Hi Bruce,
Yes this is within recon-all. I have also tried it as a stand alone command
but it stops at the same place, i.e. when the function outputs the following
statement: 'saving intensity scales to
aseg.auto_noCCseg.label_intensities.txt'. The file 'aseg.auto_noCCseg.mgz'
is not saved but the file 'aseg.auto_noCCseg.label_intensities.txt' is.
Yes, it is writeable and there is enough disk space. The only error
messages I get refer to the functions not finding the relevant files as
they were not saved. I have attached the log below:
#--------------------------------------
#@# SubCort Seg Mon Feb 18 19:02:14 GMT 2013
mri_ca_label -align -nobigventricles norm.mgz
transforms/talairach.m3z/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.gca
aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes...
reading classifier array
from/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)
mri_ca_label GCA sequential renormalization: label 28 not consistently
computed.
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
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz PREDEP40C_fsf
reading input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
mri_cc: could not read aseg volume
from/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.auto
_noCCseg.mgz
reading aseg
from/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.auto
_noCCseg.mgz
ERROR: cannot
find/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.auto
_noCCseg.mgz
No such file or directory
#--------------------------------------
#@# Merge ASeg Mon Feb 18 19:22:10 GMT 2013
cp aseg.auto.mgz aseg.mgz
cp: cannot stat `aseg.auto.mgz': No such file or directory
#--------------------------------------------
#@# Intensity Normalization2 Mon Feb 18 19:22:10 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization
reading from norm.mgz...
mri_normalize: could not read aseg from file aseg.mgz
using MR volume brainmask.mgz to mask input volume...
ERROR: cannot find
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.mgz
No such file or directory
#--------------------------------------------
#@# Mask BFS Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
mri_mask: could not read source volume brain.mgz
ERROR: cannot
find/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain.mgz
No such file or directory
#--------------------------------------------
#@# WM Segmentation Mon Feb 18 19:22:11 GMT 2013
mri_segment brain.mgz wm.seg.mgz
mri_segment: could not read source volume from brain.mgz
ERROR: cannot
find/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain.mgz
No such file or directory
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume...
mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz
reading wm segmentation from wm.seg.mgz...
ERROR: cannot
find/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.seg.mg
z
No such file or directory
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
mri_pretess: could not open wm.asegedit.mgz
ERROR: cannot
find/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.aseged
it.mgz
No such file or directory
#--------------------------------------------
#@# Fill Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...mri_fill: could not read wm.mgz
ERROR: cannot find
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.mgz
No such file or directory
#--------------------------------------------
#@# Tessellate lh Mon Feb 18 19:22:11 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz
../mri/filled-pretess255.mgz
mri_pretess: could not open ../mri/filled.mgz
ERROR: cannot find ../mri/filled.mgz
No such file or directory
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
could not open ../mri/filled-pretess255.mgz
ERROR: cannot find ../mri/filled-pretess255.mgz
No such file or directory
rm -f ../mri/filled-pretess255.mgz
?
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
Segmentation fault
#--------------------------------------------
#@# Smooth1 lh Mon Feb 18 19:22:12 GMT 2013
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
setting seed for random number generator to 1234
MRISread(../surf/lh.orig.nofix): could not open file
No such file or directory
mris_smooth: could not read surface file ../surf/lh.orig.nofix
No such file or directory
#--------------------------------------------
#@# Inflation1 lh Mon Feb 18 19:22:12 GMT 2013
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix
../surf/lh.inflated.nofix
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
MRISread(../surf/lh.smoothwm.nofix): could not open file
Not saving sulc
No such file or directory
mris_inflate: could not read surface file ../surf/lh.smoothwm.nofix
No such file or directory
#--------------------------------------------
#@# QSphere lh Mon Feb 18 19:22:12 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(../surf/lh.inflated.nofix): could not open file
No such file or directory
mris_sphere: could not read surface file ../surf/lh.inflated.nofix
No such file or directory
#--------------------------------------------
#@# Fix Topology lh Mon Feb 18 19:22:12 GMT 2013
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp: cannot stat `../surf/lh.orig.nofix': No such file or directory
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
cp: cannot stat `../surf/lh.inflated.nofix': No such file or directory
/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 PREDEP40C_fsf lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $
$Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
MRISread(/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf
/lh.qsphere.nofix): could not open file
reading input
surface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/lh.qsphe
re.nofix...
No such file or directory
mris_fix_topology: could not read input
surface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/lh.qsphe
re.nofix
No such file or directory
mris_euler_number ../surf/lh.orig
Linux ioplnx5.iop.kcl.ac.uk 2.6.32-279.19.1.el6.x86_64 #1 SMP Tue Dec 18
17:22:54 CST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013
> Date: Tue, 19 Feb 2013 16:35:50 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: horton_p...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_ca_label problem
>
> Hi Paul
>
> is this within recon-all? Does that file exist? Can you check its
> permissions to make sure it is writeable? And that you have enough disk
> space? Are any error messages printed?
> Bruce
>
>
> On Tue, 19 Feb 2013, paul horton wrote:
>
> > 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
arrayfrom/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
morphwas/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
> >
> >
> >
> >
>
>
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