Hi, there

I have a 3T MPRAGE subject which fails at the mri_ca_label step, the recon-all.log is pasted below,
Any suggestions to fix this error?

Thanks a lot!
Guang

mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/biotools/freesurfer/freesurfer-v4.5.0/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 /usr/local/biotools/freesurfer/freesurfer-v4.5.0/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 /usr/local/biotools/freesurfer/freesurfer-v4.5.0/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 = 0.20145 (24)
Left_Lateral_Ventricle (4): linear fit = 0.85 x + 0.0 (15451 voxels, overlap=0.608)
Left_Lateral_Ventricle (4): linear fit = 0.85 x + 0.0 (15451 voxels, peak = 23), gca=23.0
gca peak = 0.14982 (20)
mri peak = 0.18345 (24)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (13803 voxels, overlap=0.564)
Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (13803 voxels, peak = 20), gca=20.5
gca peak = 0.28003 (97)
mri peak = 0.12841 (110)
Right_Pallidum (52): linear fit = 1.12 x + 0.0 (445 voxels, overlap=0.000)
Right_Pallidum (52): linear fit = 1.12 x + 0.0 (445 voxels, peak = 109), gca=109.1
gca peak = 0.18160 (96)
mri peak = 0.13582 (111)
Left_Pallidum (13): linear fit = 1.15 x + 0.0 (451 voxels, overlap=0.004)
Left_Pallidum (13): linear fit = 1.15 x + 0.0 (451 voxels, peak = 110), gca=110.4
gca peak = 0.27536 (62)
mri peak = 0.07207 (76)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1453 voxels, overlap=0.164)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1453 voxels, peak = 71), gca=71.3
gca peak = 0.32745 (63)
mri peak = 0.08789 (75)
Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (1469 voxels, overlap=0.000)
Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (1469 voxels, peak = 72), gca=72.4
gca peak = 0.08597 (105)
mri peak = 0.08672 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29417 voxels, overlap=0.653)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29417 voxels, peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.08520 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (36362 voxels, overlap=0.554)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (36362 voxels, peak = 111), gca=111.3
gca peak = 0.07826 (63)
mri peak = 0.02796 (76)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (68673 voxels, overlap=0.031)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (68673 voxels, peak = 76), gca=75.6
gca peak = 0.08598 (64)
mri peak = 0.02607 (77)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (68179 voxels, overlap=0.006)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (68179 voxels, peak = 77), gca=76.8
gca peak = 0.24164 (71)
mri peak = 0.09815 (87)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (1249 voxels, overlap=0.000)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (1249 voxels, peak = 85), gca=85.2
gca peak = 0.18227 (75)
mri peak = 0.08068 (84)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (1061 voxels, overlap=0.509)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (1061 voxels, peak = 81), gca=80.6
gca peak = 0.10629 (62)
mri peak = 0.05013 (71)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (36025 voxels, overlap=0.446)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (36025 voxels, peak = 71), gca=71.3
gca peak = 0.11668 (59)
mri peak = 0.05257 (70)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (36255 voxels, overlap=0.425)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (36255 voxels, peak = 68), gca=67.8
gca peak = 0.17849 (88)
mri peak = 0.09129 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6702 voxels, overlap=0.720)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (6702 voxels, peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.09287 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5941 voxels, overlap=0.422)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5941 voxels, peak = 95), gca=94.6
gca peak = 0.41688 (64)
mri peak = 0.08561 (83)
Left_Amygdala (18): linear fit = 1.27 x + 0.0 (553 voxels, overlap=0.000)
Left_Amygdala (18): linear fit = 1.27 x + 0.0 (553 voxels, peak = 82), gca=81.6
gca peak = 0.42394 (62)
mri peak = 0.10507 (82)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (492 voxels, overlap=0.000)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (492 voxels, peak = 81), gca=80.6
gca peak = 0.10041 (96)
mri peak = 0.06936 (96)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5098 voxels, overlap=0.799)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5098 voxels, peak = 101), gca=100.8
gca peak = 0.13978 (88)
mri peak = 0.05876 (102)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4698 voxels, overlap=0.529)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4698 voxels, peak = 97), gca=96.8
gca peak = 0.08514 (81)
mri peak = 0.09350 (92)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (1465 voxels, overlap=0.545)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (1465 voxels, peak = 87), gca=87.1
gca peak = 0.09624 (82)
mri peak = 0.16556 (90)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (1124 voxels, overlap=0.363)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (1124 voxels, peak = 90), gca=90.2
gca peak = 0.07543 (88)
mri peak = 0.05860 (97)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (12206 voxels, overlap=0.421)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (12206 voxels, peak = 99), gca=99.0
gca peak = 0.12757 (95)
mri peak = 0.06982 (110)
Right_VentralDC: unreasonable value (111.6/110.0), not in range [80, 110] - rejecting
gca peak = 0.17004 (92)
mri peak = 0.08107 (112)
Left_VentralDC: unreasonable value (108.1/112.0), not in range [80, 110] - rejecting
gca peak = 0.21361 (36)
mri peak = 0.18754 (25)
Third_Ventricle (14): linear fit = 0.80 x + 0.0 (503 voxels, overlap=0.115)
Third_Ventricle (14): linear fit = 0.80 x + 0.0 (503 voxels, peak = 29), gca=28.8
gca peak = 0.26069 (23)
mri peak = 0.11881 (24)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (463 voxels, overlap=0.723)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (463 voxels, peak = 20), gca=20.1
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 1.21 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.89 x + 0.0
Left_Pallidum too bright - rescaling by 0.942 (from 1.150) to 104.0 (was 110.4)
Right_Pallidum too bright - rescaling by 0.953 (from 1.125) to 104.0 (was 109.1)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.17125 (23)
mri peak = 0.20145 (24)
Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (15451 voxels, overlap=0.669)
Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (15451 voxels, peak = 23), gca=23.0
gca peak = 0.19382 (21)
mri peak = 0.18345 (24)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (13803 voxels, overlap=0.577)
Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (13803 voxels, peak = 21), gca=21.0
gca peak = 0.22474 (104)
mri peak = 0.12841 (110)
Right_Pallidum (52): linear fit = 1.05 x + 0.0 (445 voxels, overlap=0.749)
Right_Pallidum (52): linear fit = 1.05 x + 0.0 (445 voxels, peak = 109), gca=109.2
gca peak = 0.18148 (104)
mri peak = 0.13582 (111)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (451 voxels, overlap=0.768)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (451 voxels, peak = 107), gca=106.6
gca peak = 0.24928 (71)
mri peak = 0.07207 (76)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1453 voxels, overlap=0.785)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1453 voxels, peak = 71), gca=71.0
gca peak = 0.25085 (72)
mri peak = 0.08789 (75)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1469 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1469 voxels, peak = 70), gca=70.2
gca peak = 0.08354 (108)
mri peak = 0.08672 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29417 voxels, overlap=0.739)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29417 voxels, peak = 108), gca=108.0
gca peak = 0.08793 (111)
mri peak = 0.08520 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (36362 voxels, overlap=0.718)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (36362 voxels, peak = 111), gca=111.0
gca peak = 0.06468 (76)
mri peak = 0.02796 (76)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (68673 voxels, overlap=0.222)
Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (68673 voxels, peak = 74), gca=74.1
gca peak = 0.07358 (76)
mri peak = 0.02607 (77)
Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (68179 voxels, overlap=0.207)
Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (68179 voxels, peak = 74), gca=74.1
gca peak = 0.23743 (85)
mri peak = 0.09815 (87)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (1249 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 0.98 x + 0.0 (1249 voxels, peak = 83), gca=82.9
gca peak = 0.16079 (80)
mri peak = 0.08068 (84)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1061 voxels, overlap=0.832)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1061 voxels, peak = 80), gca=80.0
gca peak = 0.09121 (70)
mri peak = 0.05013 (71)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36025 voxels, overlap=0.968)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36025 voxels, peak = 70), gca=70.0
gca peak = 0.10783 (68)
mri peak = 0.05257 (70)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36255 voxels, overlap=0.955)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36255 voxels, peak = 68), gca=68.0
gca peak = 0.17131 (94)
mri peak = 0.09129 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6702 voxels, overlap=0.990)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6702 voxels, peak = 94), gca=94.0
gca peak = 0.15537 (95)
mri peak = 0.09287 (95)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5941 voxels, overlap=0.995)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5941 voxels, peak = 95), gca=95.0
gca peak = 0.30366 (81)
mri peak = 0.08561 (83)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (553 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (553 voxels, peak = 81), gca=81.0
gca peak = 0.36454 (81)
mri peak = 0.10507 (82)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (492 voxels, overlap=0.776)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (492 voxels, peak = 81), gca=81.0
gca peak = 0.10118 (99)
mri peak = 0.06936 (96)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5098 voxels, overlap=0.924)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5098 voxels, peak = 99), gca=99.0
gca peak = 0.09695 (97)
mri peak = 0.05876 (102)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4698 voxels, overlap=0.892)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4698 voxels, peak = 99), gca=99.4
gca peak = 0.08397 (87)
mri peak = 0.09350 (92)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1465 voxels, overlap=0.855)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1465 voxels, peak = 87), gca=87.0
gca peak = 0.08263 (85)
mri peak = 0.16556 (90)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1124 voxels, overlap=0.741)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1124 voxels, peak = 85), gca=85.0
gca peak = 0.07503 (99)
mri peak = 0.05860 (97)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12206 voxels, overlap=0.801)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12206 voxels, peak = 99), gca=99.0
gca peak = 0.11812 (95)
mri peak = 0.06982 (110)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1457 voxels, overlap=0.011)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1457 voxels, peak = 109), gca=109.2
gca peak = 0.15960 (92)
mri peak = 0.08107 (112)
Left_VentralDC: unreasonable value (105.8/112.0), not in range [80, 110] - rejecting
gca peak = 0.20402 (30)
mri peak = 0.18754 (25)
Third_Ventricle (14): linear fit = 0.98 x + 0.0 (503 voxels, overlap=0.845)
Third_Ventricle (14): linear fit = 0.98 x + 0.0 (503 voxels, peak = 29), gca=29.2
gca peak = 0.24174 (20)
mri peak = 0.11881 (24)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (463 voxels, overlap=0.882)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (463 voxels, peak = 20), gca=20.5
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18244 (40)
gca peak CSF = 0.17923 (34)
gca peak Left_Accumbens_area = 0.46662 (75)
gca peak Left_VentralDC = 0.15960 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.63638 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.19452 (37)
gca peak Right_Accumbens_area = 0.27742 (86)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.82185 (37)
gca peak WM_hypointensities = 0.14997 (85)
gca peak non_WM_hypointensities = 0.10331 (55)
gca peak Optic_Chiasm = 0.34851 (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 1.00 x + 0.0
Left_Pallidum too bright - rescaling by 0.976 (from 1.025) to 104.0 (was 106.6)
Right_Pallidum too bright - rescaling by 0.953 (from 1.050) to 104.0 (was 109.2)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
Linux dnode80.mayo.edu 2.6.18-164.11.1.el5 #1 SMP Wed Jan 20 07:32:21 EST 2010 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Thu Apr 15 22:46:04 CDT 2010

---

The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy.