxel transform
 0.890  -0.003  -0.001   15.743;
-0.001   0.878  -0.121   25.885;
-0.010   0.146   1.057  -19.785;
 0.000   0.000   0.000   1.000;
done.
writing output to filled.mgz...
filling took 1.5 minutes
INFO: Modifying dst c_(r,a,s), using the transform dst
INFO: Modifying dst c_(r,a,s), using the transform dst
reading segmented volume aseg.mgz...
INFO: Modifying dst c_(r,a,s), using the transform dst
segmentation indicates cc at (127,  121,  153) --> (1.0, 25.0, 7.0)
INFO: Modifying dst c_(r,a,s), using the transform dst
talairach cc position changed to (1.00, 25.00, 7.00)
ERASING BRAINSTEMseed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, 25.00, 7.00) SRC: (112.26, 113.52, 158.49)
search lh wm seed point around talairach space (-17.00, 25.00, 7.00), SRC: (144.30, 113.48, 158.14)
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 Apr 10 09:37:47 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mri_tessellate ../mri/filled.mgz 255 ../surf/lh.orig.nofix 

$Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
slice 30: 483 vertices, 541 faces
slice 40: 4505 vertices, 4705 faces
slice 50: 11182 vertices, 11426 faces
slice 60: 19300 vertices, 19618 faces
slice 70: 28868 vertices, 29194 faces
slice 80: 38640 vertices, 38944 faces
slice 90: 48196 vertices, 48544 faces
slice 100: 59192 vertices, 59565 faces
slice 110: 69692 vertices, 70100 faces
slice 120: 80198 vertices, 80597 faces
slice 130: 90183 vertices, 90566 faces
slice 140: 99828 vertices, 100174 faces
slice 150: 107541 vertices, 107829 faces
slice 160: 113831 vertices, 114128 faces
slice 170: 120456 vertices, 120733 faces
slice 180: 126406 vertices, 126642 faces
slice 190: 131315 vertices, 131502 faces
slice 200: 134564 vertices, 134667 faces
slice 210: 134828 vertices, 134880 faces
slice 220: 134828 vertices, 134880 faces
slice 230: 134828 vertices, 134880 faces
slice 240: 134828 vertices, 134880 faces
slice 250: 134828 vertices, 134880 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using ras2vox 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;
#--------------------------------------------
#@# Smooth1 lh Tue Apr 10 09:37:55 CEST 2007

 mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

/home/xonobo/FSRFsubjects/bert/scripts
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Tue Apr 10 09:38:01 CEST 2007

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

/home/xonobo/FSRFsubjects/bert/scripts
avg radius = 48.8 mm, total surface area = 75157 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.2 minutes
Not saving sulc

step 000: RMS=0.166 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.092 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.059 (target=0.015)   
step 030: RMS=0.052 (target=0.015)   
step 035: RMS=0.046 (target=0.015)   
step 040: RMS=0.045 (target=0.015)   
step 045: RMS=0.043 (target=0.015)   
step 050: RMS=0.041 (target=0.015)   
step 055: RMS=0.040 (target=0.015)   
step 060: RMS=0.040 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Tue Apr 10 09:39:15 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
$Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
tol=1.0e+00, host=telen, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000
mom=0.90, dt=0.90

scaling brain by 0.573...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=155.893, avgs=0
005: dt: 0.9000, rms radial error=155.667, avgs=0
010: dt: 0.9000, rms radial error=155.184, avgs=0
015: dt: 0.9000, rms radial error=154.547, avgs=0
020: dt: 0.9000, rms radial error=153.821, avgs=0
025: dt: 0.9000, rms radial error=153.043, avgs=0
030: dt: 0.9000, rms radial error=152.237, avgs=0
035: dt: 0.9000, rms radial error=151.416, avgs=0
040: dt: 0.9000, rms radial error=150.589, avgs=0
045: dt: 0.9000, rms radial error=149.759, avgs=0
050: dt: 0.9000, rms radial error=148.930, avgs=0
055: dt: 0.9000, rms radial error=148.103, avgs=0
060: dt: 0.9000, rms radial error=147.279, avgs=0
065: dt: 0.9000, rms radial error=146.459, avgs=0
070: dt: 0.9000, rms radial error=145.644, avgs=0
075: dt: 0.9000, rms radial error=144.832, avgs=0
080: dt: 0.9000, rms radial error=144.025, avgs=0
085: dt: 0.9000, rms radial error=143.223, avgs=0
090: dt: 0.9000, rms radial error=142.424, avgs=0
095: dt: 0.9000, rms radial error=141.630, avgs=0
100: dt: 0.9000, rms radial error=140.841, avgs=0
105: dt: 0.9000, rms radial error=140.056, avgs=0
110: dt: 0.9000, rms radial error=139.275, avgs=0
115: dt: 0.9000, rms radial error=138.498, avgs=0
120: dt: 0.9000, rms radial error=137.727, avgs=0
125: dt: 0.9000, rms radial error=136.959, avgs=0
130: dt: 0.9000, rms radial error=136.196, avgs=0
135: dt: 0.9000, rms radial error=135.437, avgs=0
140: dt: 0.9000, rms radial error=134.683, avgs=0
145: dt: 0.9000, rms radial error=133.932, avgs=0
150: dt: 0.9000, rms radial error=133.186, avgs=0
155: dt: 0.9000, rms radial error=132.443, avgs=0
160: dt: 0.9000, rms radial error=131.705, avgs=0
165: dt: 0.9000, rms radial error=130.971, avgs=0
170: dt: 0.9000, rms radial error=130.240, avgs=0
175: dt: 0.9000, rms radial error=129.514, avgs=0
180: dt: 0.9000, rms radial error=128.792, avgs=0
185: dt: 0.9000, rms radial error=128.074, avgs=0
190: dt: 0.9000, rms radial error=127.360, avgs=0
195: dt: 0.9000, rms radial error=126.651, avgs=0
200: dt: 0.9000, rms radial error=125.945, avgs=0
205: dt: 0.9000, rms radial error=125.247, avgs=0
210: dt: 0.9000, rms radial error=124.553, avgs=0
215: dt: 0.9000, rms radial error=123.862, avgs=0
220: dt: 0.9000, rms radial error=123.175, avgs=0
225: dt: 0.9000, rms radial error=122.492, avgs=0
230: dt: 0.9000, rms radial error=121.812, avgs=0
235: dt: 0.9000, rms radial error=121.136, avgs=0
240: dt: 0.9000, rms radial error=120.463, avgs=0
245: dt: 0.9000, rms radial error=119.794, avgs=0
250: dt: 0.9000, rms radial error=119.129, avgs=0
255: dt: 0.9000, rms radial error=118.467, avgs=0
260: dt: 0.9000, rms radial error=117.809, avgs=0
265: dt: 0.9000, rms radial error=117.154, avgs=0
270: dt: 0.9000, rms radial error=116.503, avgs=0
275: dt: 0.9000, rms radial error=115.856, avgs=0
280: dt: 0.9000, rms radial error=115.212, avgs=0
285: dt: 0.9000, rms radial error=114.571, avgs=0
290: dt: 0.9000, rms radial error=113.934, avgs=0
295: dt: 0.9000, rms radial error=113.301, avgs=0
300: dtsurface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.53 (0.00-->6.21) (max @ vno 55639 --> 56786)
face area 0.09 +- 0.11 (-1.07-->2.32)
tol=1.0e-01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

301: dt: 42.15, sse: 3943.8 (0.084, 16.8, 0.419), neg: 1536 (%0.068:%0.08), avgs: 32
302: dt: 0.29, sse: 3943.5 (0.084, 16.8, 0.419), neg: 1532 (%0.067:%0.08), avgs: 32
303: dt: 0.29, sse: 3943.2 (0.084, 16.8, 0.419), neg: 1530 (%0.067:%0.08), avgs: 32
304: dt: 0.29, sse: 3942.9 (0.084, 16.8, 0.419), neg: 1533 (%0.067:%0.08), avgs: 32
305: dt: 0.29, sse: 3942.6 (0.084, 16.8, 0.419), neg: 1539 (%0.067:%0.08), avgs: 32
306: dt: 0.29, sse: 3942.4 (0.084, 16.8, 0.419), neg: 1540 (%0.067:%0.08), avgs: 32
307: dt: 0.29, sse: 3942.2 (0.084, 16.8, 0.419), neg: 1546 (%0.066:%0.08), avgs: 32
308: dt: 0.29, sse: 3941.9 (0.084, 16.8, 0.419), neg: 1546 (%0.066:%0.08), avgs: 32
309: dt: 0.29, sse: 3941.7 (0.084, 16.8, 0.419), neg: 1544 (%0.065:%0.08), avgs: 32
310: dt: 0.29, sse: 3941.5 (0.084, 16.7, 0.419), neg: 1545 (%0.065:%0.08), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.38) (max @ vno 56797 --> 56786)
face area 0.09 +- 0.11 (-0.45-->2.33)
311: dt: 0.29, sse: 3941.3 (0.084, 16.7, 0.419), neg: 1546 (%0.065:%0.08), avgs: 32
312: dt: 58.84, sse: 3939.6 (0.084, 16.8, 0.419), neg: 1604 (%0.055:%0.07), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.37) (max @ vno 51001 --> 52133)
face area 0.09 +- 0.11 (-0.29-->2.33)
313: dt: 8.63, sse: 3939.1 (0.084, 16.8, 0.419), neg: 1594 (%0.046:%0.07), avgs: 8
314: dt: 0.15, sse: 3939.0 (0.084, 16.8, 0.419), neg: 1595 (%0.045:%0.07), avgs: 8
315: dt: 0.15, sse: 3938.9 (0.084, 16.8, 0.419), neg: 1596 (%0.045:%0.07), avgs: 8
316: dt: 0.15, sse: 3938.8 (0.084, 16.8, 0.419), neg: 1594 (%0.045:%0.07), avgs: 8
317: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1592 (%0.044:%0.07), avgs: 8
318: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1592 (%0.044:%0.07), avgs: 8
319: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1591 (%0.043:%0.07), avgs: 8
320: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1596 (%0.043:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.46) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.19-->2.33)
321: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1595 (%0.043:%0.07), avgs: 8
322: dt: 0.15, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1596 (%0.042:%0.07), avgs: 8
323: dt: 0.15, sse: 3938.6 (0.084, 16.8, 0.419), neg: 1594 (%0.041:%0.07), avgs: 8
324: dt: 0.00, sse: 3938.6 (0.084, 16.8, 0.419), neg: 1594 (%0.041:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.48) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.18-->2.34)
325: dt: 0.11, sse: 3938.6 (0.084, 16.8, 0.419), neg: 1596 (%0.041:%0.07), avgs: 2
326: dt: 0.09, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1599 (%0.040:%0.07), avgs: 2
327: dt: 0.09, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1602 (%0.039:%0.07), avgs: 2
328: dt: 0.09, sse: 3938.7 (0.084, 16.8, 0.419), neg: 1609 (%0.038:%0.07), avgs: 2
329: dt: 0.09, sse: 3938.8 (0.084, 16.9, 0.419), neg: 1608 (%0.037:%0.07), avgs: 2
330: dt: 0.09, sse: 3938.9 (0.084, 16.9, 0.419), neg: 1610 (%0.036:%0.07), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.52) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.14-->2.34)
331: dt: 0.09, sse: 3939.1 (0.084, 16.9, 0.419), neg: 1616 (%0.035:%0.07), avgs: 2
332: dt: 0.09, sse: 3939.2 (0.084, 16.9, 0.419), neg: 1623 (%0.034:%0.07), avgs: 2
333: dt: 0.09, sse: 3939.5 (0.084, 16.9, 0.419), neg: 1638 (%0.033:%0.07), avgs: 2
334: dt: 0.09, sse: 3939.7 (0.084, 16.9, 0.419), neg: 1643 (%0.032:%0.07), avgs: 2
335: dt: 0.09, sse: 3939.9 (0.084, 16.9, 0.419), neg: 1642 (%0.031:%0.07), avgs: 2
336: dt: 0.00, sse: 3939.9 (0.084, 16.9, 0.419), neg: 1642 (%0.031:%0.07), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.58) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.10-->2.34)
337: dt: 0.00, sse: 3939.9 (0.084, 16.9, 0.419), neg: 1642 (%0.031:%0.07), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->5.58) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.10-->2.34)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

