[jsadinol@cluster mri]$ mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /apps/fs5/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.jeff.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 /apps/fs5/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
average std[0] = 6.9
reading transform from transforms/talairach.m3z...
zcat transforms/talairach.m3z
Atlas used for the 3D morph was /apps/fs5/average/RB_all_2008-03-26.gca
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15151 (27)
mri peak = 0.04304 (109)
CSF peak too bright - rejecting
gca peak = 0.14982 (20)
mri peak = 0.04588 (40)
Right_Lateral_Ventricle (43): linear fit = 1.73 x + 0.0 (1395 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1395 voxels, peak = 34), gca=30.0
gca peak = 0.28003 (97)
mri peak = 0.03878 (102)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (354 voxels, overlap=0.287)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (354 voxels, peak = 99), gca=99.4
gca peak = 0.18160 (96)
mri peak = 0.04933 (35)
Left_Pallidum: unreasonable value (33.6/35.0), not in range [75, 135] - rejecting
gca peak = 0.27536 (62)
mri peak = 0.07903 (92)
Right_Hippocampus (53): linear fit = 1.48 x + 0.0 (890 voxels, overlap=0.000)
Right_Hippocampus (53): linear fit = 1.48 x + 0.0 (890 voxels, peak = 91), gca=91.5
gca peak = 0.32745 (63)
mri peak = 0.12409 (86)
Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (409 voxels, overlap=0.000)
Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (409 voxels, peak = 83), gca=83.5
gca peak = 0.08597 (105)
mri peak = 0.04783 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57056 voxels, overlap=0.529)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57056 voxels, peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.09010 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62874 voxels, overlap=0.593)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62874 voxels, peak = 109), gca=108.6
gca peak = 0.07826 (63)
mri peak = 0.03055 (86)
Left_Cerebral_Cortex (3): linear fit = 1.45 x + 0.0 (35242 voxels, overlap=0.000)
Left_Cerebral_Cortex (3): linear fit = 1.45 x + 0.0 (35242 voxels, peak = 91), gca=91.4
gca peak = 0.08598 (64)
mri peak = 0.03050 (81)
Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (29212 voxels, overlap=0.000)
Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (29212 voxels, peak = 83), gca=83.2
gca peak = 0.24164 (71)
mri peak = 0.07638 (101)
Right_Caudate: unreasonable value (99.4/101.0), not in range [50, 100] - rejecting
gca peak = 0.18227 (75)
mri peak = 0.09212 (107)
Left_Caudate: unreasonable value (99.4/107.0), not in range [50, 100] - rejecting
gca peak = 0.10629 (62)
mri peak = 0.03808 (72)
Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (10844 voxels, overlap=0.029)
Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (10844 voxels, peak = 74), gca=74.4
gca peak = 0.11668 (59)
mri peak = 0.03272 (76)
Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (10784 voxels, overlap=0.001)
Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (10784 voxels, peak = 72), gca=72.3
gca peak = 0.17849 (88)
mri peak = 0.07848 (94)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (2066 voxels, overlap=0.860)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (2066 voxels, peak = 92), gca=92.4
gca peak = 0.16819 (86)
mri peak = 0.10548 (78)
Right_Cerebellum_White_Matter (46): linear fit = 0.90 x + 0.0 (240 voxels, overlap=0.197)
Right_Cerebellum_White_Matter (46): linear fit = 0.90 x + 0.0 (240 voxels, peak = 77), gca=77.4
gca peak = 0.41688 (64)
mri peak = 0.09906 (84)
Left_Amygdala (18): linear fit = 1.30 x + 0.0 (208 voxels, overlap=0.000)
Left_Amygdala (18): linear fit = 1.30 x + 0.0 (208 voxels, peak = 83), gca=83.2
gca peak = 0.42394 (62)
mri peak = 0.15075 (95)
Right_Amygdala: unreasonable value (93.0/95.0), not in range [50, 90] - rejecting
gca peak = 0.10041 (96)
mri peak = 0.08110 (96)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3206 voxels, overlap=0.826)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3206 voxels, peak = 98), gca=98.4
gca peak = 0.13978 (88)
mri peak = 0.03847 (41)
Right_Thalamus_Proper: unreasonable value (88.0/41.0), not in range [75, 120] - rejecting
gca peak = 0.08514 (81)
mri peak = 0.09052 (35)
Left_Putamen: unreasonable value (34.4/35.0), not in range [60, 107] - rejecting
gca peak = 0.09624 (82)
mri peak = 0.04443 (77)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1730 voxels, overlap=0.788)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1730 voxels, peak = 82), gca=82.0
