Hi Bruce,
Here is the last part of the recon-all.log:
#...@# SubCort Seg Mon Feb 15 01:13:58 EST 2010
\n mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z
/Applications/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
\n
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
/Applications/freesurfer/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
average std[0] = 6.9
reading transform from transforms/talairach.m3z...
gunzip -c transforms/talairach.m3z
Atlas used for the 3D morph was
/Applications/freesurfer/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 = 0.10426 ( 7)
Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (7234 voxels,
overlap=0.000)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (7234 voxels, peak =
10), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.11303 (12)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (6302 voxels,
overlap=0.000)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (6302 voxels, peak =
8), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.06830 (115)
Right_Pallidum (52): linear fit = 1.15 x + 0.0 (217 voxels, overlap=0.000)
Right_Pallidum (52): linear fit = 1.15 x + 0.0 (217 voxels, peak = 112),
gca=111.5
gca peak = 0.18160 (96)
mri peak = 0.09282 (110)
Left_Pallidum (13): linear fit = 1.15 x + 0.0 (198 voxels, overlap=0.115)
Left_Pallidum (13): linear fit = 1.15 x + 0.0 (198 voxels, peak = 110),
gca=110.4
gca peak = 0.27536 (62)
mri peak = 0.06623 (61)
Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (1190 voxels,
overlap=0.999)
Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (1190 voxels, peak = 57),
gca=57.4
gca peak = 0.32745 (63)
mri peak = 0.05769 (59)
Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1114 voxels,
overlap=0.982)
Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1114 voxels, peak = 55),
gca=55.1
gca peak = 0.08597 (105)
mri peak = 0.06013 (110)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (21713 voxels,
overlap=0.653)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (21713 voxels,
peak = 110), gca=110.2
gca peak = 0.09209 (106)
mri peak = 0.05762 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (21146 voxels,
overlap=0.661)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (21146 voxels,
peak = 111), gca=111.3
gca peak = 0.07826 (63)
mri peak = 0.02176 (57)
Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (44024 voxels,
overlap=0.000)
Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (44024 voxels, peak =
57), gca=56.7
gca peak = 0.08598 (64)
mri peak = 0.02190 (53)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (48705 voxels,
overlap=0.000)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (48705 voxels, peak =
53), gca=52.8
gca peak = 0.24164 (71)
mri peak = 0.05342 (82)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (234 voxels, overlap=0.226)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (234 voxels, peak = 78),
gca=78.1
gca peak = 0.18227 (75)
mri peak = 0.06054 (80)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (309 voxels, overlap=0.746)
Left_Caudate (11): linear fit = 0.98 x + 0.0 (309 voxels, peak = 73),
gca=73.1
gca peak = 0.10629 (62)
mri peak = 0.03469 (55)
Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (21006 voxels,
overlap=0.584)
Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (21006 voxels, peak =
59), gca=58.9
gca peak = 0.11668 (59)
mri peak = 0.03149 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21972 voxels,
overlap=0.689)
Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21972 voxels, peak
= 56), gca=56.0
gca peak = 0.17849 (88)
mri peak = 0.08063 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4201 voxels,
overlap=0.429)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4201 voxels,
peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.07601 (97)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (4494 voxels,
overlap=0.056)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (4494 voxels,
peak = 97), gca=96.8
gca peak = 0.41688 (64)
mri peak = 0.06967 (57)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (340 voxels, overlap=0.900)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (340 voxels, peak = 56),
gca=56.0
gca peak = 0.42394 (62)
mri peak = 0.10513 (61)
Right_Amygdala (54): linear fit = 0.95 x + 0.0 (398 voxels, overlap=1.000)
Right_Amygdala (54): linear fit = 0.95 x + 0.0 (398 voxels, peak = 59),
gca=58.9
gca peak = 0.10041 (96)
mri peak = 0.05003 (95)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3763 voxels,
overlap=0.957)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3763 voxels, peak =
98), gca=98.4
gca peak = 0.13978 (88)
mri peak = 0.04626 (95)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3546 voxels,
overlap=0.376)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (3546 voxels, peak =
97), gca=96.8
gca peak = 0.08514 (81)
mri peak = 0.05101 (93)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (637 voxels, overlap=0.376)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (637 voxels, peak = 91),
gca=91.1
gca peak = 0.09624 (82)
mri peak = 0.06009 (97)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (460 voxels, overlap=0.625)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (460 voxels, peak = 92),
gca=92.2
gca peak = 0.07543 (88)
mri peak = 0.04299 (93)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8870 voxels, overlap=0.657)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (8870 voxels, peak = 97),
gca=96.8
gca peak = 0.12757 (95)
mri peak = 0.06222 (110)
Right_VentralDC: unreasonable value (114.0/110.0), not in range [80, 110] -
rejecting
gca peak = 0.17004 (92)
mri peak = 0.07124 (111)
Left_VentralDC: unreasonable value (110.4/111.0), not in range [80, 110] -
rejecting
gca peak = 0.21361 (36)
mri peak = 0.14462 (17)
Third_Ventricle (14): linear fit = 0.45 x + 0.0 (272 voxels, overlap=0.000)
Third_Ventricle (14): linear fit = 0.45 x + 0.0 (272 voxels, peak = 16),
gca=16.2
gca peak = 0.26069 (23)
mri peak = 0.11940 ( 8)
Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (242 voxels, overlap=0.000)
Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (242 voxels, peak = 7),
gca=6.9
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak Third_Ventricle = 0.21361 (36)
gca peak Fourth_Ventricle = 0.26069 (23)
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 0.89 x + 0.0
estimating mean wm scale to be 1.05 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
Left_Pallidum too bright - rescaling by 0.953 (from 1.150) to 105.2 (was
110.4)
Right_Pallidum too bright - rescaling by 0.943 (from 1.150) to 105.2 (was
111.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31600 (11)
mri peak = 0.10426 ( 7)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (7234 voxels,
overlap=0.986)
Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (7234 voxels, peak =
12), gca=11.5
gca peak = 0.29325 ( 9)
mri peak = 0.11303 (12)
Right_Lateral_Ventricle (43): linear fit = 1.17 x + 0.0 (6302 voxels,
overlap=0.997)
Right_Lateral_Ventricle (43): linear fit = 1.17 x + 0.0 (6302 voxels, peak =
11), gca=10.6
gca peak = 0.23713 (106)
mri peak = 0.06830 (115)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (217 voxels, overlap=0.762)
Right_Pallidum (52): linear fit = 1.08 x + 0.0 (217 voxels, peak = 114),
gca=114.0
gca peak = 0.14634 (106)
mri peak = 0.09282 (110)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (198 voxels, overlap=0.758)
Left_Pallidum (13): linear fit = 1.05 x + 0.0 (198 voxels, peak = 111),
gca=111.3
gca peak = 0.29424 (57)
mri peak = 0.06623 (61)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1190 voxels,
overlap=1.000)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1190 voxels, peak = 57),
gca=57.0
gca peak = 0.34306 (55)
mri peak = 0.05769 (59)
Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (1114 voxels,
overlap=1.000)
Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (1114 voxels, peak = 58),
gca=57.7
gca peak = 0.08007 (112)
mri peak = 0.06013 (110)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (21713 voxels,
overlap=0.805)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (21713 voxels,
peak = 112), gca=112.0
gca peak = 0.08806 (111)
mri peak = 0.05762 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21146 voxels,
overlap=0.832)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21146 voxels,
peak = 111), gca=111.0
gca peak = 0.08431 (57)
mri peak = 0.02176 (57)
Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (44024 voxels,
overlap=0.000)
Left_Cerebral_Cortex (3): linear fit = 0.95 x + 0.0 (44024 voxels, peak =
54), gca=54.1
gca peak = 0.10547 (53)
mri peak = 0.02190 (53)
Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (48705 voxels,
overlap=0.000)
Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (48705 voxels, peak =
56), gca=55.6
gca peak = 0.29970 (81)
mri peak = 0.05342 (82)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (234 voxels, overlap=0.690)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (234 voxels, peak = 81),
gca=81.0
gca peak = 0.16560 (73)
mri peak = 0.06054 (80)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (309 voxels, overlap=0.767)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (309 voxels, peak = 73),
gca=73.0
gca peak = 0.11088 (58)
mri peak = 0.03469 (55)
Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (21006 voxels,
overlap=0.833)
Left_Cerebellum_Cortex (8): linear fit = 0.95 x + 0.0 (21006 voxels, peak =
55), gca=55.1
gca peak = 0.12351 (56)
mri peak = 0.03149 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21972 voxels,
overlap=0.924)
Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (21972 voxels, peak
= 53), gca=53.2
gca peak = 0.17247 (94)
mri peak = 0.08063 (95)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4201 voxels,
overlap=0.962)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (4201 voxels,
peak = 96), gca=96.3
gca peak = 0.15522 (97)
mri peak = 0.07601 (97)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4494 voxels,