338: dt: 387.05, sse: 298.6 (0.084, 16.7, 0.419), neg: 1683 (%0.035:%0.08), avgs: 32
339: dt: 0.29, sse: 298.9 (0.084, 16.7, 0.419), neg: 1700 (%0.034:%0.08), avgs: 32
340: dt: 0.29, sse: 299.1 (0.084, 16.7, 0.419), neg: 1719 (%0.034:%0.08), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.65) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.32-->2.34)
341: dt: 0.29, sse: 299.3 (0.084, 16.7, 0.419), neg: 1729 (%0.034:%0.08), avgs: 32
342: dt: 0.29, sse: 299.5 (0.084, 16.8, 0.419), neg: 1732 (%0.034:%0.08), avgs: 32
343: dt: 0.29, sse: 299.6 (0.084, 16.8, 0.419), neg: 1740 (%0.033:%0.08), avgs: 32
344: dt: 0.29, sse: 299.7 (0.084, 16.8, 0.419), neg: 1749 (%0.033:%0.08), avgs: 32
345: dt: 0.29, sse: 299.8 (0.084, 16.8, 0.419), neg: 1747 (%0.033:%0.08), avgs: 32
346: dt: 0.29, sse: 299.8 (0.084, 16.8, 0.419), neg: 1754 (%0.032:%0.08), avgs: 32
347: dt: 0.29, sse: 299.9 (0.084, 16.8, 0.419), neg: 1758 (%0.032:%0.08), avgs: 32
348: dt: 0.29, sse: 299.8 (0.084, 16.8, 0.419), neg: 1761 (%0.031:%0.08), avgs: 32
349: dt: 107.12, sse: 296.2 (0.084, 16.7, 0.419), neg: 1683 (%0.023:%0.06), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.61) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.23-->2.34)
350: dt: 13.07, sse: 294.8 (0.084, 16.7, 0.419), neg: 1704 (%0.020:%0.06), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.64) (max @ vno 51001 --> 52133)
face area 0.09 +- 0.11 (-0.07-->2.34)
351: dt: 0.15, sse: 294.9 (0.084, 16.7, 0.419), neg: 1709 (%0.020:%0.06), avgs: 8
352: dt: 0.15, sse: 295.0 (0.084, 16.7, 0.419), neg: 1714 (%0.020:%0.06), avgs: 8
353: dt: 0.15, sse: 295.0 (0.084, 16.7, 0.419), neg: 1720 (%0.020:%0.06), avgs: 8
354: dt: 0.15, sse: 295.1 (0.084, 16.7, 0.419), neg: 1724 (%0.020:%0.06), avgs: 8
355: dt: 0.15, sse: 295.1 (0.084, 16.7, 0.419), neg: 1730 (%0.020:%0.06), avgs: 8
356: dt: 0.15, sse: 295.1 (0.084, 16.7, 0.419), neg: 1728 (%0.020:%0.06), avgs: 8
357: dt: 0.15, sse: 295.1 (0.084, 16.7, 0.419), neg: 1727 (%0.020:%0.06), avgs: 8
358: dt: 0.15, sse: 295.1 (0.084, 16.8, 0.419), neg: 1730 (%0.020:%0.06), avgs: 8
359: dt: 0.15, sse: 295.1 (0.084, 16.8, 0.419), neg: 1735 (%0.020:%0.06), avgs: 8
360: dt: 0.15, sse: 295.0 (0.084, 16.8, 0.419), neg: 1733 (%0.020:%0.06), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.66) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.07-->2.34)
: 0.9000, rms radial error=112.670, avgs=0

spherical inflation complete.
epoch 1 (K=20.0), pass 1, starting sse = 3948.74
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.00/37 = 0.00006
epoch 2 (K=80.0), pass 1, starting sse = 306.76
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 361: dt: 68.63, sse: 292.7 (0.084, 16.8, 0.419), neg: 1811 (%0.024:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.73) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.41-->2.34)
362: dt: 0.60, sse: 291.5 (0.084, 16.8, 0.419), neg: 1817 (%0.020:%0.06), avgs: 2
363: dt: 0.09, sse: 291.5 (0.084, 16.8, 0.419), neg: 1813 (%0.020:%0.06), avgs: 2
364: dt: 0.09, sse: 291.4 (0.084, 16.8, 0.419), neg: 1816 (%0.020:%0.06), avgs: 2
365: dt: 0.09, sse: 291.3 (0.084, 16.8, 0.419), neg: 1817 (%0.019:%0.06), avgs: 2
366: dt: 0.09, sse: 291.1 (0.084, 16.8, 0.419), neg: 1808 (%0.018:%0.06), avgs: 2
367: dt: 0.09, sse: 290.9 (0.084, 16.8, 0.419), neg: 1814 (%0.018:%0.06), avgs: 2
368: dt: 0.09, sse: 290.7 (0.084, 16.8, 0.419), neg: 1821 (%0.017:%0.06), avgs: 2
369: dt: 0.09, sse: 290.5 (0.084, 16.8, 0.419), neg: 1824 (%0.017:%0.06), avgs: 2
370: dt: 0.09, sse: 290.4 (0.084, 16.8, 0.419), neg: 1827 (%0.016:%0.06), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.08-->2.34)
371: dt: 0.09, sse: 290.3 (0.084, 16.8, 0.419), neg: 1825 (%0.016:%0.06), avgs: 2
372: dt: 0.09, sse: 290.1 (0.084, 16.8, 0.419), neg: 1832 (%0.016:%0.06), avgs: 2
373: dt: 0.47, sse: 289.9 (0.084, 16.8, 0.419), neg: 1839 (%0.016:%0.06), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 51001 --> 52133)
face area 0.09 +- 0.11 (-0.05-->2.34)
374: dt: 0.11, sse: 289.8 (0.084, 16.8, 0.419), neg: 1841 (%0.015:%0.06), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 51001 --> 52133)
face area 0.09 +- 0.11 (-0.05-->2.34)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

375: dt: 78.58, sse: 18.4 (0.084, 16.8, 0.419), neg: 1827 (%0.015:%0.05), avgs: 32
376: dt: 0.29, sse: 18.4 (0.084, 16.8, 0.419), neg: 1834 (%0.015:%0.05), avgs: 32
377: dt: 0.29, sse: 18.4 (0.084, 16.8, 0.419), neg: 1835 (%0.015:%0.05), avgs: 32
378: dt: 0.29, sse: 18.4 (0.084, 16.8, 0.419), neg: 1840 (%0.015:%0.06), avgs: 32
379: dt: 0.29, sse: 18.5 (0.084, 16.8, 0.419), neg: 1850 (%0.015:%0.06), avgs: 32
380: dt: 0.29, sse: 18.5 (0.084, 16.8, 0.419), neg: 1849 (%0.015:%0.06), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.75) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.09-->2.34)
381: dt: 0.29, sse: 18.5 (0.084, 16.8, 0.419), neg: 1850 (%0.015:%0.06), avgs: 32
382: dt: 0.29, sse: 18.5 (0.084, 16.8, 0.419), neg: 1855 (%0.015:%0.06), avgs: 32
383: dt: 0.29, sse: 18.5 (0.084, 16.8, 0.419), neg: 1857 (%0.015:%0.06), avgs: 32
384: dt: 0.29, sse: 18.6 (0.084, 16.8, 0.419), neg: 1861 (%0.015:%0.06), avgs: 32
385: dt: 0.29, sse: 18.6 (0.084, 16.8, 0.419), neg: 1863 (%0.016:%0.06), avgs: 32
386: dt: 51.40, sse: 18.5 (0.084, 16.8, 0.419), neg: 1870 (%0.015:%0.06), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.74) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.12-->2.34)
387: dt: 12.94, sse: 18.2 (0.084, 16.8, 0.419), neg: 1861 (%0.014:%0.06), avgs: 8
388: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1859 (%0.014:%0.06), avgs: 8
389: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1861 (%0.014:%0.06), avgs: 8
390: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1863 (%0.014:%0.06), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.74) (max @ vno 52133 --> 51001)
face area 0.09 +- 0.11 (-0.09-->2.34)
391: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1865 (%0.014:%0.06), avgs: 8
392: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1865 (%0.014:%0.06), avgs: 8
393: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1866 (%0.014:%0.06), avgs: 8
394: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1866 (%0.014:%0.06), avgs: 8
395: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1867 (%0.014:%0.06), avgs: 8
396: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1874 (%0.014:%0.06), avgs: 8
397: dt: 0.15, sse: 18.2 (0.084, 16.8, 0.419), neg: 1874 (%0.014:%0.06), avgs: 8
398: dt: 10.61, sse: 18.1 (0.084, 16.8, 0.419), neg: 1880 (%0.014:%0.06), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.74) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.08-->2.34)
399: dt: 0.46, sse: 18.0 (0.084, 16.8, 0.419), neg: 1884 (%0.014:%0.06), avgs: 2
400: dt: 0.09, sse: 18.0 (0.084, 16.8, 0.419), neg: 1882 (%0.014:%0.06), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.75) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.07-->2.34)
401: dt: 0.09, sse: 17.9 (0.084, 16.8, 0.419), neg: 1884 (%0.013:%0.06), avgs: 2
402: dt: 0.09, sse: 17.9 (0.084, 16.8, 0.419), neg: 1888 (%0.013:%0.06), avgs: 2
403: dt: 0.09, sse: 17.8 (0.084, 16.8, 0.419), neg: 1890 (%0.013:%0.05), avgs: 2
404: dt: 0.09, sse: 17.8 (0.084, 16.8, 0.419), neg: 1889 (%0.013:%0.05), avgs: 2
405: dt: 0.09, sse: 17.8 (0.084, 16.8, 0.419), neg: 1891 (%0.013:%0.06), avgs: 2
406: dt: 0.09, sse: 17.7 (0.084, 16.8, 0.419), neg: 1889 (%0.013:%0.06), avgs: 2
407: dt: 0.09, sse: 17.7 (0.084, 16.8, 0.419), neg: 1886 (%0.012:%0.06), avgs: 2
408: dt: 0.09, sse: 17.6 (0.084, 16.8, 0.419), neg: 1883 (%0.012:%0.05), avgs: 2
409: dt: 0.09, sse: 17.6 (0.084, 16.8, 0.419), neg: 1890 (%0.012:%0.05), avgs: 2
410: dt: 1.32, sse: 17.5 (0.084, 16.8, 0.419), neg: 1891 (%0.012:%0.06), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 54565 --> 53422)
face area 0.09 +- 0.12 (-0.06-->2.34)
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 54565 --> 53422)
face area 0.09 +- 0.12 (-0.06-->2.34)
411: dt: 0.00, sse: 17.5 (0.084, 16.8, 0.419), neg: 1891 (%0.012:%0.06), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->5.76) (max @ vno 54565 --> 53422)
face area 0.09 +- 0.12 (-0.06-->2.34)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

412: dt: 22.16, sse: 4.4 (0.084, 16.8, 0.419), neg: 1891 (%0.011:%0.05), avgs: 32
and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.06/37 = 0.00149
epoch 3 (K=320.0), pass 1, starting sse = 18.62
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.06/37 = 0.00156
epoch 4 (K=1280.0), pass 1, starting sse = 4.44
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and to413: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1894 (%0.011:%0.05), avgs: 32
414: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1900 (%0.011:%0.05), avgs: 32
415: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1897 (%0.011:%0.06), avgs: 32
416: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1894 (%0.011:%0.06), avgs: 32
417: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1892 (%0.011:%0.06), avgs: 32
418: dt: 0.29, sse: 4.3 (0.084, 16.8, 0.419), neg: 1894 (%0.011:%0.06), avgs: 32
419: dt: 0.29, sse: 4.2 (0.084, 16.8, 0.419), neg: 1890 (%0.011:%0.06), avgs: 32
420: dt: 0.29, sse: 4.2 (0.084, 16.8, 0.419), neg: 1887 (%0.011:%0.06), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.78) (max @ vno 54565 --> 53422)
face area 0.09 +- 0.12 (-0.05-->2.34)
421: dt: 0.29, sse: 4.2 (0.084, 16.8, 0.419), neg: 1884 (%0.011:%0.06), avgs: 32
422: dt: 0.29, sse: 4.2 (0.084, 16.8, 0.419), neg: 1884 (%0.011:%0.06), avgs: 32
423: dt: 38.05, sse: 4.2 (0.084, 16.8, 0.419), neg: 1891 (%0.011:%0.05), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->5.79) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.05-->2.34)
424: dt: 4.59, sse: 4.1 (0.084, 16.8, 0.419), neg: 1884 (%0.010:%0.05), avgs: 8
425: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1886 (%0.010:%0.05), avgs: 8
426: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1889 (%0.010:%0.05), avgs: 8
427: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1888 (%0.010:%0.05), avgs: 8
428: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1889 (%0.010:%0.05), avgs: 8
429: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1892 (%0.010:%0.06), avgs: 8
430: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1893 (%0.010:%0.06), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.80) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.06-->2.34)
431: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1893 (%0.010:%0.06), avgs: 8
432: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1893 (%0.010:%0.06), avgs: 8
433: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1894 (%0.010:%0.06), avgs: 8
434: dt: 0.15, sse: 4.1 (0.084, 16.8, 0.419), neg: 1894 (%0.010:%0.06), avgs: 8
435: dt: 4.75, sse: 4.0 (0.084, 16.8, 0.419), neg: 1895 (%0.010:%0.05), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->5.80) (max @ vno 54565 --> 53422)
face area 0.09 +- 0.12 (-0.07-->2.34)
436: dt: 1.63, sse: 4.0 (0.084, 16.8, 0.419), neg: 1876 (%0.010:%0.05), avgs: 2
437: dt: 0.00, sse: 4.0 (0.084, 16.8, 0.419), neg: 1876 (%0.010:%0.05), avgs: 2
438: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1882 (%0.010:%0.05), avgs: 2
439: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1878 (%0.010:%0.05), avgs: 2
440: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1882 (%0.009:%0.05), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.80) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.04-->2.34)
441: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1879 (%0.009:%0.05), avgs: 2
442: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1889 (%0.009:%0.05), avgs: 2
443: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1892 (%0.009:%0.05), avgs: 2
444: dt: 0.09, sse: 3.9 (0.084, 16.8, 0.419), neg: 1893 (%0.009:%0.05), avgs: 2
445: dt: 0.09, sse: 3.8 (0.084, 16.8, 0.419), neg: 1900 (%0.009:%0.06), avgs: 2
446: dt: 0.09, sse: 3.8 (0.084, 16.8, 0.419), neg: 1897 (%0.009:%0.05), avgs: 2
447: dt: 0.09, sse: 3.8 (0.084, 16.8, 0.419), neg: 1891 (%0.009:%0.05), avgs: 2
448: dt: 0.00, sse: 3.8 (0.084, 16.8, 0.419), neg: 1891 (%0.009:%0.05), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->5.80) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.03-->2.34)
449: dt: 0.00, sse: 3.8 (0.084, 16.8, 0.419), neg: 1891 (%0.009:%0.05), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->5.80) (max @ vno 53422 --> 54565)
face area 0.09 +- 0.12 (-0.03-->2.34)
449: dt: 0.00, sse: 3924.1 (0.084, 16.8, 0.419), neg: 1891 (%0.009:%0.05), avgs: 32
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.18 hours
l=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.15/38 = 0.00382
final distance error %100000.00
optimization complete.
unfolding took 0.13 hours
#--------------------------------------------
#@# Fix Topology lh Tue Apr 10 09:50:15 CEST 2007

 cp ../surf/lh.orig.nofix ../surf/lh.orig 


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated 

/home/xonobo/FSRFsubjects/bert/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga bert lh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters

*************************************************************
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 1.41.2.1 2007/01/05 16:58:33 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
before topology correction, eno=-40 (nv=134828, nf=269760, ne=404628, g=21)
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...
4268 ambiguous faces found in tessellation
segmenting defects...
39 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
39 defects to be corrected 
0 vertices coincident
Computing Initial Surface Statistics
      -face       loglikelihood: -8.5261  (-4.2630)
      -vertex     loglikelihood: -5.3846  (-2.6923)
      -normal dot loglikelihood: -3.5890  (-3.5890)
      -quad curv  loglikelihood: -6.1131  (-3.0566)
      Total Loglikelihood : -23.6128

CORRECTING DEFECT 0 (vertices=28, convex hull=53)
l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 
After retessellation of defect 0, euler #=-36 (132252,395784,263496) : difference with theory (-36) = 0 

CORRECTING DEFECT 1 (vertices=38, convex hull=71)
After retessellation of defect 1, euler #=-35 (132276,395883,263572) : difference with theory (-35) = 0 

CORRECTING DEFECT 2 (vertices=45, convex hull=54)
After retessellation of defect 2, euler #=-34 (132285,395931,263612) : difference with theory (-34) = 0 

CORRECTING DEFECT 3 (vertices=8, convex hull=38)
After retessellation of defect 3, euler #=-33 (132288,395951,263630) : difference with theory (-33) = 0 

CORRECTING DEFECT 4 (vertices=47, convex hull=87)
After retessellation of defect 4, euler #=-32 (132317,396076,263727) : difference with theory (-32) = 0 

CORRECTING DEFECT 5 (vertices=156, convex hull=227)
After retessellation of defect 5, euler #=-31 (132342,396256,263883) : difference with theory (-31) = 0 

CORRECTING DEFECT 6 (vertices=15, convex hull=40)
After retessellation of defect 6, euler #=-30 (132348,396286,263908) : difference with theory (-30) = 0 

CORRECTING DEFECT 7 (vertices=10, convex hull=31)
After retessellation of defect 7, euler #=-29 (132352,396306,263925) : difference with theory (-29) = 0 

CORRECTING DEFECT 8 (vertices=187, convex hull=149)
After retessellation of defect 8, euler #=-28 (132417,396571,264126) : difference with theory (-28) = 0 

CORRECTING DEFECT 9 (vertices=62, convex hull=82)
After retessellation of defect 9, euler #=-27 (132442,396682,264213) : difference with theory (-27) = 0 

CORRECTING DEFECT 10 (vertices=52, convex hull=77)
After retessellation of defect 10, euler #=-26 (132478,396822,264318) : difference with theory (-26) = 0 

CORRECTING DEFECT 11 (vertices=236, convex hull=105)
After retessellation of defect 11, euler #=-25 (132493,396916,264398) : difference with theory (-25) = 0 

CORRECTING DEFECT 12 (vertices=20, convex hull=50)
After retessellation of defect 12, euler #=-24 (132506,396975,264445) : difference with theory (-24) = 0 

CORRECTING DEFECT 13 (vertices=46, convex hull=87)
After retessellation of defect 13, euler #=-23 (132525,397065,264517) : difference with theory (-23) = 0 

CORRECTING DEFECT 14 (vertices=10, convex hull=26)
After retessellation of defect 14, euler #=-22 (132527,397078,264529) : difference with theory (-22) = 0 

CORRECTING DEFECT 15 (vertices=9, convex hull=26)
After retessellation of defect 15, euler #=-21 (132528,397088,264539) : difference with theory (-21) = 0 

CORRECTING DEFECT 16 (vertices=233, convex hull=99)
After retessellation of defect 16, euler #=-20 (132582,397293,264691) : difference with theory (-20) = 0 

CORRECTING DEFECT 17 (vertices=9, convex hull=32)
After retessellation of defect 17, euler #=-19 (132587,397318,264712) : difference with theory (-19) = 0 

CORRECTING DEFECT 18 (vertices=40, convex hull=54)
After retessellation of defect 18, euler #=-18 (132606,397394,264770) : difference with theory (-18) = 0 

CORRECTING DEFECT 19 (vertices=82, convex hull=83)
After retessellation of defect 19, euler #=-17 (132624,397484,264843) : difference with theory (-17) = 0 

CORRECTING DEFECT 20 (vertices=13, convex hull=23)
After retessellation of defect 20, euler #=-16 (132627,397497,264854) : difference with theory (-16) = 0 

CORRECTING DEFECT 21 (vertices=43, convex hull=79)
After retessellation of defect 21, euler #=-15 (132657,397619,264947) : difference with theory (-15) = 0 

CORRECTING DEFECT 22 (vertices=8, convex hull=25)
After retessellation of defect 22, euler #=-14 (132658,397631,264959) : difference with theory (-14) = 0 

CORRECTING DEFECT 23 (vertices=10, convex hull=30)
After retessellation of defect 23, euler #=-13 (132664,397659,264982) : difference with theory (-13) = 0 

CORRECTING DEFECT 24 (vertices=223, convex hull=61)
After retessellation of defect 24, euler #=-12 (132673,397717,265032) : difference with theory (-12) = 0 

CORRECTING DEFECT 25 (vertices=9, convex hull=23)
After retessellation of defect 25, euler #=-11 (132676,397735,265048) : difference with theory (-11) = 0 

CORRECTING DEFECT 26 (vertices=12, convex hull=35)
After retessellation of defect 26, euler #=-10 (132682,397765,265073) : difference with theory (-10) = 0 

CORRECTING DEFECT 27 (vertices=77, convex hull=108)
After retessellation of defect 27, euler #=-9 (132711,397898,265178) : difference with theory (-9) = 0 

CORRECTING DEFECT 28 (vertices=12, convex hull=17)
After retessellation of defect 28, euler #=-8 (132714,397912,265190) : difference with theory (-8) = 0 

CORRECTING DEFECT 29 (vertices=36, convex hull=67)
After retessellation of defect 29, euler #=-7 (132733,397998,265258) : difference with theory (-7) = 0 

CORRECTING DEFECT 30 (vertices=10, convex hull=27)
After retessellation of defect 30, euler #=-6 (132734,398007,265267) : difference with theory (-6) = 0 

CORRECTING DEFECT 31 (vertices=45, convex hull=20)
After retessellation of defect 31, euler #=-5 (132735,398014,265274) : difference with theory (-5) = 0 

CORRECTING DEFECT 32 (vertices=69, convex hull=93)
After retessellation of defect 32, euler #=-4 (132750,398104,265350) : difference with theory (-4) = 0 

CORRECTING DEFECT 33 (vertices=12, convex hull=18)
After retessellation of defect 33, euler #=-3 (132753,398118,265362) : difference with theory (-3) = 0 

CORRECTING DEFECT 34 (vertices=350, convex hull=91)
After retessellation of defect 34, euler #=-2 (132779,398236,265455) : difference with theory (-2) = 0 

CORRECTING DEFECT 35 (vertices=62, convex hull=63)
After retessellation of defect 35, euler #=-1 (132795,398310,265514) : difference with theory (-1) = 0 

CORRECTING DEFECT 36 (vertices=47, convex hull=84)
After retessellation of defect 36, euler #=0 (132812,398396,265584) : difference with theory (0) = 0 

CORRECTING DEFECT 37 (vertices=147, convex hull=40)
After retessellation of defect 37, euler #=1 (132821,398438,265618) : difference with theory (1) = 0 

CORRECTING DEFECT 38 (vertices=72, convex hull=48)
After retessellation of defect 38, euler #=2 (132825,398469,265646) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.06-->4.33) (max @ vno 132594 --> 53021)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.06-->4.33) (max @ vno 132594 --> 53021)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
118 mutations (33.3%), 236 crossovers (66.7%), 161 vertices were eliminated
building final representation...
2003 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=132825, nf=265646, ne=398469, g=0)
writing corrected surface to /home/xonobo/FSRFsubjects/bert/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 60.1 minutes
reading input surface /home/xonobo/FSRFsubjects/bert/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
0 defective edges
removing intersecting faces
000: 123 intersecting
/home/xonobo/FSRFsubjects/bert/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 53 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make Final Surf lh Tue Apr 10 10:50:32 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_make_surfaces -mgz -T1 brain.finalsurfs bert lh 

INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading volume /home/xonobo/FSRFsubjects/bert/mri/filled.mgz...
reading volume /home/xonobo/FSRFsubjects/bert/mri/brain.finalsurfs.mgz...
reading volume /home/xonobo/FSRFsubjects/bert/mri/wm.mgz...
22493 bright wm thresholded.
2987 bright non-wm voxels segmented.
reading original surface position from /home/xonobo/FSRFsubjects/bert/surf/lh.orig...
computing class statistics...
border white:    257339 voxels (1.53%)
border gray      278721 voxels (1.66%)
WM: 104.2 +- 5.4 [70.0 --> 110.0]
GM: 87.2 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 75.6 (was 70)
setting MAX_BORDER_WHITE to 112.4 (was 105)
setting MIN_BORDER_WHITE to 85.0 (was 85)
setting MAX_CSF to 66.2 (was 40)
setting MAX_GRAY to 101.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 80.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 56.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->3.99) (max @ vno 53021 --> 132357)
face area 0.28 +- 0.12 (0.00-->2.36)
mean absolute distance = 0.91 +- 1.08
3743 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
intensity peaks found at WM=107,    GM=85
using class modes intead of means....
mean inside = 101.3, mean outside = 90.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=91.3, 22 (22) missing vertices, mean dist 0.4 [0.8 (%27.2)->0.9 (%72.8))]
%57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=4, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.91 +- 0.24 (0.06-->4.74) (max @ vno 53021 --> 132357)
face area 0.28 +- 0.12 (0.00-->3.59)
vertex spacing 0.92 +- 0.26 (0.05-->4.94) (max @ vno 53021 --> 132357)
face area 0.28 +- 0.13 (0.00-->3.95)
smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.12-->4.95) (max @ vno 53021 --> 132357)
face area 0.28 +- 0.13 (0.00-->3.99)
mean absolute distance = 0.44 +- 0.68
4087 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2446666.0, rms=7.68
001: dt: 0.5000, sse=3360869.2, rms=5.75
002: dt: 0.5000, sse=3654057.0, rms=4.34
003: dt: 0.5000, sse=3808047.5, rms=3.31
004: dt: 0.5000, sse=3880899.2, rms=2.59
005: dt: 0.5000, sse=3890991.0, rms=2.14
006: dt: 0.5000, sse=3891278.5, rms=1.89
007: dt: 0.5000, sse=3871887.0, rms=1.75
008: dt: 0.5000, sse=3879059.0, rms=1.67
rms = 1.63, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=3877128.2, rms=1.63
010: dt: 0.2500, sse=2854124.0, rms=1.33
rms = 1.30, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=2774059.0, rms=1.30
rms = 1.29, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=2746235.5, rms=1.29
positioning took 9.9 minutes
inhibiting deformation at non-cortical midline structures...
mean border=93.5, 35 (3) missing vertices, mean dist -0.3 [0.5 (%70.4)->0.3 (%29.6))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=2, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.90 +- 0.24 (0.08-->5.02) (max @ vno 53021 --> 132357)
face area 0.35 +- 0.16 (0.00-->5.45)
vertex spacing 0.90 +- 0.24 (0.09-->5.10) (max @ vno 53021 --> 132357)
face area 0.35 +- 0.16 (0.00-->5.73)
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.09-->5.10) (max @ vno 53021 --> 132357)
face area 0.35 +- 0.16 (0.00-->5.73)
mean absolute distance = 0.33 +- 0.45
4424 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2929532.2, rms=3.48
013: dt: 0.5000, sse=3259157.0, rms=2.13
014: dt: 0.5000, sse=3414723.5, rms=1.62
015: dt: 0.5000, sse=3423957.2, rms=1.42
016: dt: 0.5000, sse=3536676.2, rms=1.34
rms = 1.34, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=3555082.5, rms=1.34
018: dt: 0.2500, sse=3061406.2, rms=1.14
rms = 1.12, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=2987567.2, rms=1.12
rms = 1.12, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=2965689.2, rms=1.12
positioning took 5.4 minutes
inhibiting deformation at non-cortical midline structures...
mean border=95.6, 40 (2) missing vertices, mean dist -0.2 [0.4 (%73.2)->0.2 (%26.8))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=1, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.89 +- 0.24 (0.11-->5.14) (max @ vno 53021 --> 132357)
face area 0.34 +- 0.16 (0.00-->5.80)
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.11-->5.14) (max @ vno 53021 --> 132357)
face area 0.34 +- 0.16 (0.00-->5.83)
mean absolute distance = 0.25 +- 0.33
3415 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2972875.2, rms=2.87
021: dt: 0.5000, sse=3325274.2, rms=1.53
022: dt: 0.5000, sse=3413991.5, rms=1.25
023: dt: 0.5000, sse=3408030.8, rms=1.18
rms = 1.19, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=3223333.5, rms=1.08
rms = 1.04, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=3153207.8, rms=1.04
rms = 1.04, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3132777.5, rms=1.04
positioning took 4.5 minutes
inhibiting deformation at non-cortical midline structures...
mean border=96.1, 38 (1) missing vertices, mean dist -0.0 [0.3 (%55.1)->0.2 (%44.9))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=0, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

