Hi Paul
is this within recon-all? Does that file exist? Can you check its permissions to make sure it is writeable? And that you have enough disk space? Are any error messages printed? Bruce
On Tue, 19 Feb 2013, paul horton wrote:
Hi guys, I am wondering if you can help me. I have run command: mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails: i.e. it stops after the 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' line and does not save the file: aseg.auto_noCCseg.mgz. However, it does save the file: aseg.auto_noCCseg.label_intensities.txt. I have tried it several times and it stops at the same place. I have also tried recon-all, where it jumps from 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' to the command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz', where, again, the file: aseg.auto_noCCseg.mgz is not saved. I am using freesurfer version 4.5.0. So is there a way I can solve this problem. Many Thanks Paul Ps, i have attached the output log below ################ renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.gca ... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.gca
average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, overlap=0.484) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak = 22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, overlap=0.766) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, peak = 20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, overlap=0.353) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104), gca=104.3 gca peak = 0.18160 (96) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, overlap=0.638) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, overlap=0.818) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak = 68), gca=68.2 gca peak = 0.32745 (63) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak = 65), gca=64.6 gca peak = 0.08597 (105) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels, overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0 gca peak = 0.07826 (63) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, overlap=0.547) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak = 71), gca=70.9 gca peak = 0.08598 (64) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, overlap=0.642) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, peak = 69), gca=68.8 gca peak = 0.24164 (71) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82), gca=81.7 gca peak = 0.18227 (75) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, overlap=0.988) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66), gca=65.6 gca peak = 0.42394 (62) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, overlap=0.434) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70), gca=69.8 gca peak = 0.10041 (96) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, overlap=0.910) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, overlap=0.376) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak = 99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0 gca peak = 0.09624 (82) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, overlap=0.815) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84), gca=84.0 gca peak = 0.07543 (88) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.05862 (107) Right_VentralDC: unreasonable value (111.6/107.0), not in range [80, 110] - rejecting gca peak = 0.17004 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] - rejecting gca peak = 0.21361 (36) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25), gca=25.2 gca peak = 0.26069 (23) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, overlap=0.640) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak = 21), gca=20.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_VentralDC = 0.17004 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_VentralDC = 0.12757 (95) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was 100.8) Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5 (was 104.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14515 (23) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, overlap=0.897) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak = 24), gca=23.6 gca peak = 0.19392 (21) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, peak = 21), gca=21.0 gca peak = 0.25607 (102) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105), gca=104.5 gca peak = 0.17462 (103) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103), gca=103.0 gca peak = 0.24759 (68) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak = 68), gca=68.0 gca peak = 0.28061 (65) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak = 62), gca=61.8 gca peak = 0.08360 (108) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels, overlap=0.831) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels, peak = 108), gca=108.0 gca peak = 0.09206 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0 gca peak = 0.06916 (71) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, overlap=0.733) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak = 69), gca=69.2 gca peak = 0.08227 (69) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, overlap=0.734) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, peak = 69), gca=69.0 gca peak = 0.22329 (81) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81), gca=81.0 gca peak = 0.18180 (77) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, overlap=0.937) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77), gca=77.0 gca peak = 0.10419 (63) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak = 65), gca=64.6 gca peak = 0.12084 (64) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, overlap=0.985) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, peak = 62), gca=62.4 gca peak = 0.17137 (94) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels, peak = 94), gca=94.0 gca peak = 0.15715 (93) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels, peak = 93), gca=93.0 gca peak = 0.32238 (65) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65), gca=65.0 gca peak = 0.49832 (70) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70), gca=70.0 gca peak = 0.10606 (98) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, overlap=0.901) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak = 98), gca=98.0 gca peak = 0.12505 (99) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, overlap=0.961) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak = 99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0 gca peak = 0.09838 (78) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, overlap=0.982) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78), gca=78.0 gca peak = 0.07177 (90) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92), gca=92.2 gca peak = 0.13316 (95) mri peak = 0.05862 (107) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, overlap=0.010) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak = 109), gca=109.2 gca peak = 0.16834 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] - rejecting gca peak = 0.25342 (25) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, overlap=0.998) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25), gca=25.0 gca peak = 0.20850 (21) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, overlap=0.808) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26363 (36) gca peak CSF = 0.17919 (33) gca peak Left_Accumbens_area = 0.40223 (72) gca peak Left_VentralDC = 0.16834 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.29122 (35) gca peak Right_Accumbens_area = 0.25605 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (36) gca peak WM_hypointensities = 0.15216 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was 103.0) Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6 (was 104.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt