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. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=P...
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
The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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is there space left on your disk? Can you see if the file aseg.auto_noCCseg.label_intensities.txt exists? Do you have permission to write it?
On Thu, 22 Apr 2010, 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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Hello, Bruce,
Yes, I have space and permission and write the aseg.auto_noCCseg.label_intensities.txt. I found the the aseg.auto_noCCseg.label_intensities.txt in the /mri folder, and pasted below
Thanks! Guang
1 Left_Cerebral_Exterior 1.00 0.0 0 2 Left_Cerebral_White_Matter 1.00 0.0 108 3 Left_Cerebral_Cortex 1.00 0.0 76 4 Left_Lateral_Ventricle 0.98 0.0 24 5 Left_Inf_Lat_Vent 1.00 0.0 41 7 Left_Cerebellum_White_Matter 1.00 0.0 96 8 Left_Cerebellum_Cortex 1.00 0.0 73 9 Left_Thalamus 0.99 0.0 0 10 Left_Thalamus_Proper 1.00 0.0 98 11 Left_Caudate 1.00 0.0 79 12 Left_Putamen 1.00 0.0 87 13 Left_Pallidum 1.00 0.0 103 14 Third_Ventricle 0.98 0.0 29 15 Fourth_Ventricle 1.05 0.0 23 16 Brain_Stem 1.02 0.0 99 17 Left_Hippocampus 1.00 0.0 74 18 Left_Amygdala 1.00 0.0 78 24 CSF 1.00 0.0 42 26 Left_Accumbens_area 1.00 0.0 74 28 Left_VentralDC 1.15 0.0 109 40 Right_Cerebral_Exterior 1.00 0.0 0 41 Right_Cerebral_White_Matter 1.00 0.0 108 42 Right_Cerebral_Cortex 0.98 0.0 75 43 Right_Lateral_Ventricle 1.00 0.0 21 44 Right_Inf_Lat_Vent 1.00 0.0 36 46 Right_Cerebellum_White_Matter 1.00 0.0 95 47 Right_Cerebellum_Cortex 1.00 0.0 68 48 Right_Thalamus 0.99 0.0 0 49 Right_Thalamus_Proper 0.98 0.0 97 50 Right_Caudate 1.00 0.0 83 51 Right_Putamen 0.98 0.0 81 52 Right_Pallidum 0.99 0.0 103 53 Right_Hippocampus 1.00 0.0 70 54 Right_Amygdala 0.98 0.0 79 58 Right_Accumbens_area 1.00 0.0 86 60 Right_VentralDC 1.15 0.0 109 72 Fifth_Ventricle 1.00 0.0 38 75 Left_Lateral_Ventricles 1.00 0.0 0 76 Right_Lateral_Ventricles 1.00 0.0 0 77 WM_hypointensities 1.00 0.0 84 78 Left_WM_hypointensities 1.00 0.0 0 79 Right_WM_hypointensities 1.00 0.0 0 80 non_WM_hypointensities 1.00 0.0 54 81 Left_non_WM_hypointensities 1.00 0.0 0 82 Right_non_WM_hypointensities 1.00 0.0 0 186 1.00 0.0 0 187 1.00 0.0 0
Date: Thu, 22 Apr 2010 10:34:06 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] a 3T MPRAGE subject fails at mri_ca_label
is there space left on your disk? Can you see if the file aseg.auto_noCCseg.label_intensities.txt exists? Do you have permission to write it?
On Thu, 22 Apr 2010, 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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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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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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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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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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That would be fine
On Apr 22, 2010, at 3:57 PM, Guang Zeng freesurfer_zg@hotmail.com wrote:
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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