writing white matter surface to /home/xonobo/FSRFsubjects/bert/surf/lh.white...
writing smoothed curvature to lh.curv
writing smoothed area to lh.area
vertex spacing 0.89 +- 0.24 (0.09-->5.17) (max @ vno 51918 --> 51926)
face area 0.33 +- 0.15 (0.00-->5.81)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3121739.0, rms=1.30
027: dt: 0.5000, sse=3773580.8, rms=0.88
rms = 1.05, time step reduction 1 of 3 to 0.250...
rms = 0.85, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=3598286.8, rms=0.85
rms = 0.86, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=3598286.8, rms=0.85
positioning took 2.5 minutes
generating cortex label...
writing cortex label to /home/xonobo/FSRFsubjects/bert/label/lh.cortex.label...
LabelWrite: saving to /home/xonobo/FSRFsubjects/bert/label/lh.cortex.label
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/lh.curv
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/lh.area
smoothing surface for 5 iterations...
mean border=75.5, 53 (53) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.5 (%100.0))]
%24 local maxima, %49 large gradients and %22 min vals, 2118 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 0.87 +- 0.28 (0.05-->5.93) (max @ vno 51918 --> 51926)
face area 0.29 +- 0.17 (0.00-->6.19)
vertex spacing 0.95 +- 0.35 (0.03-->6.50) (max @ vno 51918 --> 51926)
face area 0.29 +- 0.19 (0.00-->5.79)
vertex spacing 1.00 +- 0.40 (0.05-->6.94) (max @ vno 51918 --> 51926)
face area 0.29 +- 0.20 (0.00-->5.73)
vertex spacing 0.99 +- 0.40 (0.05-->7.12) (max @ vno 51918 --> 51926)
face area 0.29 +- 0.21 (0.00-->5.99)
000: dt: 0.0000, sse=4691833.5, rms=21.55
001: dt: 0.5000, sse=4193591.0, rms=19.16
002: dt: 0.5000, sse=3782250.8, rms=17.05
003: dt: 0.5000, sse=3528679.0, rms=15.26
004: dt: 0.5000, sse=3476627.2, rms=13.74
005: dt: 0.5000, sse=3477865.5, rms=12.43
006: dt: 0.5000, sse=3527896.5, rms=11.28
007: dt: 0.5000, sse=3600306.5, rms=10.25
008: dt: 0.5000, sse=3674113.2, rms=9.22
009: dt: 0.5000, sse=3765940.5, rms=8.14
010: dt: 0.5000, sse=3898277.0, rms=7.04
011: dt: 0.5000, sse=4016285.2, rms=5.92
012: dt: 0.5000, sse=4173977.2, rms=4.93
013: dt: 0.5000, sse=4338368.0, rms=4.17
014: dt: 0.5000, sse=4467508.0, rms=3.67
015: dt: 0.5000, sse=4559289.5, rms=3.37
016: dt: 0.5000, sse=4649609.0, rms=3.20
017: dt: 0.5000, sse=4676383.0, rms=3.12
018: dt: 0.5000, sse=4718242.0, rms=3.07
rms = 3.04, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=4723206.0, rms=3.04
020: dt: 0.2500, sse=3233262.5, rms=2.35
021: dt: 0.2500, sse=3077057.5, rms=2.16
rms = 2.12, time step reduction 2 of 3 to 0.125...
022: dt: 0.2smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
500, sse=3009164.8, rms=2.12
023: dt: 0.1250, sse=2909555.2, rms=2.04
rms = 2.02, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=2893709.8, rms=2.02
positioning took 21.6 minutes
mean border=73.3, 779 (8) missing vertices, mean dist 0.2 [0.2 (%41.1)->0.5 (%58.9))]
%49 local maxima, %31 large gradients and %15 min vals, 675 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 1.00 +- 0.41 (0.05-->7.34) (max @ vno 51918 --> 51926)
face area 0.39 +- 0.28 (0.00-->8.03)
vertex spacing 1.00 +- 0.41 (0.09-->7.43) (max @ vno 51918 --> 51926)
face area 0.39 +- 0.28 (0.00-->8.20)
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3164882.8, rms=4.16
025: dt: 0.5000, sse=3476277.0, rms=3.14
026: dt: 0.5000, sse=4252453.5, rms=3.03
rms = 3.03, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=4331070.0, rms=3.03
028: dt: 0.2500, sse=3510663.8, rms=2.24
029: dt: 0.2500, sse=3425681.0, rms=2.02
rms = 2.00, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3370390.0, rms=2.00
031: dt: 0.1250, sse=3289902.5, rms=1.90
rms = 1.88, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=3270777.0, rms=1.88
positioning took 6.4 minutes
mean border=71.9, 939 (6) missing vertices, mean dist 0.1 [0.2 (%37.7)->0.3 (%62.3))]
%63 local maxima, %17 large gradients and %15 min vals, 685 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 1.00 +- 0.41 (0.07-->7.49) (max @ vno 51918 --> 51926)
face area 0.39 +- 0.29 (0.00-->8.48)
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3304462.2, rms=2.67
033: dt: 0.5000, sse=3468279.5, rms=2.56
rms = 2.86, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3335857.5, rms=2.08
035: dt: 0.2500, sse=3424303.5, rms=1.89
rms = 1.85, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=3403189.5, rms=1.85
037: dt: 0.1250, sse=3343082.2, rms=1.77
rms = 1.76, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=3336550.8, rms=1.76
positioning took 5.4 minutes
mean border=71.4, 1769 (3) missing vertices, mean dist 0.0 [0.2 (%48.2)->0.3 (%51.8))]
%66 local maxima, %14 large gradients and %14 min vals, 559 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 1.00 +- 0.41 (0.06-->7.55) (max @ vno 51918 --> 51926)
face area 0.39 +- 0.29 (0.00-->8.56)
writing pial surface to /home/xonobo/FSRFsubjects/bert/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
writing smoothed area to lh.area.pial
vertex spacing 1.00 +- 0.41 (0.06-->7.57) (max @ vno 51918 --> 51926)
face area 0.39 +- 0.29 (0.00-->8.60)
measuring cortical thickness...
000: dt: 0.0000, sse=3334519.8, rms=1.86
rms = 2.05, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=3310842.0, rms=1.76
rms = 1.73, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=3396336.0, rms=1.73
rms = 1.69, time step reduction 3 of 3 to 0.062...
041: dt: 0.1250, sse=3351516.2, rms=1.69
positioning took 3.0 minutes
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/lh.curv.pial
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/lh.area.pial
0 of 132825 vertices processed
25000 of 132825 vertices processed
50000 of 132825 vertices processed
75000 of 132825 vertices processed
100000 of 132825 vertices processed
125000 of 132825 vertices processed
0 of 132825 vertices processed
25000 of 132825 vertices processed
50000 of 132825 vertices processed
75000 of 132825 vertices processed
100000 of 132825 vertices processed
125000 of 132825 vertices processed
thickness calculation complete, 412:675 truncations.
32474 vertices at 0 distance
89773 vertices at 1 distance
79398 vwriting cortical thickness estimate to 'thickness' file.
positioning took 96.5 minutes
ertices at 2 distance
34742 vertices at 3 distance
11579 vertices at 4 distance
3530 vertices at 5 distance
1140 vertices at 6 distance
412 vertices at 7 distance
139 vertices at 8 distance
76 vertices at 9 distance
40 vertices at 10 distance
19 vertices at 11 distance
11 vertices at 12 distance
16 vertices at 13 distance
2 vertices at 14 distance
5 vertices at 15 distance
2 vertices at 16 distance
6 vertices at 17 distance
7 vertices at 18 distance
1 vertices at 19 distance
4 vertices at 20 distance
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/lh.thickness
#--------------------------------------------
#@# Smooth2 lh Tue Apr 10 12:27:04 CEST 2007

 mris_smooth -n 3 -nw ../surf/lh.white ../surf/lh.smoothwm 

/home/xonobo/FSRFsubjects/bert/scripts
smoothing for 3 iterations
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation2 lh Tue Apr 10 12:27:10 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated 

avg radius = 48.9 mm, total surface area = 81031 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc
inflation took 1.3 minutes

step 000: RMS=0.166 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.085 (target=0.015)   
step 015: RMS=0.069 (target=0.015)   
step 020: RMS=0.057 (target=0.015)   
step 025: RMS=0.048 (target=0.015)   
step 030: RMS=0.039 (target=0.015)   
step 035: RMS=0.033 (target=0.015)   
step 040: RMS=0.029 (target=0.015)   
step 045: RMS=0.026 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
#--------------------------------------------
#@# Cortical ribbon mask lh Tue Apr 10 12:28:27 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_surf2vol --mkmask --hemi lh --fillribbon --template orig.mgz --volregidentity bert --outvol lh.ribbon.mgz 

gdiagno = -1
Using identity matrix for registration
Qa2v: SurfXYZ to VolCRS: ------------------------------
-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;
--------------------------------------------------
subjects dir   /home/xonobo/FSRFsubjects
hemi           lh
mksurfmask     1
projfrac       0
volreg file    (null)
outvol   path  lh.ribbon.mgz
template path  orig.mgz
------- Anat2Vol Registration (TkReg)----
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
-----------------------------------------
height = 256
 width = 256
 depth = 256
 xsize = 1.000000
 ysize = 1.000000
 zsize = 1.000000
  cdc  = -1.000000 0.000000 0.000000
  rdc  = 0.000000 0.000000 -1.000000
  sdc  = 0.000000 1.000000 0.000000
  xyz0 = 5.399719 18.000000 0.000000
Gdiag_no  -1
Reading surface /home/xonobo/FSRFsubjects/bert/surf/lh.white
Done reading source surface
Reading thickness /home/xonobo/FSRFsubjects/bert/surf/lh.thickness
Done
surf nframes = 1
INFO: mapping vertices to closest voxel
INFO: resampling surface to volume at projfrac=0.00, 84749 hits
INFO: resampling surface to volume at projfrac=0.05, 86224 hits
INFO: resampling surface to volume at projfrac=0.10, 87720 hits
INFO: resampling surface to volume at projfrac=0.15, 88820 hits
INFO: resampling surface to volume at projfrac=0.20, 89191 hits
INFO: resampling surface to volume at projfrac=0.25, 88902 hits
INFO: resampling surface to volume at projfrac=0.30, 88106 hits
INFO: resampling surface to volume at projfrac=0.35, 86966 hits
INFO: resampling surface to volume at projfrac=0.40, 85665 hits
INFO: resampling surface to volume at projfrac=0.45, 84702 hits
INFO: resampling surface to volume at projfrac=0.50, 83574 hits
INFO: resampling surface to volume at projfrac=0.55, 82672 hits
INFO: resampling surface to volume at projfrac=0.60, 81644 hits
INFO: resampling surface to volume at projfrac=0.65, 80813 hits
INFO: resampling surface to volume at projfrac=0.70, 79967 hits
INFO: resampling surface to volume at projfrac=0.75, 79072 hits
INFO: resampling surface to volume at projfrac=0.80, 78267 hits
INFO: resampling surface to volume at projfrac=0.85, 77368 hits
INFO: resampling surface to volume at projfrac=0.90, 76446 hits
INFO: resampling surface to volume at projfrac=0.95, 75689 hits
INFO: writing output volume to lh.ribbon.mgz
done
#--------------------------------------------
#@# Tessellate rh Tue Apr 10 12:29:03 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mri_tessellate ../mri/filled.mgz 127 ../surf/rh.orig.nofix 

$Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
slice 30: 610 vertices, 695 faces
slice 40: 4365 vertices, 4539 faces
slice 50: 11216 vertices, 11472 faces
slice 60: 19650 vertices, 19944 faces
slice 70: 29659 vertices, 30034 faces
slice 80: 39520 vertices, 39851 faces
slice 90: 49596 vertices, 49969 faces
slice 100: 60795 vertices, 61189 faces
slice 110: 71049 vertices, 71461 faces
slice 120: 81365 vertices, 81745 faces
slice 130: 90987 vertices, 91349 faces
slice 140: 99892 vertices, 100205 faces
slice 150: 107077 vertices, 107357 faces
slice 160: 113239 vertices, 113510 faces
slice 170: 119812 vertices, 120081 faces
slice 180: 125647 vertices, 125896 faces
slice 190: 130523 vertices, 130729 faces
slice 200: 133921 vertices, 134032 faces
slice 210: 134322 vertices, 134376 faces
slice 220: 134322 vertices, 134376 faces
slice 230: 134322 vertices, 134376 faces
slice 240: 134322 vertices, 134376 faces
slice 250: 134322 vertices, 134376 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using ras2vox 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;
#--------------------------------------------
#@# Smooth1 rh Tue Apr 10 12:29:10 CEST 2007

 mris_smooth -nw ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

/home/xonobo/FSRFsubjects/bert/scripts
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 rh Tue Apr 10 12:29:16 CEST 2007

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

/home/xonobo/FSRFsubjects/bert/scripts
avg radius = 48.8 mm, total surface area = 75244 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.2 minutes
Not saving sulc

step 000: RMS=0.163 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.064 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.049 (target=0.015)   
step 035: RMS=0.045 (target=0.015)   
step 040: RMS=0.041 (target=0.015)   
step 045: RMS=0.040 (target=0.015)   
step 050: RMS=0.039 (target=0.015)   
step 055: RMS=0.038 (target=0.015)   
step 060: RMS=0.037 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Tue Apr 10 12:30:30 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_sphere -q ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
$Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
tol=1.0e+00, host=telen, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000
mom=0.90, dt=0.90

scaling brain by 0.568...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=156.111, avgs=0
005: dt: 0.9000, rms radial error=155.884, avgs=0
010: dt: 0.9000, rms radial error=155.395, avgs=0
015: dt: 0.9000, rms radial error=154.752, avgs=0
020: dt: 0.9000, rms radial error=154.022, avgs=0
025: dt: 0.9000, rms radial error=153.242, avgs=0
030: dt: 0.9000, rms radial error=152.434, avgs=0
035: dt: 0.9000, rms radial error=151.611, avgs=0
040: dt: 0.9000, rms radial error=150.783, avgs=0
045: dt: 0.9000, rms radial error=149.953, avgs=0
050: dt: 0.9000, rms radial error=149.124, avgs=0
055: dt: 0.9000, rms radial error=148.297, avgs=0
060: dt: 0.9000, rms radial error=147.474, avgs=0
065: dt: 0.9000, rms radial error=146.656, avgs=0
070: dt: 0.9000, rms radial error=145.841, avgs=0
075: dt: 0.9000, rms radial error=145.031, avgs=0
080: dt: 0.9000, rms radial error=144.224, avgs=0
085: dt: 0.9000, rms radial error=143.423, avgs=0
090: dt: 0.9000, rms radial error=142.626, avgs=0
095: dt: 0.9000, rms radial error=141.833, avgs=0
100: dt: 0.9000, rms radial error=141.044, avgs=0
105: dt: 0.9000, rms radial error=140.260, avgs=0
110: dt: 0.9000, rms radial error=139.480, avgs=0
115: dt: 0.9000, rms radial error=138.704, avgs=0
120: dt: 0.9000, rms radial error=137.932, avgs=0
125: dt: 0.9000, rms radial error=137.165, avgs=0
130: dt: 0.9000, rms radial error=136.402, avgs=0
135: dt: 0.9000, rms radial error=135.643, avgs=0
140: dt: 0.9000, rms radial error=134.888, avgs=0
145: dt: 0.9000, rms radial error=134.138, avgs=0
150: dt: 0.9000, rms radial error=133.392, avgs=0
155: dt: 0.9000, rms radial error=132.650, avgs=0
160: dt: 0.9000, rms radial error=131.913, avgs=0
165: dt: 0.9000, rms radial error=131.179, avgs=0
170: dt: 0.9000, rms radial error=130.450, avgs=0
175: dt: 0.9000, rms radial error=129.724, avgs=0
180: dt: 0.9000, rms radial error=129.002, avgs=0
185: dt: 0.9000, rms radial error=128.285, avgs=0
190: dt: 0.9000, rms radial error=127.571, avgs=0
195: dt: 0.9000, rms radial error=126.861, avgs=0
200: dt: 0.9000, rms radial error=126.155, avgs=0
205: dt: 0.9000, rms radial error=125.453, avgs=0
210: dt: 0.9000, rms radial error=124.755, avgs=0
215: dt: 0.9000, rms radial error=124.060, avgs=0
220: dt: 0.9000, rms radial error=123.370, avgs=0
225: dt: 0.9000, rms radial error=122.683, avgs=0
230: dt: 0.9000, rms radial error=122.000, avgs=0
235: dt: 0.9000, rms radial error=121.321, avgs=0
240: dt: 0.9000, rms radial error=120.645, avgs=0
245: dt: 0.9000, rms radial error=119.974, avgs=0
250: dt: 0.9000, rms radial error=119.307, avgs=0
255: dt: 0.9000, rms radial error=118.643, avgs=0
260: dt: 0.9000, rms radial error=117.983, avgs=0
265: dt: 0.9000, rms radial error=117.327, avgs=0
270: dt: 0.9000, rms radial error=116.674, avgs=0
275: dt: 0.9000, rms radial error=116.025, avgs=0
280: dt: 0.9000, rms radial error=115.379, avgs=0
285: dt: 0.9000, rms radial error=114.737, avgs=0
290: dt: 0.9000, rms radial error=114.099, avgs=0
295: dt: 0.9000, rms radial error=113.464, avgs=0
300: dtsurface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.53 (0.00-->7.10) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.79-->2.03)
tol=1.0e-01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

301: dt: 20.03, sse: 3973.2 (0.084, 15.4, 0.418), neg: 1423 (%0.109:%0.12), avgs: 32
302: dt: 0.29, sse: 3972.8 (0.084, 15.4, 0.418), neg: 1425 (%0.109:%0.12), avgs: 32
303: dt: 0.29, sse: 3972.4 (0.083, 15.4, 0.418), neg: 1425 (%0.108:%0.12), avgs: 32
304: dt: 0.29, sse: 3972.1 (0.083, 15.4, 0.418), neg: 1425 (%0.108:%0.12), avgs: 32
305: dt: 0.29, sse: 3971.8 (0.083, 15.4, 0.418), neg: 1425 (%0.107:%0.12), avgs: 32
306: dt: 0.29, sse: 3971.5 (0.083, 15.4, 0.418), neg: 1423 (%0.106:%0.12), avgs: 32
307: dt: 0.29, sse: 3971.2 (0.083, 15.4, 0.418), neg: 1428 (%0.105:%0.12), avgs: 32
308: dt: 0.29, sse: 3970.9 (0.083, 15.4, 0.418), neg: 1432 (%0.104:%0.12), avgs: 32
309: dt: 0.29, sse: 3970.6 (0.083, 15.4, 0.418), neg: 1435 (%0.103:%0.12), avgs: 32
310: dt: 0.29, sse: 3970.4 (0.083, 15.4, 0.418), neg: 1443 (%0.102:%0.12), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.90) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.11 (-0.58-->2.04)
311: dt: 0.29, sse: 3970.1 (0.083, 15.4, 0.418), neg: 1443 (%0.101:%0.12), avgs: 32
312: dt: 29.53, sse: 3969.2 (0.083, 15.4, 0.418), neg: 1509 (%0.089:%0.12), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.82) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.11 (-0.46-->2.04)
313: dt: 5.61, sse: 3968.9 (0.083, 15.4, 0.418), neg: 1512 (%0.081:%0.12), avgs: 8
314: dt: 0.15, sse: 3968.8 (0.083, 15.4, 0.418), neg: 1522 (%0.080:%0.12), avgs: 8
315: dt: 0.15, sse: 3968.7 (0.083, 15.4, 0.418), neg: 1526 (%0.080:%0.12), avgs: 8
316: dt: 0.15, sse: 3968.6 (0.083, 15.4, 0.418), neg: 1528 (%0.079:%0.12), avgs: 8
317: dt: 0.15, sse: 3968.5 (0.083, 15.4, 0.418), neg: 1530 (%0.078:%0.12), avgs: 8
318: dt: 0.15, sse: 3968.5 (0.083, 15.4, 0.418), neg: 1542 (%0.078:%0.12), avgs: 8
319: dt: 0.15, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1546 (%0.077:%0.12), avgs: 8
320: dt: 0.15, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1553 (%0.076:%0.12), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.76) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.11 (-0.29-->2.04)
321: dt: 0.15, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1564 (%0.075:%0.12), avgs: 8
322: dt: 0.15, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1577 (%0.075:%0.12), avgs: 8
323: dt: 0.15, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1585 (%0.074:%0.12), avgs: 8
324: dt: 0.18, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1584 (%0.074:%0.12), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.26-->2.04)
325: dt: 0.08, sse: 3968.3 (0.083, 15.4, 0.418), neg: 1585 (%0.073:%0.12), avgs: 2
326: dt: 0.09, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1595 (%0.072:%0.12), avgs: 2
327: dt: 0.09, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1598 (%0.071:%0.12), avgs: 2
328: dt: 0.09, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1608 (%0.070:%0.12), avgs: 2
329: dt: 0.09, sse: 3968.4 (0.083, 15.4, 0.418), neg: 1616 (%0.068:%0.12), avgs: 2
330: dt: 0.09, sse: 3968.5 (0.083, 15.4, 0.418), neg: 1623 (%0.067:%0.12), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.74) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.16-->2.05)
331: dt: 0.09, sse: 3968.6 (0.083, 15.4, 0.418), neg: 1622 (%0.066:%0.11), avgs: 2
332: dt: 0.09, sse: 3968.8 (0.083, 15.5, 0.418), neg: 1631 (%0.064:%0.11), avgs: 2
333: dt: 0.09, sse: 3969.0 (0.083, 15.5, 0.418), neg: 1641 (%0.063:%0.11), avgs: 2
334: dt: 0.09, sse: 3969.2 (0.083, 15.5, 0.418), neg: 1661 (%0.062:%0.12), avgs: 2
335: dt: 0.09, sse: 3969.5 (0.083, 15.5, 0.418), neg: 1674 (%0.061:%0.12), avgs: 2
336: dt: 0.00, sse: 3969.5 (0.083, 15.5, 0.418), neg: 1674 (%0.061:%0.12), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.73) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.09-->2.05)
337: dt: 0.00, sse: 3969.5 (0.083, 15.5, 0.418), neg: 1674 (%0.061:%0.12), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->6.73) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.09-->2.05)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