overlap=0.982)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4494 voxels,
peak = 97), gca=97.0
gca peak = 0.53643 (56)
mri peak = 0.06967 (57)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (340 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (340 voxels, peak = 56),
gca=56.0
gca peak = 0.56686 (59)
mri peak = 0.10513 (61)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (398 voxels, overlap=1.000)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (398 voxels, peak = 60),
gca=60.5
gca peak = 0.10643 (98)
mri peak = 0.05003 (95)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3763 voxels,
overlap=0.995)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3763 voxels, peak =
98), gca=98.0
gca peak = 0.09695 (97)
mri peak = 0.04626 (95)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3546 voxels,
overlap=0.967)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3546 voxels, peak =
99), gca=99.4
gca peak = 0.08938 (98)
mri peak = 0.05101 (93)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (637 voxels, overlap=0.840)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (637 voxels, peak = 98),
gca=98.0
gca peak = 0.08286 (85)
mri peak = 0.06009 (97)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (460 voxels, overlap=0.753)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (460 voxels, peak = 85),
gca=85.0
gca peak = 0.06571 (97)
mri peak = 0.04299 (93)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8870 voxels, overlap=0.882)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8870 voxels, peak = 97),
gca=97.0
gca peak = 0.12854 (95)
mri peak = 0.06222 (110)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1099 voxels, overlap=0.003)
Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1099 voxels, peak = 109),
gca=109.2
gca peak = 0.16156 (92)
mri peak = 0.07124 (111)
Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] -
rejecting
gca peak = 0.35640 (14)
mri peak = 0.14462 (17)
Third_Ventricle (14): linear fit = 1.17 x + 0.0 (272 voxels, overlap=0.993)
Third_Ventricle (14): linear fit = 1.17 x + 0.0 (272 voxels, peak = 16),
gca=16.4
gca peak = 0.33827 ( 9)
mri peak = 0.11940 ( 8)
Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (242 voxels, overlap=0.954)
Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (242 voxels, peak = 7),
gca=7.2
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.27467 (31)
gca peak CSF = 0.28683 (18)
gca peak Left_Accumbens_area = 0.57061 (68)
gca peak Left_VentralDC = 0.16156 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.43967 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.24679 (29)
gca peak Right_Accumbens_area = 0.35744 (79)
gca peak Right_vessel = 0.58378 (60)
gca peak Right_choroid_plexus = 0.10278 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.14917 (86)
gca peak non_WM_hypointensities = 0.09071 (55)
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 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.05 x + 0.0
Left_Pallidum too bright - rescaling by 0.952 (from 1.050) to 105.9 (was
111.3)
Right_Pallidum too bright - rescaling by 0.930 (from 1.075) to 105.9 (was
114.0)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
Darwin sarah-readings-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0:
Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
recon-all exited with ERRORS at Mon Feb 15 01:39:43 EST 2010
On 2/15/10 10:40 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> Hi Julie,
>
> can you send us the last couple of hundred or so lines of the
> recon-all.log? You can generate this with tail -n 200 recon-all.log
>
> cheers,
> Bruce
>
>
> On Mon, 15
> Feb 2010, Julie McEntee wrote:
>
>> Hello,
>>
>> The initial command to recon-all:
>>
>> recon-all -i $FREESURFER_HOME/subjects/PPG1156/1156MPRage.nii.gz -autorecon1
>> -autorecon2 -subjid MGZ
>>
>> exited with errors during SubCort Seg. At this point, I am attempting to
>> obtain subcortical segmentation only (aseg.mgz, wm.mgz, aseg.stats), but
>> would like to eventually run entire recon. I previosly tried to attach the
>> recon-all.log, but the file is too large (>200KB).
>>
>> I checked the tal transform and skullstrip- both looked OK. The scan is of a
>> subject with Huntington's Disease so the ventricles are a bit enlarged and
>> there is significant asymmetrical atrophy such that at least one area of
>> brainmask.mgz was labeled as 57 (Right-Lesion). Also, there seems to be
>> intensity variations (artifact?) A-P across cortex on slices around mid-line
>> in sagittal view.
>>
>> Any ideas? Please let me know if you'd like me to upload any/all files.
>>
>> Thank you for your help,
>>
>> Julie
>>
>> Julie E. McEntee, M.A., C.C.R.P.
>> Senior Research Program Coordinator
>> Department of Psychiatry- Neuroimaging
>> Johns Hopkins University School of Medicine
>> 600 N. Wolfe St./ Phipps 300
>> Baltimore, MD 21287
>> Phone: 410-502-0468
>> Fax: 410-614-3676
>>
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