Hello, Nick,

I see, thanks!

But what is the correct way to install it.
What I did is I rename the old one as mri_ca_label.old, and then copy the new one to the freesurfer bin folder.

Thanks!
Guang

> Subject: RE: [Freesurfer] a 3T MPRAGE subject fails at mri_ca_label
> From: nicks@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Date: Thu, 22 Apr 2010 15:10:58 -0400
>
> i dont think the newer mri_ca_label was installed properly. it should
> have the following -all-info output:
>
> ProgramName: mri_ca_label ProgramArguments: --all-info ProgramVersion:
> $Name: stable4 $ TimeStamp: 2010/04/22-19:08:18-GMT BuildTimeStamp:
> Nov 24 2009 04:00:54 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30
> 23:22:53 nicks Exp $ User: nicks Machine: terrier Platform: Linux
> PlatformVersion: 2.6.18-164.el5 CompilerName: GCC CompilerVersion:
> 30400
>
> the critical info being 'BuildTimeStamp', which should be 'Nov 24 2009'
>
>
> n.
>
>
> On Thu, 2010-04-22 at 13:36 -0500, Guang Zeng wrote:
> > Hello, Nick,
> >
> > The mri_ca_label --all-info result is:
> >
> > ProgramName: mri_ca_label ProgramArguments: --all-info
> > ProgramVersion: $Name: stable4 $ TimeStamp: 2010/04/22-18:30:38-GMT
> > BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_label.c,v
> > 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: m047599 Machine:
> > dnode33.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5
> > CompilerName: GCC CompilerVersion: 30400
> >
> > Thanks!
> > Guang
> >
> > > Subject: RE: [Freesurfer] a 3T MPRAGE subject fails at mri_ca_label
> > > From: nicks@nmr.mgh.harvard.edu
> > > To: freesurfer_zg@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Date: Thu, 22 Apr 2010 14:30:09 -0400
> > >
> > > what is the output of
> > >
> > > mri_ca_label --all-info
> > >
> > >
> > >
> > > On Thu, 2010-04-22 at 09:29 -0500, Guang Zeng wrote:
> > > > Hello, Nick,
> > > >
> > > > Thanks a lot for your help. I downloaded the new version for the
> > > > website, and reran the subject again.
> > > > It failed at the same place, it looks like the new version does
> > not
> > > > work for my case.
> > > >
> > > > Thanks!
> > > > Guang
> > > >
> > > > mri_ca_label -align -nobigventricles norm.mgz
> > > >
> > transforms/talairach.m3z /data1/radiology/m047599/temp_fs_2/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 /data1/radiology/m047599/temp_fs_2/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 /data1/radiology/m047599/temp_fs_2/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 = 0.19455 (22)
> > > > Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (14935
> > voxels,
> > > > overlap=0.730)
> > > > Left_Lateral_Ventricle (4): linear fit = 0.90 x + 0.0 (14935
> > voxels,
> > > > peak = 24), gca=24.3
> > > > gca peak = 0.14982 (20)
> > > > mri peak = 0.17994 (24)
> > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (13315
> > voxels,
> > > > overlap=0.564)
> > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (13315
> > voxels,
> > > > peak = 20), gca=20.5
> > > > gca peak = 0.28003 (97)
> > > > mri peak = 0.16459 (110)
> > > > Right_Pallidum (52): linear fit = 1.12 x + 0.0 (393 voxels,
> > > > overlap=0.000)
> > > > Right_Pallidum (52): linear fit = 1.12 x + 0.0 (393 voxels, peak =