338: dt: 123.89, sse: 299.1 (0.083, 15.4, 0.418), neg: 1691 (%0.045:%0.09), avgs: 32
339: dt: 0.29, sse: 299.4 (0.084, 15.4, 0.418), neg: 1702 (%0.045:%0.09), avgs: 32
340: dt: 0.29, sse: 299.7 (0.084, 15.4, 0.418), neg: 1710 (%0.045:%0.09), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.70) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.09-->2.05)
341: dt: 0.29, sse: 300.0 (0.084, 15.4, 0.418), neg: 1717 (%0.046:%0.09), avgs: 32
342: dt: 0.29, sse: 300.2 (0.084, 15.4, 0.418), neg: 1731 (%0.046:%0.09), avgs: 32
343: dt: 0.29, sse: 300.5 (0.084, 15.4, 0.418), neg: 1740 (%0.046:%0.09), avgs: 32
344: dt: 0.29, sse: 300.6 (0.084, 15.4, 0.418), neg: 1745 (%0.046:%0.09), avgs: 32
345: dt: 0.29, sse: 300.8 (0.084, 15.5, 0.418), neg: 1750 (%0.046:%0.09), avgs: 32
346: dt: 0.29, sse: 300.9 (0.084, 15.5, 0.418), neg: 1764 (%0.046:%0.09), avgs: 32
347: dt: 0.29, sse: 301.1 (0.084, 15.5, 0.418), neg: 1766 (%0.046:%0.09), avgs: 32
348: dt: 0.29, sse: 301.2 (0.084, 15.5, 0.418), neg: 1778 (%0.046:%0.09), avgs: 32
349: dt: 88.94, sse: 299.4 (0.084, 15.5, 0.418), neg: 2020 (%0.041:%0.10), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.65) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.10-->2.05)
350: dt: 53.78, sse: 296.0 (0.084, 15.5, 0.418), neg: 1993 (%0.044:%0.10), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.67) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.09-->2.05)
351: dt: 0.15, sse: 296.0 (0.084, 15.5, 0.418), neg: 1993 (%0.044:%0.10), avgs: 8
352: dt: 0.15, sse: 296.0 (0.084, 15.5, 0.418), neg: 1989 (%0.044:%0.09), avgs: 8
353: dt: 0.15, sse: 296.0 (0.084, 15.5, 0.418), neg: 1987 (%0.043:%0.09), avgs: 8
354: dt: 0.15, sse: 296.0 (0.084, 15.5, 0.418), neg: 1990 (%0.043:%0.09), avgs: 8
355: dt: 0.15, sse: 296.0 (0.084, 15.5, 0.418), neg: 1996 (%0.043:%0.09), avgs: 8
356: dt: 0.15, sse: 295.9 (0.084, 15.5, 0.418), neg: 1990 (%0.042:%0.09), avgs: 8
357: dt: 0.15, sse: 295.8 (0.084, 15.5, 0.418), neg: 1988 (%0.042:%0.09), avgs: 8
358: dt: 0.15, sse: 295.8 (0.084, 15.5, 0.418), neg: 1991 (%0.041:%0.09), avgs: 8
359: dt: 0.15, sse: 295.7 (0.084, 15.5, 0.418), neg: 1991 (%0.041:%0.09), avgs: 8
360: dt: 0.15, sse: 295.6 (0.084, 15.5, 0.418), neg: 1994 (%0.040:%0.09), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.66) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.07-->2.05)
: 0.9000, rms radial error=112.832, avgs=0

spherical inflation complete.
epoch 1 (K=20.0), pass 1, starting sse = 3977.40
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.00/37 = 0.00005
epoch 2 (K=80.0), pass 1, starting sse = 304.15
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 361: dt: 44.70, sse: 293.5 (0.084, 15.5, 0.418), neg: 2018 (%0.039:%0.10), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.68) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.06-->2.05)
362: dt: 6.37, sse: 291.7 (0.084, 15.5, 0.418), neg: 2004 (%0.034:%0.09), avgs: 2
363: dt: 0.09, sse: 291.6 (0.084, 15.5, 0.418), neg: 2012 (%0.034:%0.09), avgs: 2
364: dt: 0.09, sse: 291.5 (0.084, 15.5, 0.418), neg: 2012 (%0.033:%0.09), avgs: 2
365: dt: 0.09, sse: 291.4 (0.084, 15.5, 0.418), neg: 2011 (%0.033:%0.09), avgs: 2
366: dt: 0.09, sse: 291.3 (0.084, 15.5, 0.418), neg: 2006 (%0.032:%0.09), avgs: 2
367: dt: 0.09, sse: 291.2 (0.084, 15.5, 0.418), neg: 2018 (%0.032:%0.09), avgs: 2
368: dt: 0.09, sse: 291.1 (0.084, 15.5, 0.418), neg: 2026 (%0.032:%0.09), avgs: 2
369: dt: 0.09, sse: 291.0 (0.084, 15.5, 0.418), neg: 2029 (%0.032:%0.09), avgs: 2
370: dt: 0.09, sse: 290.9 (0.084, 15.5, 0.418), neg: 2030 (%0.032:%0.09), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.69) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.03-->2.05)
371: dt: 0.09, sse: 290.8 (0.084, 15.5, 0.418), neg: 2040 (%0.032:%0.09), avgs: 2
372: dt: 0.09, sse: 290.8 (0.084, 15.5, 0.418), neg: 2052 (%0.032:%0.09), avgs: 2
373: dt: 10.41, sse: 289.5 (0.084, 15.5, 0.418), neg: 2035 (%0.034:%0.09), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.71) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.05-->2.05)
374: dt: 0.30, sse: 288.7 (0.084, 15.5, 0.418), neg: 2048 (%0.030:%0.08), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->6.71) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.02-->2.05)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

375: dt: 173.49, sse: 18.3 (0.084, 15.4, 0.418), neg: 1837 (%0.022:%0.09), avgs: 32
376: dt: 16.83, sse: 18.0 (0.084, 15.4, 0.418), neg: 1876 (%0.020:%0.08), avgs: 32
377: dt: 0.29, sse: 18.0 (0.084, 15.4, 0.418), neg: 1873 (%0.020:%0.08), avgs: 32
378: dt: 0.29, sse: 18.0 (0.084, 15.4, 0.418), neg: 1887 (%0.020:%0.08), avgs: 32
379: dt: 0.29, sse: 18.1 (0.084, 15.4, 0.418), neg: 1892 (%0.021:%0.08), avgs: 32
380: dt: 0.29, sse: 18.1 (0.084, 15.4, 0.418), neg: 1890 (%0.021:%0.08), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.71) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.03-->2.05)
381: dt: 0.29, sse: 18.1 (0.084, 15.4, 0.418), neg: 1898 (%0.021:%0.08), avgs: 32
382: dt: 0.29, sse: 18.2 (0.084, 15.4, 0.418), neg: 1901 (%0.021:%0.08), avgs: 32
383: dt: 0.29, sse: 18.2 (0.084, 15.4, 0.418), neg: 1904 (%0.021:%0.08), avgs: 32
384: dt: 0.29, sse: 18.3 (0.084, 15.4, 0.418), neg: 1907 (%0.021:%0.08), avgs: 32
385: dt: 0.29, sse: 18.3 (0.084, 15.4, 0.418), neg: 1909 (%0.022:%0.08), avgs: 32
386: dt: 0.29, sse: 18.3 (0.084, 15.4, 0.418), neg: 1914 (%0.022:%0.08), avgs: 32
387: dt: 0.00, sse: 18.3 (0.084, 15.4, 0.418), neg: 1914 (%0.022:%0.08), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.71) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.04-->2.05)
388: dt: 5.75, sse: 18.1 (0.084, 15.4, 0.418), neg: 1935 (%0.021:%0.08), avgs: 8
389: dt: 0.15, sse: 18.1 (0.084, 15.4, 0.418), neg: 1937 (%0.021:%0.08), avgs: 8
390: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1938 (%0.021:%0.08), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.72) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.04-->2.05)
391: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1945 (%0.021:%0.08), avgs: 8
392: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1948 (%0.021:%0.08), avgs: 8
393: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1951 (%0.021:%0.08), avgs: 8
394: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1956 (%0.021:%0.08), avgs: 8
395: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1955 (%0.021:%0.08), avgs: 8
396: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1954 (%0.021:%0.08), avgs: 8
397: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1956 (%0.021:%0.08), avgs: 8
398: dt: 0.15, sse: 18.2 (0.084, 15.4, 0.418), neg: 1959 (%0.021:%0.08), avgs: 8
399: dt: 27.41, sse: 17.8 (0.084, 15.4, 0.418), neg: 1924 (%0.020:%0.08), avgs: 8
400: dt: 4.64, sse: 17.7 (0.084, 15.4, 0.418), neg: 1922 (%0.019:%0.08), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.72) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.03-->2.05)
vertex spacing 0.92 +- 0.53 (0.00-->6.72) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.03-->2.05)
401: dt: 2.15, sse: 17.4 (0.084, 15.4, 0.418), neg: 1902 (%0.018:%0.08), avgs: 2
402: dt: 0.98, sse: 17.3 (0.084, 15.4, 0.418), neg: 1890 (%0.017:%0.07), avgs: 2
403: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1891 (%0.017:%0.07), avgs: 2
404: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1899 (%0.017:%0.07), avgs: 2
405: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1904 (%0.017:%0.07), avgs: 2
406: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1914 (%0.017:%0.08), avgs: 2
407: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1912 (%0.017:%0.08), avgs: 2
408: dt: 0.09, sse: 17.3 (0.084, 15.4, 0.418), neg: 1912 (%0.017:%0.08), avgs: 2
409: dt: 0.09, sse: 17.2 (0.084, 15.4, 0.418), neg: 1915 (%0.017:%0.08), avgs: 2
410: dt: 0.09, sse: 17.2 (0.084, 15.4, 0.418), neg: 1917 (%0.017:%0.08), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.73) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
411: dt: 0.09, sse: 17.2 (0.084, 15.4, 0.418), neg: 1919 (%0.017:%0.08), avgs: 2
412: dt: 0.09, sse: 17.2 (0.084, 15.4, 0.418), neg: 1918 (%0.017:%0.08), avgs: 2
413: dt: 4.26, sse: 17.0 (0.084, 15.4, 0.418), neg: 1896 (%0.017:%0.07), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.74) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
414: dt: 0.23, sse: 16.9 (0.084, 15.4, 0.418), neg: 1899 (%0.016:%0.07), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->6.74) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
tol=1.8e+01, host=telen, nav=32, nbrs=1, l_nlarea=1.000
using quadratic fit line minimization

415: dt: 62.39, sse: 4.6 (0.084, 15.4, 0.418), neg: 1874 (%0.014:%0.08), avgs: 32
416: dt: 12.87, sse: 4.4 (0.084, 15.4, 0.418), neg: 1834 (%0.013:%0.07), avgs: 32
and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.05/37 = 0.00138
epoch 3 (K=320.0), pass 1, starting sse = 20.01
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.15/40 = 0.00382
epoch 4 (K=1280.0), pass 1, starting sse = 5.01
integrating with navgs=32 and tol=3.200e+00
taking momentum steps...
integrating with navgs=32 and to417: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1831 (%0.013:%0.07), avgs: 32
418: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1834 (%0.013:%0.07), avgs: 32
419: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1836 (%0.013:%0.07), avgs: 32
420: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1835 (%0.013:%0.07), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.74) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
421: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1837 (%0.013:%0.07), avgs: 32
422: dt: 0.29, sse: 4.4 (0.084, 15.4, 0.418), neg: 1841 (%0.013:%0.07), avgs: 32
423: dt: 0.29, sse: 4.3 (0.084, 15.4, 0.418), neg: 1842 (%0.013:%0.07), avgs: 32
424: dt: 0.29, sse: 4.3 (0.084, 15.4, 0.418), neg: 1848 (%0.013:%0.07), avgs: 32
425: dt: 0.29, sse: 4.3 (0.084, 15.4, 0.418), neg: 1851 (%0.013:%0.08), avgs: 32
426: dt: 0.29, sse: 4.3 (0.084, 15.4, 0.418), neg: 1850 (%0.013:%0.07), avgs: 32
427: dt: 17.41, sse: 4.3 (0.084, 15.4, 0.418), neg: 1836 (%0.013:%0.07), avgs: 32
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
428: dt: 9.85, sse: 4.2 (0.084, 15.4, 0.418), neg: 1836 (%0.013:%0.07), avgs: 8
429: dt: 5.47, sse: 4.2 (0.084, 15.4, 0.418), neg: 1826 (%0.012:%0.07), avgs: 8
430: dt: 0.15, sse: 4.2 (0.084, 15.4, 0.418), neg: 1831 (%0.012:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
431: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1828 (%0.012:%0.07), avgs: 8
432: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1828 (%0.012:%0.07), avgs: 8
433: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1828 (%0.012:%0.07), avgs: 8
434: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1829 (%0.012:%0.07), avgs: 8
435: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1828 (%0.012:%0.07), avgs: 8
436: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1825 (%0.012:%0.07), avgs: 8
437: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1826 (%0.012:%0.07), avgs: 8
438: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1824 (%0.012:%0.07), avgs: 8
439: dt: 0.15, sse: 4.1 (0.084, 15.4, 0.418), neg: 1829 (%0.012:%0.07), avgs: 8
440: dt: 14.74, sse: 4.0 (0.084, 15.4, 0.418), neg: 1807 (%0.012:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 57089 --> 55854)
face area 0.09 +- 0.12 (-0.02-->2.05)
441: dt: 2.48, sse: 4.0 (0.084, 15.4, 0.418), neg: 1818 (%0.011:%0.07), avgs: 8
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
442: dt: 1.17, sse: 3.9 (0.084, 15.4, 0.418), neg: 1806 (%0.011:%0.07), avgs: 2
443: dt: 0.00, sse: 3.9 (0.084, 15.4, 0.418), neg: 1805 (%0.011:%0.07), avgs: 2
444: dt: 0.09, sse: 3.9 (0.084, 15.4, 0.418), neg: 1818 (%0.011:%0.07), avgs: 2
445: dt: 0.09, sse: 3.9 (0.084, 15.4, 0.418), neg: 1829 (%0.011:%0.07), avgs: 2
446: dt: 0.09, sse: 3.9 (0.084, 15.4, 0.418), neg: 1831 (%0.011:%0.07), avgs: 2
447: dt: 0.09, sse: 3.9 (0.084, 15.4, 0.418), neg: 1832 (%0.011:%0.07), avgs: 2
448: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1835 (%0.011:%0.08), avgs: 2
449: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1831 (%0.011:%0.08), avgs: 2
450: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1832 (%0.011:%0.08), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.75) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
451: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1837 (%0.010:%0.07), avgs: 2
452: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1836 (%0.010:%0.07), avgs: 2
453: dt: 0.09, sse: 3.8 (0.084, 15.4, 0.418), neg: 1837 (%0.010:%0.08), avgs: 2
454: dt: 0.00, sse: 3.8 (0.084, 15.4, 0.418), neg: 1837 (%0.010:%0.08), avgs: 2
vertex spacing 0.92 +- 0.53 (0.00-->6.76) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
455: dt: 0.00, sse: 3.8 (0.084, 15.4, 0.418), neg: 1837 (%0.010:%0.08), avgs: 0
vertex spacing 0.92 +- 0.53 (0.00-->6.76) (max @ vno 55854 --> 57089)
face area 0.09 +- 0.12 (-0.02-->2.05)
455: dt: 0.00, sse: 3953.5 (0.084, 15.4, 0.418), neg: 1837 (%0.010:%0.08), avgs: 32
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.20 hours
l=3.200e+00
integrating with navgs=32 and tol=3.200e+00
integrating with navgs=8 and tol=1.671e+00
taking momentum steps...
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=8 and tol=1.671e+00
integrating with navgs=2 and tol=9.648e-01
taking momentum steps...
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=2 and tol=9.648e-01
integrating with navgs=0 and tol=5.570e-01
pass 1 complete, delta sse/iter = 0.25/41 = 0.00610
final distance error %100000.00
optimization complete.
unfolding took 0.15 hours
#--------------------------------------------
#@# Fix Topology rh Tue Apr 10 12:42:37 CEST 2007