gca peak = 0.07543 (88)
mri peak = 0.04772 (74)
Brain_Stem: unreasonable value (77.0/74.0), not in range [80, 110] - rejecting
gca peak = 0.12757 (95)
mri peak = 0.13617 (95)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1050 voxels, overlap=0.747)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1050 voxels, peak = 97), gca=97.4
gca peak = 0.17004 (92)
mri peak = 0.07614 (97)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (829 voxels, overlap=0.844)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (829 voxels, peak = 94), gca=94.3
gca peak = 0.21361 (36)
mri peak = 0.07754 (41)
gca peak = 0.26069 (23)
mri peak = 1.00000 (67)
CSF peak too bright - rejecting
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Lateral_Ventricle = 0.15151 (27)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak Left_Caudate = 0.18227 (75)
gca peak Left_Putamen = 0.08514 (81)
gca peak Left_Pallidum = 0.18160 (96)
gca peak Third_Ventricle = 0.21361 (36)
gca peak Fourth_Ventricle = 0.26069 (23)
gca peak Brain_Stem = 0.07543 (88)
gca peak CSF = 0.14367 (38)
gca peak Left_Accumbens_area = 0.57033 (70)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65201 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.31129 (32)
gca peak Right_Thalamus_Proper = 0.13978 (88)
gca peak Right_Caudate = 0.24164 (71)
gca peak Right_Amygdala = 0.42394 (62)
gca peak Right_Accumbens_area = 0.30219 (72)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.72939 (42)
gca peak WM_hypointensities = 0.14821 (82)
gca peak non_WM_hypointensities = 0.10354 (53)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
setting label Right_Lateral_Ventricle based on Left_Lateral_Ventricle = 1.50 x +  0
setting label Left_Amygdala based on Right_Amygdala = 1.30 x +  0
setting label Left_Thalamus_Proper based on Right_Thalamus_Proper = 1.02 x +  0
setting label Right_Putamen based on Left_Putamen = 1.00 x +  0
setting label Right_Pallidum based on Left_Pallidum = 1.02 x +  0
estimating mean gm scale to be 1.36 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.50 x + 0.0
saving intensity scales to aseg.auto_noCCseg.jeff.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.12189 (41)
mri peak = 0.04304 (109)
CSF peak too bright - rejecting
gca peak = 0.12264 (30)
mri peak = 0.04588 (40)
Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (1395 voxels, overlap=0.218)
Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (1395 voxels, peak = 34), gca=34.5
gca peak = 0.30362 (100)
mri peak = 0.03878 (102)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (354 voxels, overlap=0.284)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (354 voxels, peak = 100), gca=100.0
gca peak = 0.16158 (98)
mri peak = 0.04933 (35)
Left_Pallidum: unreasonable value (31.8/35.0), not in range [75, 135] - rejecting
gca peak = 0.19709 (92)
mri peak = 0.07903 (92)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (890 voxels, overlap=0.812)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (890 voxels, peak = 92), gca=92.0
gca peak = 0.21659 (83)
mri peak = 0.12409 (86)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (409 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (409 voxels, peak = 81), gca=80.9
gca peak = 0.08345 (108)
mri peak = 0.04783 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57056 voxels, overlap=0.565)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57056 voxels, peak = 108), gca=108.0
gca peak = 0.08488 (108)
mri peak = 0.09010 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (62874 voxels, overlap=0.626)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (62874 voxels, peak = 108), gca=108.0
gca peak = 0.05407 (91)
mri peak = 0.03055 (86)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (35242 voxels, overlap=0.200)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (35242 voxels, peak = 91), gca=91.0
gca peak = 0.06771 (82)
mri peak = 0.03050 (81)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29212 voxels, overlap=0.491)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29212 voxels, peak = 82), gca=82.0
gca peak = 0.22598 (100)
mri peak = 0.07638 (101)
Right_Caudate: unreasonable value (102.5/101.0), not in range [50, 100] - rejecting
gca peak = 0.12960 (101)
mri peak = 0.09212 (107)
Left_Caudate: unreasonable value (98.5/107.0), not in range [50, 100] - rejecting
gca peak = 0.08741 (73)