> > > > 109), gca=109.1
> > > > gca peak = 0.18160 (96)
> > > > mri peak = 0.15057 (110)
> > > > Left_Pallidum (13): linear fit = 1.10 x + 0.0 (454 voxels,
> > > > overlap=0.069)
> > > > Left_Pallidum (13): linear fit = 1.10 x + 0.0 (454 voxels, peak =
> > > > 106), gca=105.6
> > > > gca peak = 0.27536 (62)
> > > > mri peak = 0.07277 (75)
> > > > Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1544 voxels,
> > > > overlap=0.140)
> > > > Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (1544 voxels,
> > peak =
> > > > 70), gca=69.8
> > > > gca peak = 0.32745 (63)
> > > > mri peak = 0.09303 (75)
> > > > Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (1519 voxels,
> > > > overlap=0.181)
> > > > Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (1519 voxels,
> > peak =
> > > > 74), gca=74.0
> > > > gca peak = 0.08597 (105)
> > > > mri peak = 0.08247 (106)
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (28258
> > > > voxels, overlap=0.656)
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (28258
> > > > voxels, peak = 108), gca=107.6
> > > > gca peak = 0.09209 (106)
> > > > mri peak = 0.07428 (109)
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (34792
> > > > voxels, overlap=0.661)
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (34792
> > > > voxels, peak = 109), gca=108.6
> > > > gca peak = 0.07826 (63)
> > > > mri peak = 0.02775 (74)
> > > > Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (69386 voxels,
> > > > overlap=0.031)
> > > > Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (69386 voxels,
> > > > peak = 76), gca=75.6
> > > > gca peak = 0.08598 (64)
> > > > mri peak = 0.02662 (74)
> > > > Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (69439
> > voxels,
> > > > overlap=0.015)
> > > > Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (69439
> > voxels,
> > > > peak = 78), gca=78.4
> > > > gca peak = 0.24164 (71)
> > > > mri peak = 0.09277 (84)
> > > > Right_Caudate (50): linear fit = 1.17 x + 0.0 (1505 voxels,
> > > > overlap=0.000)
> > > > Right_Caudate (50): linear fit = 1.17 x + 0.0 (1505 voxels, peak =
> > > > 83), gca=83.4
> > > > gca peak = 0.18227 (75)
> > > > mri peak = 0.10121 (86)
> > > > Left_Caudate (11): linear fit = 1.05 x + 0.0 (1290 voxels,
> > > > overlap=0.481)
> > > > Left_Caudate (11): linear fit = 1.05 x + 0.0 (1290 voxels, peak =
> > 79),
> > > > gca=78.8
> > > > gca peak = 0.10629 (62)
> > > > mri peak = 0.05510 (72)
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (35554
> > voxels,
> > > > overlap=0.245)
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (35554
> > voxels,
> > > > peak = 74), gca=74.4
> > > > gca peak = 0.11668 (59)
> > > > mri peak = 0.04765 (71)
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (36178
> > voxels,
> > > > overlap=0.425)
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (36178
> > voxels,
> > > > peak = 68), gca=67.8
> > > > gca peak = 0.17849 (88)
> > > > mri peak = 0.10359 (97)
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5829
> > > > voxels, overlap=0.251)
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (5829
> > > > voxels, peak = 97), gca=96.8
> > > > gca peak = 0.16819 (86)
> > > > mri peak = 0.08973 (95)
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0
> > (5682
> > > > voxels, overlap=0.276)
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0
> > (5682
> > > > voxels, peak = 95), gca=94.6
> > > > gca peak = 0.41688 (64)
> > > > mri peak = 0.08920 (76)
> > > > Left_Amygdala (18): linear fit = 1.23 x + 0.0 (565 voxels,
> > > > overlap=0.000)
> > > > Left_Amygdala (18): linear fit = 1.23 x + 0.0 (565 voxels, peak =
> > 78),
> > > > gca=78.4
> > > > gca peak = 0.42394 (62)
> > > > mri peak = 0.08525 (81)
> > > > Right_Amygdala (54): linear fit = 1.30 x + 0.0 (481 voxels,
> > > > overlap=0.000)
> > > > Right_Amygdala (54): linear fit = 1.30 x + 0.0 (481 voxels, peak =
> > > > 81), gca=80.6
> > > > gca peak = 0.10041 (96)
> > > > mri peak = 0.07187 (96)
> > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5596 voxels,
> > > > overlap=0.613)
> > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5596 voxels,
> > > > peak = 98), gca=98.4
> > > > gca peak = 0.13978 (88)
> > > > mri peak = 0.05644 (99)
> > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5116
> > voxels,
> > > > overlap=0.582)
> > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5116
> > voxels,
> > > > peak = 99), gca=99.0
> > > > gca peak = 0.08514 (81)
> > > > mri peak = 0.11174 (88)
> > > > Left_Putamen (12): linear fit = 1.08 x + 0.0 (1383 voxels,
> > > > overlap=0.545)
> > > > Left_Putamen (12): linear fit = 1.08 x + 0.0 (1383 voxels, peak =
> > 87),
> > > > gca=87.1
> > > > gca peak = 0.09624 (82)
> > > > mri peak = 0.11806 (88)
> > > > Right_Putamen (51): linear fit = 1.10 x + 0.0 (983 voxels,
> > > > overlap=0.585)
> > > > Right_Putamen (51): linear fit = 1.10 x + 0.0 (983 voxels, peak =
> > 90),
> > > > gca=90.2
> > > > gca peak = 0.07543 (88)
> > > > mri peak = 0.06257 (98)
> > > > Brain_Stem (16): linear fit = 1.10 x + 0.0 (12615 voxels,
> > > > overlap=0.400)
> > > > Brain_Stem (16): linear fit = 1.10 x + 0.0 (12615 voxels, peak =
> > 97),
> > > > gca=96.8
> > > > gca peak = 0.12757 (95)
> > > > mri peak = 0.07190 (107)
> > > > Right_VentralDC: unreasonable value (111.6/107.0), not in range
> > [80,
> > > > 110] - rejecting
> > > > gca peak = 0.17004 (92)
> > > > mri peak = 0.08220 (112)
> > > > Left_VentralDC: unreasonable value (105.8/112.0), not in range
> > [80,
> > > > 110] - rejecting
> > > > gca peak = 0.21361 (36)
> > > > mri peak = 0.17046 (27)
> > > > Third_Ventricle (14): linear fit = 0.80 x + 0.0 (423 voxels,
> > > > overlap=0.115)
> > > > Third_Ventricle (14): linear fit = 0.80 x + 0.0 (423 voxels, peak
> > =
> > > > 29), gca=28.8
> > > > gca peak = 0.26069 (23)
> > > > mri peak = 0.12203 (25)
> > > > Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (467 voxels,
> > > > overlap=0.806)
> > > > Fourth_Ventricle (15): linear fit = 0.95 x + 0.0 (467 voxels, peak
> > =
> > > > 22), gca=21.9
> > > > 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 1.02 x + 0.0
> > > > estimating mean csf scale to be 0.92 x + 0.0
> > > > Left_Pallidum too bright - rescaling by 0.973 (from 1.100) to
> > 102.7
> > > > (was 105.6)
> > > > Right_Pallidum too bright - rescaling by 0.941 (from 1.125) to
> > 102.7
> > > > (was 109.1)
> > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > > renormalizing by structure alignment....
> > > > renormalizing input #0
> > > > gca peak = 0.14647 (25)
> > > > mri peak = 0.19455 (22)
> > > > Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (14935
> > voxels,
> > > > overlap=0.867)
> > > > Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (14935
> > voxels,
> > > > peak = 24), gca=24.4
> > > > gca peak = 0.19378 (21)
> > > > mri peak = 0.17994 (24)
> > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (13315
> > voxels,
> > > > overlap=0.577)
> > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (13315
> > voxels,
> > > > peak = 21), gca=21.0
> > > > gca peak = 0.26518 (104)
> > > > mri peak = 0.16459 (110)
> > > > Right_Pallidum (52): linear fit = 1.05 x + 0.0 (393 voxels,
> > > > overlap=0.718)
> > > > Right_Pallidum (52): linear fit = 1.05 x + 0.0 (393 voxels, peak =
> > > > 109), gca=109.2
> > > > gca peak = 0.18126 (103)
> > > > mri peak = 0.15057 (110)
> > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (454 voxels,
> > > > overlap=0.599)
> > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (454 voxels, peak =
> > > > 108), gca=108.1
> > > > gca peak = 0.25544 (70)
> > > > mri peak = 0.07277 (75)
> > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1544 voxels,
> > > > overlap=0.987)
> > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1544 voxels,
> > peak =
> > > > 70), gca=70.0
> > > > gca peak = 0.28137 (74)
> > > > mri peak = 0.09303 (75)
> > > > Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1519 voxels,
> > > > overlap=0.999)
> > > > Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1519 voxels,
> > peak =
> > > > 74), gca=74.0
> > > > gca peak = 0.08350 (108)
> > > > mri peak = 0.08247 (106)
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28258
> > > > voxels, overlap=0.753)
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (28258
> > > > voxels, peak = 108), gca=108.0
> > > > gca peak = 0.08542 (108)
> > > > mri peak = 0.07428 (109)
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34792
> > > > voxels, overlap=0.746)
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34792
> > > > voxels, peak = 108), gca=108.0
> > > > gca peak = 0.06459 (76)
> > > > mri peak = 0.02775 (74)
> > > > Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (69386 voxels,
> > > > overlap=0.183)
> > > > Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (69386 voxels,
> > > > peak = 76), gca=76.0
> > > > gca peak = 0.07121 (77)
> > > > mri peak = 0.02662 (74)
> > > > Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (69439
> > voxels,
> > > > overlap=0.174)
> > > > Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (69439
> > voxels,
> > > > peak = 75), gca=75.1
> > > > gca peak = 0.21592 (83)
> > > > mri peak = 0.09277 (84)
> > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1505 voxels,
> > > > overlap=0.996)
> > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1505 voxels, peak =
> > > > 83), gca=83.0
> > > > gca peak = 0.15916 (79)
> > > > mri peak = 0.10121 (86)
> > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1290 voxels,
> > > > overlap=0.882)
> > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1290 voxels, peak =
> > 79),
> > > > gca=79.0
> > > > gca peak = 0.08763 (73)
> > > > mri peak = 0.05510 (72)
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (35554
> > voxels,
> > > > overlap=0.948)
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (35554
> > voxels,
> > > > peak = 73), gca=73.0
> > > > gca peak = 0.10762 (68)
> > > > mri peak = 0.04765 (71)
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36178
> > voxels,
> > > > overlap=0.974)
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (36178
> > voxels,
> > > > peak = 68), gca=68.0
> > > > gca peak = 0.16966 (96)
> > > > mri peak = 0.10359 (97)
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5829
> > > > voxels, overlap=0.978)
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5829
> > > > voxels, peak = 96), gca=96.0
> > > > gca peak = 0.15537 (95)
> > > > mri peak = 0.08973 (95)
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0
> > (5682
> > > > voxels, overlap=0.983)
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0
> > (5682
> > > > voxels, peak = 95), gca=95.0
> > > > gca peak = 0.30364 (78)
> > > > mri peak = 0.08920 (76)
> > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (565 voxels,
> > > > overlap=1.000)
> > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (565 voxels, peak =
> > 78),
> > > > gca=78.0
> > > > gca peak = 0.37855 (81)
> > > > mri peak = 0.08525 (81)
> > > > Right_Amygdala (54): linear fit = 0.98 x + 0.0 (481 voxels,
> > > > overlap=1.000)
> > > > Right_Amygdala (54): linear fit = 0.98 x + 0.0 (481 voxels, peak =
> > > > 79), gca=79.0
> > > > gca peak = 0.10643 (98)
> > > > mri peak = 0.07187 (96)
> > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5596 voxels,
> > > > overlap=0.793)
> > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5596 voxels,
> > > > peak = 98), gca=98.0
> > > > gca peak = 0.12116 (99)
> > > > mri peak = 0.05644 (99)
> > > > Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (5116
> > voxels,
> > > > overlap=0.867)
> > > > Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (5116
> > voxels,
> > > > peak = 97), gca=96.5
> > > > gca peak = 0.08623 (87)
> > > > mri peak = 0.11174 (88)
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (1383 voxels,
> > > > overlap=0.855)
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (1383 voxels, peak =
> > 87),
> > > > gca=87.0
> > > > gca peak = 0.09047 (83)
> > > > mri peak = 0.11806 (88)
> > > > Right_Putamen (51): linear fit = 0.98 x + 0.0 (983 voxels,
> > > > overlap=0.834)
> > > > Right_Putamen (51): linear fit = 0.98 x + 0.0 (983 voxels, peak =
> > 81),
> > > > gca=80.9
> > > > gca peak = 0.06833 (97)
> > > > mri peak = 0.06257 (98)
> > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12615 voxels,
> > > > overlap=0.781)
> > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12615 voxels, peak =
> > 99),
> > > > gca=99.4
> > > > gca peak = 0.13036 (95)
> > > > mri peak = 0.07190 (107)
> > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1487 voxels,
> > > > overlap=0.012)
> > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1487 voxels, peak
> > =
> > > > 109), gca=109.2
> > > > gca peak = 0.16234 (92)
> > > > mri peak = 0.08220 (112)
> > > > Left_VentralDC: unreasonable value (105.8/112.0), not in range
> > [80,
> > > > 110] - rejecting
> > > > gca peak = 0.20402 (30)
> > > > mri peak = 0.17046 (27)
> > > > Third_Ventricle (14): linear fit = 0.98 x + 0.0 (423 voxels,
> > > > overlap=0.788)
> > > > Third_Ventricle (14): linear fit = 0.98 x + 0.0 (423 voxels, peak
> > =
> > > > 29), gca=29.2
> > > > gca peak = 0.20373 (22)
> > > > mri peak = 0.12203 (25)
> > > > Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (467 voxels,
> > > > overlap=0.862)
> > > > Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (467 voxels, peak
> > =
> > > > 23), gca=23.1
> > > > gca peak Unknown = 0.94427 ( 0)
> > > > gca peak Left_Inf_Lat_Vent = 0.23861 (41)
> > > > gca peak CSF = 0.19583 (42)
> > > > gca peak Left_Accumbens_area = 0.34736 (74)
> > > > gca peak Left_VentralDC = 0.16234 (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 = 0.22085 (36)
> > > > gca peak Right_Accumbens_area = 0.25693 (86)
> > > > gca peak Right_vessel = 0.83418 (60)
> > > > gca peak Right_choroid_plexus = 0.10189 (48)
> > > > gca peak Fifth_Ventricle = 0.82185 (38)
> > > > gca peak WM_hypointensities = 0.14848 (84)
> > > > gca peak non_WM_hypointensities = 0.11940 (54)
> > > > gca peak Optic_Chiasm = 0.34508 (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 0.949 (from 1.050) to
> > 102.6
> > > > (was 108.1)
> > > > Right_Pallidum too bright - rescaling by 0.940 (from 1.050) to
> > 102.6
> > > > (was 109.2)
> > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > > Linux dnode33.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25
> > 13:45:47
> > > > EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
> > > >
> > > > recon-all exited with ERRORS at Wed Apr 21 17:58:54 CDT 2010
> > > >
> > > >
> > > > > From: nicks@nmr.mgh.harvard.edu
> > > > > To: freesurfer_zg@hotmail.com
> > > > > Date: Tue, 20 Apr 2010 18:18:14 -0400
> > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] a 3T MPRAGE subject fails at
> > mri_ca_label
> > > > >
> > > > > you can download a newer mri_ca_label for your platform from
> > here:
> > > > >
> > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/
> > > > >
> > > > > which fixes this problem.
> > > > >
> > > > > n.
> > > > >
> > > > >
> > > > > On Tue, 2010-04-20 at 15:21 -0500, Guang Zeng wrote:
> > > > > > 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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > >
> > ______________________________________________________________________
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