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

/home/xonobo/FSRFsubjects/bert/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga bert rh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters

*************************************************************
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 1.41.2.1 2007/01/05 16:58:33 nicks Exp $
  $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
before topology correction, eno=-44 (nv=134322, nf=268752, ne=403118, g=23)
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...
4112 ambiguous faces found in tessellation
segmenting defects...
30 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
30 defects to be corrected 
0 vertices coincident
vertex 104823: degenerate normal
vertex 104823: degenerate normal
vertex 104823: degenerate normal
Computing Initial Surface Statistics
      -face       loglikelihood: -8.5177  (-4.2589)
      -vertex     loglikelihood: -5.3885  (-2.6942)
      -normal dot loglikelihood: -3.5629  (-3.5629)
      -quad curv  loglikelihood: -6.4132  (-3.2066)
      Total Loglikelihood : -23.8823

CORRECTING DEFECT 0 (vertices=24, convex hull=60)
l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 
After retessellation of defect 0, euler #=-20 (131872,394685,262793) : difference with theory (-27) = -7 

CORRECTING DEFECT 1 (vertices=33, convex hull=77)
After retessellation of defect 1, euler #=-19 (131888,394767,262860) : difference with theory (-26) = -7 

CORRECTING DEFECT 2 (vertices=44, convex hull=64)
After retessellation of defect 2, euler #=-18 (131898,394822,262906) : difference with theory (-25) = -7 

CORRECTING DEFECT 3 (vertices=20, convex hull=49)
After retessellation of defect 3, euler #=-17 (131906,394862,262939) : difference with theory (-24) = -7 

CORRECTING DEFECT 4 (vertices=53, convex hull=97)
After retessellation of defect 4, euler #=-16 (131943,395012,263053) : difference with theory (-23) = -7 

CORRECTING DEFECT 5 (vertices=924, convex hull=307)
normal vector of length zero at vertex 132755 with 4 faces
normal vector of length zero at vertex 132826 with 3 faces
normal vector of length zero at vertex 132799 with 3 faces
normal vector of length zero at vertex 132799 with 3 faces
normal vector of length zero at vertex 132814 with 3 faces
normal vector of length zero at vertex 132790 with 5 faces
After retessellation of defect 5, euler #=-20 (132129,395759,263610) : difference with theory (-22) = -2 

CORRECTING DEFECT 6 (vertices=20, convex hull=50)
After retessellation of defect 6, euler #=-19 (132140,395812,263653) : difference with theory (-21) = -2 

CORRECTING DEFECT 7 (vertices=45, convex hull=61)
After retessellation of defect 7, euler #=-18 (132149,395863,263696) : difference with theory (-20) = -2 

CORRECTING DEFECT 8 (vertices=6, convex hull=16)
After retessellation of defect 8, euler #=-17 (132150,395870,263703) : difference with theory (-19) = -2 

CORRECTING DEFECT 9 (vertices=178, convex hull=88)
After retessellation of defect 9, euler #=-17 (132161,395946,263768) : difference with theory (-18) = -1 

CORRECTING DEFECT 10 (vertices=76, convex hull=124)
After retessellation of defect 10, euler #=-16 (132194,396100,263890) : difference with theory (-17) = -1 

CORRECTING DEFECT 11 (vertices=14, convex hull=30)
After retessellation of defect 11, euler #=-15 (132196,396118,263907) : difference with theory (-16) = -1 

CORRECTING DEFECT 12 (vertices=15, convex hull=42)
After retessellation of defect 12, euler #=-14 (132205,396158,263939) : difference with theory (-15) = -1 

CORRECTING DEFECT 13 (vertices=105, convex hull=63)
After retessellation of defect 13, euler #=-13 (132214,396214,263987) : difference with theory (-14) = -1 

CORRECTING DEFECT 14 (vertices=87, convex hull=30)
After retessellation of defect 14, euler #=-12 (132222,396247,264013) : difference with theory (-13) = -1 

CORRECTING DEFECT 15 (vertices=112, convex hull=107)
After retessellation of defect 15, euler #=-11 (132241,396355,264103) : difference with theory (-12) = -1 

CORRECTING DEFECT 16 (vertices=41, convex hull=93)
After retessellation of defect 16, euler #=-10 (132258,396444,264176) : difference with theory (-11) = -1 

CORRECTING DEFECT 17 (vertices=14, convex hull=26)
After retessellation of defect 17, euler #=-9 (132261,396461,264191) : difference with theory (-10) = -1 

CORRECTING DEFECT 18 (vertices=36, convex hull=50)
After retessellation of defect 18, euler #=-8 (132279,396536,264249) : difference with theory (-9) = -1 

CORRECTING DEFECT 19 (vertices=28, convex hull=68)
After retessellation of defect 19, euler #=-7 (132294,396605,264304) : difference with theory (-8) = -1 

CORRECTING DEFECT 20 (vertices=114, convex hull=37)
After retessellation of defect 20, euler #=-6 (132300,396640,264334) : difference with theory (-7) = -1 

CORRECTING DEFECT 21 (vertices=12, convex hull=37)
After retessellation of defect 21, euler #=-5 (132302,396659,264352) : difference with theory (-6) = -1 

CORRECTING DEFECT 22 (vertices=108, convex hull=66)
After retessellation of defect 22, euler #=-4 (132333,396778,264441) : difference with theory (-5) = -1 

CORRECTING DEFECT 23 (vertices=134, convex hull=118)
After retessellation of defect 23, euler #=-4 (132384,396992,264604) : difference with theory (-4) = 0 

CORRECTING DEFECT 24 (vertices=11, convex hull=47)
After retessellation of defect 24, euler #=-3 (132391,397031,264637) : difference with theory (-3) = 0 

CORRECTING DEFECT 25 (vertices=64, convex hull=76)
After retessellation of defect 25, euler #=-2 (132410,397119,264707) : difference with theory (-2) = 0 

CORRECTING DEFECT 26 (vertices=28, convex hull=63)
After retessellation of defect 26, euler #=-1 (132425,397188,264762) : difference with theory (-1) = 0 

CORRECTING DEFECT 27 (vertices=9, convex hull=25)
After retessellation of defect 27, euler #=0 (132426,397200,264774) : difference with theory (0) = 0 

CORRECTING DEFECT 28 (vertices=84, convex hull=115)
After retessellation of defect 28, euler #=1 (132466,397374,264909) : difference with theory (1) = 0 

CORRECTING DEFECT 29 (vertices=23, convex hull=50)
After retessellation of defect 29, euler #=2 (132474,397416,264944) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.09-->5.79) (max @ vno 109400 --> 108834)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.09-->5.79) (max @ vno 109400 --> 108834)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
81 mutations (34.9%), 151 crossovers (65.1%), 158 vertices were eliminated
building final representation...
1848 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=132474, nf=264944, ne=397416, g=0)
writing corrected surface to /home/xonobo/FSRFsubjects/bert/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 47.3 minutes
reading input surface /home/xonobo/FSRFsubjects/bert/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
0 defective edges
removing intersecting faces
000: 176 intersecting
/home/xonobo/FSRFsubjects/bert/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 121 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make Final Surf rh Tue Apr 10 13:30:07 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_make_surfaces -mgz -T1 brain.finalsurfs bert rh 

INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $
$Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $
reading volume /home/xonobo/FSRFsubjects/bert/mri/filled.mgz...
reading volume /home/xonobo/FSRFsubjects/bert/mri/brain.finalsurfs.mgz...
reading volume /home/xonobo/FSRFsubjects/bert/mri/wm.mgz...
22493 bright wm thresholded.
2987 bright non-wm voxels segmented.
reading original surface position from /home/xonobo/FSRFsubjects/bert/surf/rh.orig...
computing class statistics...
border white:    257339 voxels (1.53%)
border gray      278721 voxels (1.66%)
WM: 104.2 +- 5.4 [70.0 --> 110.0]
GM: 87.2 +- 9.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 75.6 (was 70)
setting MAX_BORDER_WHITE to 113.4 (was 105)
setting MIN_BORDER_WHITE to 85.0 (was 85)
setting MAX_CSF to 66.2 (was 40)
setting MAX_GRAY to 102.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 80.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 56.7 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->4.21) (max @ vno 131949 --> 58542)
face area 0.28 +- 0.12 (0.00-->2.73)
mean absolute distance = 0.94 +- 1.07
3491 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
intensity peaks found at WM=108,    GM=85
using class modes intead of means....
mean inside = 101.7, mean outside = 90.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=91.5, 57 (57) missing vertices, mean dist 0.5 [0.9 (%25.1)->1.0 (%74.9))]
%57 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=4, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.91 +- 0.24 (0.09-->4.32) (max @ vno 132128 --> 63251)
face area 0.28 +- 0.13 (0.00-->3.28)
vertex spacing 0.92 +- 0.26 (0.06-->4.85) (max @ vno 132086 --> 132126)
face area 0.28 +- 0.14 (0.00-->3.50)
smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.09-->4.87) (max @ vno 132086 --> 132126)
face area 0.28 +- 0.14 (0.00-->3.53)
mean absolute distance = 0.46 +- 0.67
4107 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2463482.5, rms=7.84
001: dt: 0.5000, sse=3264646.8, rms=5.88
002: dt: 0.5000, sse=3544175.2, rms=4.44
003: dt: 0.5000, sse=3712358.5, rms=3.39
004: dt: 0.5000, sse=3772276.0, rms=2.64
005: dt: 0.5000, sse=3788479.2, rms=2.16
006: dt: 0.5000, sse=3760276.5, rms=1.88
007: dt: 0.5000, sse=3760686.0, rms=1.73
008: dt: 0.5000, sse=3745422.0, rms=1.64
rms = 1.59, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=3757471.8, rms=1.59
010: dt: 0.2500, sse=2849448.5, rms=1.34
rms = 1.31, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=2783931.5, rms=1.31
rms = 1.30, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=2755847.2, rms=1.30
positioning took 10.0 minutes
inhibiting deformation at non-cortical midline structures...
mean border=93.7, 82 (32) missing vertices, mean dist -0.3 [0.5 (%70.5)->0.3 (%29.5))]
%71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=2, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.91 +- 0.25 (0.01-->5.20) (max @ vno 132086 --> 132126)
face area 0.35 +- 0.16 (0.00-->4.74)
vertex spacing 0.90 +- 0.24 (0.11-->5.42) (max @ vno 132086 --> 132126)
face area 0.35 +- 0.16 (0.00-->5.00)
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.11-->5.42) (max @ vno 132086 --> 132126)
face area 0.35 +- 0.16 (0.00-->5.00)
mean absolute distance = 0.35 +- 0.44
4541 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2946887.0, rms=3.62
013: dt: 0.5000, sse=3246262.8, rms=2.26
014: dt: 0.5000, sse=3373176.5, rms=1.70
015: dt: 0.5000, sse=3383409.8, rms=1.45
016: dt: 0.5000, sse=3487532.0, rms=1.36
rms = 1.34, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=3496628.0, rms=1.34
018: dt: 0.2500, sse=3028475.5, rms=1.15
rms = 1.13, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=2960963.5, rms=1.13
rms = 1.13, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=2939635.8, rms=1.13
positioning took 5.4 minutes
inhibiting deformation at non-cortical midline structures...
mean border=96.0, 79 (22) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.2 (%25.5))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=1, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

