Hi guys,
I am wondering if you can help me.
I have run command: mri_ca_label -align -nobigventricles norm.mgz
transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca
aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails: i.e. it stops
after the 'saving intensity scales to
aseg.auto_noCCseg.label_intensities.txt' line and does not save the file:
aseg.auto_noCCseg.mgz. However, it does save the file:
aseg.auto_noCCseg.label_intensities.txt. I have tried
it several times and it stops at the same place. I have also tried
recon-all, where it jumps from
'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' to the
command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz', where, again,
the file: aseg.auto_noCCseg.mgz is not saved. I am using freesurfer version
4.5.0.
So is there a way I can solve this problem.
Many Thanks
Paul
Ps, i have attached the output log below
################
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/software/system/freesurfer/freesurfer-4.5.0//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/software/system/freesurfer/freesurfer-4.5.0//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 = 0.15062 (23)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels,
overlap=0.484)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak =
22), gca=22.3
gca peak = 0.14982 (20)
mri peak = 0.16025 (24)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels,
overlap=0.766)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, peak =
20), gca=20.5
gca peak = 0.28003 (97)
mri peak = 0.11295 (106)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, overlap=0.353)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104),
gca=104.3
gca peak = 0.18160 (96)
mri peak = 0.12433 (104)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, overlap=0.638)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101),
gca=100.8
gca peak = 0.27536 (62)
mri peak = 0.08252 (69)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels,
overlap=0.818)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak = 68),
gca=68.2
gca peak = 0.32745 (63)
mri peak = 0.07934 (66)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels,
overlap=1.000)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak = 65),
gca=64.6
gca peak = 0.08597 (105)
mri peak = 0.06861 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels,
overlap=0.744)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels,
peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.07113 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
overlap=0.820)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
peak = 106), gca=106.0
gca peak = 0.07826 (63)
mri peak = 0.02785 (72)
Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels,
overlap=0.547)
Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak =
71), gca=70.9
gca peak = 0.08598 (64)
mri peak = 0.02894 (68)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
overlap=0.642)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, peak =
69), gca=68.8
gca peak = 0.24164 (71)
mri peak = 0.13663 (85)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, overlap=0.000)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82),
gca=81.7
gca peak = 0.18227 (75)
mri peak = 0.14739 (80)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, overlap=0.988)
Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77),
gca=76.9
gca peak = 0.10629 (62)
mri peak = 0.05203 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
overlap=0.948)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak =
64), gca=63.5
gca peak = 0.11668 (59)
mri peak = 0.05041 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels,
overlap=0.926)
Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, peak
= 63), gca=63.4
gca peak = 0.17849 (88)
mri peak = 0.09573 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels,
overlap=0.601)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels,
peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.10076 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels,
overlap=0.590)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels,
peak = 92), gca=92.5
gca peak = 0.41688 (64)
mri peak = 0.07820 (67)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66),
gca=65.6
gca peak = 0.42394 (62)
mri peak = 0.10919 (71)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, overlap=0.434)
Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70),
gca=69.8
gca peak = 0.10041 (96)
mri peak = 0.07146 (97)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels,
overlap=0.910)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak =
98), gca=98.4
gca peak = 0.13978 (88)
mri peak = 0.06159 (103)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels,
overlap=0.376)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak =
99), gca=99.0
gca peak = 0.08514 (81)
mri peak = 0.06222 (85)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81),
gca=81.0
gca peak = 0.09624 (82)
mri peak = 0.09383 (84)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, overlap=0.815)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84),
gca=84.0
gca peak = 0.07543 (88)
mri peak = 0.05306 (86)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92),
gca=92.4
gca peak = 0.12757 (95)
mri peak = 0.05862 (107)
Right_VentralDC: unreasonable value (111.6/107.0), not in range [80, 110] -
rejecting
gca peak = 0.17004 (92)
mri peak = 0.06574 (111)
Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] -
rejecting
gca peak = 0.21361 (36)
mri peak = 0.12619 (24)
Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, overlap=0.000)
Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25),
gca=25.2
gca peak = 0.26069 (23)
mri peak = 0.16285 (24)
Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, overlap=0.640)
Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak = 21),
gca=20.7
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak CSF = 0.14367 (38)
gca peak Left_Accumbens_area = 0.57033 (70)
gca peak Left_VentralDC = 0.17004 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65201 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.31129 (32)