mri peak = 0.03808 (72)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10844 voxels, overlap=0.888)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (10844 voxels, peak = 73), gca=73.0
gca peak = 0.11030 (73)
mri peak = 0.03272 (76)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10784 voxels, overlap=0.754)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10784 voxels, peak = 75), gca=74.8
gca peak = 0.16855 (92)
mri peak = 0.07848 (94)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2066 voxels, overlap=0.984)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2066 voxels, peak = 92), gca=92.0
gca peak = 0.20184 (78)
mri peak = 0.10548 (78)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (240 voxels, overlap=0.783)
Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (240 voxels, peak = 76), gca=76.1
gca peak = 0.29647 (83)
mri peak = 0.09906 (84)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (208 voxels, overlap=0.968)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (208 voxels, peak = 83), gca=83.0
gca peak = 0.37659 (81)
mri peak = 0.15075 (95)
Right_Amygdala: unreasonable value (95.2/95.0), not in range [50, 90] - rejecting
gca peak = 0.10923 (98)
mri peak = 0.08110 (96)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3206 voxels, overlap=0.843)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3206 voxels, peak = 98), gca=98.0
gca peak = 0.12570 (90)
mri peak = 0.03847 (41)
Right_Thalamus_Proper: unreasonable value (87.8/41.0), not in range [75, 120] - rejecting
gca peak = 0.08404 (81)
mri peak = 0.09052 (35)
Left_Putamen: unreasonable value (34.4/35.0), not in range [60, 107] - rejecting
gca peak = 0.10040 (76)
mri peak = 0.04443 (77)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1730 voxels, overlap=0.790)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1730 voxels, peak = 76), gca=76.0
gca peak = 0.06766 (87)
mri peak = 0.04772 (74)
Brain_Stem: unreasonable value (74.0/74.0), not in range [80, 110] - rejecting
gca peak = 0.14457 (97)
mri peak = 0.13617 (95)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1050 voxels, overlap=0.801)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1050 voxels, peak = 97), gca=97.0
gca peak = 0.15815 (95)
mri peak = 0.07614 (97)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (829 voxels, overlap=0.888)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (829 voxels, peak = 95), gca=95.0
gca peak = 0.13658 (54)
mri peak = 0.07754 (41)
gca peak = 0.13883 (35)
mri peak = 1.00000 (67)
CSF peak too bright - rejecting
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Lateral_Ventricle = 0.12189 (41)
gca peak Left_Inf_Lat_Vent = 0.20578 (47)
gca peak Left_Caudate = 0.12960 (101)
gca peak Left_Putamen = 0.08404 (81)
gca peak Left_Pallidum = 0.16158 (98)
gca peak Third_Ventricle = 0.13658 (54)
gca peak Fourth_Ventricle = 0.13883 (35)
gca peak Brain_Stem = 0.06766 (87)
gca peak CSF = 0.24587 (58)
gca peak Left_Accumbens_area = 0.35149 (95)
gca peak Left_undetermined = 0.95107 (47)
gca peak Left_vessel = 0.63638 (62)
gca peak Left_choroid_plexus = 0.12525 (48)
gca peak Right_Inf_Lat_Vent = 0.26826 (47)
gca peak Right_Thalamus_Proper = 0.12570 (90)
gca peak Right_Caudate = 0.22598 (100)
gca peak Right_Amygdala = 0.37659 (81)
gca peak Right_Accumbens_area = 0.30079 (98)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.13245 (46)
gca peak Fifth_Ventricle = 0.45827 (62)
gca peak WM_hypointensities = 0.13959 (84)
gca peak non_WM_hypointensities = 0.11940 (54)
gca peak Optic_Chiasm = 0.38324 (75)
not using caudate to estimate GM means
setting label Right_Lateral_Ventricle based on Left_Lateral_Ventricle = 1.15 x +  0
setting label Left_Amygdala based on Right_Amygdala = 1.00 x +  0
setting label Left_Thalamus_Proper based on Right_Thalamus_Proper = 1.00 x +  0
setting label Right_Putamen based on Left_Putamen = 1.00 x +  0
setting label Right_Pallidum based on Left_Pallidum = 1.00 x +  0
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.15 x + 0.0
saving intensity scales to aseg.auto_noCCseg.jeff.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.jeff.label_intensities.txt
57643 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
739 hippocampal voxels changed.
21 amygdala voxels changed.
pass 1: 75074 changed. image ll: -2.461, PF=1.000
pass 2: 16374 changed. image ll: -2.458, PF=1.000
pass 3: 6352 changed.
pass 4: 2881 changed.
writing labeled volume to aseg.auto_noCCseg.jeff.mgz...
auto-labeling took 46 minutes and 12 seconds.