vertex spacing 0.89 +- 0.24 (0.08-->5.62) (max @ vno 132086 --> 132126)
face area 0.34 +- 0.16 (0.00-->4.98)
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.08-->5.63) (max @ vno 132086 --> 132126)
face area 0.34 +- 0.16 (0.00-->4.99)
mean absolute distance = 0.25 +- 0.32
3434 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2950257.2, rms=3.03
021: dt: 0.5000, sse=3284791.5, rms=1.60
022: dt: 0.5000, sse=3402152.5, rms=1.25
023: dt: 0.5000, sse=3397721.8, rms=1.17
rms = 1.18, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=3216090.5, rms=1.08
rms = 1.05, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=3144449.8, rms=1.05
rms = 1.05, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3122458.0, rms=1.05
positioning took 4.5 minutes
inhibiting deformation at non-cortical midline structures...
mean border=96.5, 81 (21) missing vertices, mean dist -0.1 [0.3 (%56.1)->0.2 (%43.9))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, host=telen, nav=0, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50

writing white matter surface to /home/xonobo/FSRFsubjects/bert/surf/rh.white...
writing smoothed curvature to rh.curv
writing smoothed area to rh.area
vertex spacing 0.89 +- 0.24 (0.08-->5.68) (max @ vno 132086 --> 132126)
face area 0.33 +- 0.15 (0.00-->4.90)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3109730.2, rms=1.32
027: dt: 0.5000, sse=3748051.2, rms=0.89
rms = 1.05, time step reduction 1 of 3 to 0.250...
rms = 0.87, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=3579963.0, rms=0.87
rms = 0.88, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=3579963.0, rms=0.87
positioning took 2.5 minutes
generating cortex label...
writing cortex label to /home/xonobo/FSRFsubjects/bert/label/rh.cortex.label...
LabelWrite: saving to /home/xonobo/FSRFsubjects/bert/label/rh.cortex.label
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/rh.curv
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/rh.area
smoothing surface for 5 iterations...
mean border=75.8, 77 (77) missing vertices, mean dist 1.9 [0.7 (%0.0)->2.6 (%100.0))]
%25 local maxima, %48 large gradients and %23 min vals, 1898 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 0.87 +- 0.28 (0.03-->6.11) (max @ vno 132128 --> 63251)
face area 0.30 +- 0.17 (0.00-->4.92)
vertex spacing 0.95 +- 0.35 (0.03-->6.38) (max @ vno 132128 --> 63251)
face area 0.30 +- 0.19 (0.00-->4.41)
vertex spacing 0.99 +- 0.39 (0.02-->6.47) (max @ vno 132128 --> 63251)
face area 0.30 +- 0.20 (0.00-->4.05)
vertex spacing 0.99 +- 0.40 (0.03-->6.32) (max @ vno 132128 --> 63251)
face area 0.30 +- 0.21 (0.00-->4.07)
000: dt: 0.0000, sse=4688910.5, rms=21.63
001: dt: 0.5000, sse=4192258.5, rms=19.26
002: dt: 0.5000, sse=3773738.5, rms=17.14
003: dt: 0.5000, sse=3490233.8, rms=15.34
004: dt: 0.5000, sse=3393256.5, rms=13.84
005: dt: 0.5000, sse=3419803.5, rms=12.53
006: dt: 0.5000, sse=3477540.5, rms=11.38
007: dt: 0.5000, sse=3596022.2, rms=10.35
008: dt: 0.5000, sse=3708261.5, rms=9.33
009: dt: 0.5000, sse=3806257.8, rms=8.27
010: dt: 0.5000, sse=3914495.8, rms=7.16
011: dt: 0.5000, sse=4014971.0, rms=6.00
012: dt: 0.5000, sse=4151902.2, rms=4.93
013: dt: 0.5000, sse=4312429.5, rms=4.15
014: dt: 0.5000, sse=4467482.5, rms=3.66
015: dt: 0.5000, sse=4565784.0, rms=3.37
016: dt: 0.5000, sse=4628952.0, rms=3.22
017: dt: 0.5000, sse=4693309.5, rms=3.11
018: dt: 0.5000, sse=4722098.5, rms=3.06
rms = 3.02, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=4727295.0, rms=3.02
020: dt: 0.2500, sse=3199311.0, rms=2.30
021: dt: 0.2500, sse=3055645.8, rms=2.12
rms = 2.09, time step reduction 2 of 3 to 0.125...
022: dt: 0.2smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
500, sse=2991119.5, rms=2.09
023: dt: 0.1250, sse=2889110.8, rms=2.01
rms = 2.00, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=2874157.8, rms=2.00
positioning took 22.0 minutes
mean border=73.5, 799 (25) missing vertices, mean dist 0.2 [0.2 (%39.7)->0.5 (%60.3))]
%50 local maxima, %29 large gradients and %16 min vals, 551 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 1.00 +- 0.41 (0.03-->7.15) (max @ vno 97087 --> 96298)
face area 0.39 +- 0.28 (0.00-->5.36)
vertex spacing 1.00 +- 0.41 (0.03-->8.38) (max @ vno 97087 --> 96298)
face area 0.39 +- 0.28 (0.00-->5.38)
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3140227.8, rms=4.18
025: dt: 0.5000, sse=3409493.5, rms=3.08
026: dt: 0.5000, sse=4192153.5, rms=2.95
rms = 3.01, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=3593225.5, rms=2.36
028: dt: 0.2500, sse=3359097.2, rms=2.07
029: dt: 0.2500, sse=3324677.0, rms=2.01
rms = 1.98, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3302651.0, rms=1.98
031: dt: 0.1250, sse=3229184.5, rms=1.90
rms = 1.89, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=3222492.0, rms=1.89
positioning took 7.0 minutes
mean border=72.1, 928 (16) missing vertices, mean dist 0.1 [0.2 (%37.4)->0.3 (%62.6))]
%64 local maxima, %15 large gradients and %16 min vals, 555 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 1.00 +- 0.41 (0.03-->9.46) (max @ vno 97087 --> 96298)
face area 0.39 +- 0.29 (0.00-->5.48)
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3254092.8, rms=2.68
033: dt: 0.5000, sse=3417417.0, rms=2.57
rms = 2.82, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3292215.5, rms=2.09
035: dt: 0.2500, sse=3367251.0, rms=1.87
rms = 1.84, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=3349905.0, rms=1.84
037: dt: 0.1250, sse=3291507.0, rms=1.76
rms = 1.75, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=3289932.0, rms=1.75
positioning took 5.5 minutes
mean border=71.7, 1829 (15) missing vertices, mean dist 0.0 [0.2 (%48.0)->0.3 (%52.0))]
%65 local maxima, %13 large gradients and %16 min vals, 427 gradients ignored
tol=1.0e-04, host=telen, 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

vertex spacing 0.99 +- 0.41 (0.03-->10.18) (max @ vno 97087 --> 96298)
face area 0.39 +- 0.29 (0.00-->5.49)
writing pial surface to /home/xonobo/FSRFsubjects/bert/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
writing smoothed area to rh.area.pial
vertex spacing 0.99 +- 0.41 (0.03-->10.09) (max @ vno 97087 --> 96298)
face area 0.39 +- 0.29 (0.00-->6.44)
measuring cortical thickness...
000: dt: 0.0000, sse=3287924.0, rms=1.84
rms = 2.02, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=3271016.2, rms=1.74
rms = 1.71, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=3342011.0, rms=1.71
rms = 1.68, time step reduction 3 of 3 to 0.062...
041: dt: 0.1250, sse=3308335.5, rms=1.68
positioning took 3.1 minutes
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/rh.curv.pial
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/rh.area.pial
0 of 132474 vertices processed
25000 of 132474 vertices processed
50000 of 132474 vertices processed
75000 of 132474 vertices processed
100000 of 132474 vertices processed
125000 of 132474 vertices processed
0 of 132474 vertices processed
25000 of 132474 vertices processed
50000 of 132474 vertices processed
75000 of 132474 vertices processed
100000 of 132474 vertices processed
125000 of 132474 vertices processed
thickness calculation complete, 466:606 truncations.
32178 vertices at 0 distance
88738 vertices at 1 distance
81088 vwriting cortical thickness estimate to 'thickness' file.
positioning took 98.0 minutes
ertices at 2 distance
34643 vertices at 3 distance
11269 vertices at 4 distance
3371 vertices at 5 distance
1109 vertices at 6 distance
391 vertices at 7 distance
148 vertices at 8 distance
58 vertices at 9 distance
28 vertices at 10 distance
20 vertices at 11 distance
18 vertices at 12 distance
13 vertices at 13 distance
10 vertices at 14 distance
10 vertices at 15 distance
7 vertices at 16 distance
10 vertices at 17 distance
1 vertices at 18 distance
2 vertices at 19 distance
8 vertices at 20 distance
writing curvature file /home/xonobo/FSRFsubjects/bert/surf/rh.thickness
#--------------------------------------------
#@# Smooth2 rh Tue Apr 10 15:08:09 CEST 2007

 mris_smooth -n 3 -nw ../surf/rh.white ../surf/rh.smoothwm 

/home/xonobo/FSRFsubjects/bert/scripts
smoothing for 3 iterations
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation2 rh Tue Apr 10 15:08:15 CEST 2007
/home/xonobo/FSRFsubjects/bert/scripts

 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated 

avg radius = 49.2 mm, total surface area = 81053 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc
inflation took 1.3 minutes

step 000: RMS=0.166 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.086 (target=0.015)   
step 015: RMS=0.069 (target=0.015)   
step 020: RMS=0.057 (target=0.015)   
step 025: RMS=0.048 (target=0.015)   
step 030: RMS=0.041 (target=0.015)   
step 035: RMS=0.034 (target=0.015)   
step 040: RMS=0.029 (target=0.015)   
step 045: RMS=0.026 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
#--------------------------------------------
#@# Cortical ribbon mask rh Tue Apr 10 15:09:31 CEST 2007
/home/xonobo/FSRFsubjects/bert/mri

 mri_surf2vol --mkmask --hemi rh --fillribbon --template orig.mgz --volregidentity bert --outvol rh.ribbon.mgz 

gdiagno = -1
Using identity matrix for registration
Qa2v: SurfXYZ to VolCRS: ------------------------------
-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;
--------------------------------------------------
subjects dir   /home/xonobo/FSRFsubjects
hemi           rh
mksurfmask     1
projfrac       0
volreg file    (null)
outvol   path  rh.ribbon.mgz
template path  orig.mgz
------- Anat2Vol Registration (TkReg)----
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
-----------------------------------------
height = 256
 width = 256
 depth = 256
 xsize = 1.000000
 ysize = 1.000000
 zsize = 1.000000
  cdc  = -1.000000 0.000000 0.000000
  rdc  = 0.000000 0.000000 -1.000000
  sdc  = 0.000000 1.000000 0.000000
  xyz0 = 5.399719 18.000000 0.000000
Gdiag_no  -1
Reading surface /home/xonobo/FSRFsubjects/bert/surf/rh.white
Done reading source surface
Reading thickness /home/xonobo/FSRFsubjects/bert/surf/rh.thickness
Done
surf nframes = 1
INFO: mapping vertices to closest voxel
INFO: resampling surface to volume at projfrac=0.00, 84699 hits
INFO: resampling surface to volume at projfrac=0.05, 86133 hits
INFO: resampling surface to volume at projfrac=0.10, 87746 hits
INFO: resampling surface to volume at projfrac=0.15, 88613 hits
INFO: resampling surface to volume at projfrac=0.20, 88899 hits
INFO: resampling surface to volume at projfrac=0.25, 88620 hits
INFO: resampling surface to volume at projfrac=0.30, 87931 hits
INFO: resampling surface to volume at projfrac=0.35, 86713 hits
INFO: resampling surface to volume at projfrac=0.40, 85505 hits
INFO: resampling surface to volume at projfrac=0.45, 84326 hits
INFO: resampling surface to volume at projfrac=0.50, 83254 hits
INFO: resampling surface to volume at projfrac=0.55, 82198 hits
INFO: resampling surface to volume at projfrac=0.60, 81301 hits
INFO: resampling surface to volume at projfrac=0.65, 80378 hits
INFO: resampling surface to volume at projfrac=0.70, 79455 hits
INFO: resampling surface to volume at projfrac=0.75, 78627 hits
INFO: resampling surface to volume at projfrac=0.80, 77727 hits
INFO: resampling surface to volume at projfrac=0.85, 76846 hits
INFO: resampling surface to volume at projfrac=0.90, 75938 hits
INFO: resampling surface to volume at projfrac=0.95, 75067 hits
INFO: writing output volume to rh.ribbon.mgz
done

#------------------------------------------

recon-all finished without error at Tue Apr 10 16:23:58 CEST 2007
done