gca peak Right_Accumbens_area = 0.30219 (72)
gca peak Right_VentralDC = 0.12757 (95)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.72939 (42)
gca peak WM_hypointensities = 0.14821 (82)
gca peak non_WM_hypointensities = 0.10354 (53)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.08 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 0.86 x + 0.0
Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was
100.8)
Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5 (was
104.3)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.14515 (23)
mri peak = 0.15062 (23)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels,
overlap=0.897)
Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak =
24), gca=23.6
gca peak = 0.19392 (21)
mri peak = 0.16025 (24)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels,
overlap=0.745)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, peak =
21), gca=21.0
gca peak = 0.25607 (102)
mri peak = 0.11295 (106)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, overlap=1.000)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105),
gca=104.5
gca peak = 0.17462 (103)
mri peak = 0.12433 (104)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, overlap=0.999)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103),
gca=103.0
gca peak = 0.24759 (68)
mri peak = 0.08252 (69)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels,
overlap=0.999)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak = 68),
gca=68.0
gca peak = 0.28061 (65)
mri peak = 0.07934 (66)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels,
overlap=0.999)
Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak = 62),
gca=61.8
gca peak = 0.08360 (108)
mri peak = 0.06861 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels,
overlap=0.831)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels,
peak = 108), gca=108.0
gca peak = 0.09206 (106)
mri peak = 0.07113 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
overlap=0.820)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
peak = 106), gca=106.0
gca peak = 0.06916 (71)
mri peak = 0.02785 (72)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels,
overlap=0.733)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak =
69), gca=69.2
gca peak = 0.08227 (69)
mri peak = 0.02894 (68)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
overlap=0.734)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, peak =
69), gca=69.0
gca peak = 0.22329 (81)
mri peak = 0.13663 (85)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81),
gca=81.0
gca peak = 0.18180 (77)
mri peak = 0.14739 (80)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, overlap=0.937)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77),
gca=77.0
gca peak = 0.10419 (63)
mri peak = 0.05203 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
overlap=0.982)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak =
65), gca=64.6
gca peak = 0.12084 (64)
mri peak = 0.05041 (65)
Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels,
overlap=0.985)
Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, peak
= 62), gca=62.4
gca peak = 0.17137 (94)
mri peak = 0.09573 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels,
overlap=0.978)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels,
peak = 94), gca=94.0
gca peak = 0.15715 (93)
mri peak = 0.10076 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels,
overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels,
peak = 93), gca=93.0
gca peak = 0.32238 (65)
mri peak = 0.07820 (67)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65),
gca=65.0
gca peak = 0.49832 (70)
mri peak = 0.10919 (71)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, overlap=1.000)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70),
gca=70.0
gca peak = 0.10606 (98)
mri peak = 0.07146 (97)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels,
overlap=0.901)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak =
98), gca=98.0
gca peak = 0.12505 (99)
mri peak = 0.06159 (103)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels,
overlap=0.961)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak =
99), gca=99.0
gca peak = 0.08514 (81)
mri peak = 0.06222 (85)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81),
gca=81.0
gca peak = 0.09838 (78)
mri peak = 0.09383 (84)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, overlap=0.982)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78),
gca=78.0
gca peak = 0.07177 (90)
mri peak = 0.05306 (86)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92),
gca=92.2
gca peak = 0.13316 (95)
mri peak = 0.05862 (107)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, overlap=0.010)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak = 109),
gca=109.2
gca peak = 0.16834 (92)
mri peak = 0.06574 (111)
Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] -
rejecting
gca peak = 0.25342 (25)
mri peak = 0.12619 (24)
Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, overlap=0.998)
Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25),
gca=25.0
gca peak = 0.20850 (21)
mri peak = 0.16285 (24)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, overlap=0.808)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak = 22),
gca=21.5
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.26363 (36)
gca peak CSF = 0.17919 (33)
gca peak Left_Accumbens_area = 0.40223 (72)
gca peak Left_VentralDC = 0.16834 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.63670 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.29122 (35)
gca peak Right_Accumbens_area = 0.25605 (83)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.81716 (36)
gca peak WM_hypointensities = 0.15216 (83)
gca peak non_WM_hypointensities = 0.09346 (54)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.01 x + 0.0
Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was
103.0)
Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6 (was
104.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
