External Email - Use Caution Please find the logfile attached.
Thank you Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > Can you send the log file? > > On 6/4/2020 9:12 AM, Boris Rauchmann wrote: > > External Email - Use Caution > Dear FS experts, > > In my dataset I have 4 subjects where the T1 was acquired, planning the > FOV very close to the occipital lobe. I guess that triggers the error: > getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 > slices behind head! ERROR: xcerebralseg and results in gtmseg exited with > errors. > How can I fix this? > > Best regards, > Boris > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Log file for gtmseg Thu Jun 4 14:40:20 CEST 2020 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/gtmseg --s 098_S_6655_20190107 freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux xcerebralseg --s 098_S_6655_20190107 Thu Jun 4 14:40:20 CEST 2020 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/xcerebralseg --s 098_S_6655_20190107 freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: xcerebralseg,v 1.12 2017/01/18 21:21:00 zkaufman Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh sysname Linux hostname linuxrechner2 machine x86_64 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh == Number of threads available to mri_ca_label for OpenMP = 1 == 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/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca reading input volume from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz average std[0] = 20.4 reading transform from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.01 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 20.4 using min determinant for regularization = 41.8 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.24861 (36) mri peak = 0.08632 (27) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, overlap=0.008) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, peak = 25), gca=25.0 gca peak = 0.29857 (37) mri peak = 0.08013 (27) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, overlap=0.010) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, peak = 24), gca=23.9 gca peak = 0.94219 (108) mri peak = 0.08247 (108) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (333 voxels, overlap=1.049) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (333 voxels, peak = 107), gca=107.5 gca peak = 0.53160 (105) mri peak = 0.09871 (108) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (464 voxels, overlap=1.045) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (464 voxels, peak = 107), gca=106.6 gca peak = 0.29818 (86) mri peak = 0.07672 (78) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (455 voxels, overlap=0.705) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (455 voxels, peak = 80), gca=79.6 gca peak = 0.51707 (84) mri peak = 0.07839 (83) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (336 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (336 voxels, peak = 79), gca=79.4 gca peak = 0.11572 (108) mri peak = 0.06269 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38550 voxels, overlap=0.986) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38550 voxels, peak = 108), gca=108.0 gca peak = 0.12550 (107) mri peak = 0.06717 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38729 voxels, overlap=0.953) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38729 voxels, peak = 108), gca=107.5 gca peak = 0.13594 (79) mri peak = 0.04341 (76) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (13779 voxels, overlap=0.993) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (13779 voxels, peak = 76), gca=76.2 gca peak = 0.14160 (79) mri peak = 0.04592 (72) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (13271 voxels, overlap=0.441) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (13271 voxels, peak = 70), gca=69.9 gca peak = 0.44729 (91) mri peak = 0.08617 (95) Right_Caudate (50): linear fit = 1.02 x + 0.0 (451 voxels, overlap=0.998) Right_Caudate (50): linear fit = 1.02 x + 0.0 (451 voxels, peak = 93), gca=93.3 gca peak = 0.56906 (92) mri peak = 0.07719 (88) Left_Caudate (11): linear fit = 0.94 x + 0.0 (621 voxels, overlap=1.015) Left_Caudate (11): linear fit = 0.94 x + 0.0 (621 voxels, peak = 87), gca=86.9 gca peak = 0.09134 (83) mri peak = 0.05687 (83) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (20374 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (20374 voxels, peak = 83), gca=82.6 gca peak = 0.08707 (81) mri peak = 0.04162 (79) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (19098 voxels, overlap=0.867) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (19098 voxels, peak = 78), gca=78.2 gca peak = 0.18417 (104) mri peak = 0.06782 (113) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5492 voxels, overlap=0.609) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5492 voxels, peak = 113), gca=112.8 gca peak = 0.23199 (105) mri peak = 0.07640 (111) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5672 voxels, overlap=0.614) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5672 voxels, peak = 111), gca=110.8 gca peak = 0.39551 (85) mri peak = 0.12121 (77) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (117 voxels, overlap=0.653) Left_Amygdala (18): linear fit = 0.95 x + 0.0 (117 voxels, peak = 81), gca=81.2 gca peak = 0.40047 (85) mri peak = 0.09091 (79) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (154 voxels, overlap=0.922) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (154 voxels, peak = 80), gca=80.3 gca peak = 0.14337 (103) mri peak = 0.05975 (100) Left_Thalamus (10): linear fit = 0.96 x + 0.0 (3269 voxels, overlap=0.951) Left_Thalamus (10): linear fit = 0.96 x + 0.0 (3269 voxels, peak = 99), gca=99.4 gca peak = 0.15911 (103) mri peak = 0.06677 (103) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3304 voxels, overlap=1.002) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3304 voxels, peak = 104), gca=103.5 gca peak = 0.12855 (93) mri peak = 0.06873 (94) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1199 voxels, overlap=0.581) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1199 voxels, peak = 88), gca=87.9 gca peak = 0.13191 (95) mri peak = 0.07476 (91) Right_Putamen (51): linear fit = 0.89 x + 0.0 (1632 voxels, overlap=0.377) Right_Putamen (51): linear fit = 0.89 x + 0.0 (1632 voxels, peak = 85), gca=85.0 gca peak = 0.34872 (102) mri peak = 0.08591 (106) Brain_Stem (16): linear fit = 1.03 x + 0.0 (5891 voxels, overlap=0.974) Brain_Stem (16): linear fit = 1.03 x + 0.0 (5891 voxels, peak = 106), gca=105.6 gca peak = 0.24156 (107) mri peak = 0.20588 (110) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, overlap=0.868) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, peak = 108), gca=107.5 gca peak = 0.19573 (107) mri peak = 0.18266 (110) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1136 voxels, overlap=0.878) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1136 voxels, peak = 108), gca=107.5 gca peak = 0.42363 (50) mri peak = 0.09604 (30) Third_Ventricle (14): linear fit = 0.60 x + 0.0 (711 voxels, overlap=0.069) Third_Ventricle (14): linear fit = 0.60 x + 0.0 (711 voxels, peak = 30), gca=29.8 gca peak = 0.34418 (40) mri peak = 0.10506 (29) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (419 voxels, overlap=0.031) Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (419 voxels, peak = 27), gca=27.0 gca peak Unknown = 1.00000 ( 0) gca peak Left_Inf_Lat_Vent = 0.52654 (51) gca peak Third_Ventricle = 0.42363 (50) gca peak CSF = 0.28546 (57) gca peak Left_Accumbens_area = 0.78299 (92) gca peak Left_vessel = 0.92095 (72) gca peak Left_choroid_plexus = 0.16464 (56) gca peak Right_Inf_Lat_Vent = 0.86099 (49) gca peak Right_Accumbens_area = 0.67115 (94) gca peak Right_vessel = 0.81418 (74) gca peak Right_choroid_plexus = 0.17128 (58) gca peak Fifth_Ventricle = 1.00000 (62) gca peak WM_hypointensities = 0.32749 (79) gca peak non_WM_hypointensities = 0.17249 (59) gca peak Optic_Chiasm = 0.77564 (85) gca peak Air = 0.62365 ( 2) gca peak = 0.04778 (23) gca peak = 0.17873 (77) gca peak = 0.19213 (104) gca peak CC_Posterior = 0.70026 (113) gca peak CC_Mid_Posterior = 0.69090 (107) gca peak CC_Central = 0.89754 (108) gca peak CC_Mid_Anterior = 0.58555 (109) gca peak CC_Anterior = 0.23011 (113) gca peak = 0.08554 (44) gca peak = 0.02810 (91) not using caudate to estimate GM means estimating mean gm scale to be 0.94 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.67 x + 0.0 Left_Pallidum too bright - rescaling by 0.981 (from 1.015) to 104.5 (was 106.6) Right_Pallidum too bright - rescaling by 0.973 (from 0.995) to 104.5 (was 107.5) saving intensity scales to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29796 (25) mri peak = 0.08632 (27) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (14329 voxels, overlap=0.998) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (14329 voxels, peak = 26), gca=26.4 gca peak = 0.39818 (24) mri peak = 0.08013 (27) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (12114 voxels, overlap=1.001) Right_Lateral_Ventricle (43): linear fit = 1.11 x + 0.0 (12114 voxels, peak = 27), gca=26.5 gca peak = 0.72761 (105) mri peak = 0.08247 (108) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (333 voxels, overlap=1.035) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (333 voxels, peak = 107), gca=106.6 gca peak = 0.85330 (105) mri peak = 0.09871 (108) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (464 voxels, overlap=1.038) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (464 voxels, peak = 107), gca=106.6 gca peak = 0.34338 (78) mri peak = 0.07672 (78) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (455 voxels, overlap=1.014) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (455 voxels, peak = 80), gca=79.9 gca peak = 0.54055 (80) mri peak = 0.07839 (83) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (336 voxels, overlap=1.014) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (336 voxels, peak = 80), gca=80.0 gca peak = 0.11561 (108) mri peak = 0.06269 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38550 voxels, overlap=0.986) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (38550 voxels, peak = 108), gca=108.0 gca peak = 0.12062 (107) mri peak = 0.06717 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38729 voxels, overlap=0.963) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (38729 voxels, peak = 108), gca=107.5 gca peak = 0.14100 (77) mri peak = 0.04341 (76) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (13779 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (13779 voxels, peak = 76), gca=75.8 gca peak = 0.15895 (70) mri peak = 0.04592 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13271 voxels, overlap=0.999) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13271 voxels, peak = 69), gca=69.0 gca peak = 0.38071 (93) mri peak = 0.08617 (95) Right_Caudate (50): linear fit = 1.00 x + 0.0 (451 voxels, overlap=0.993) Right_Caudate (50): linear fit = 1.00 x + 0.0 (451 voxels, peak = 93), gca=93.0 gca peak = 0.62677 (87) mri peak = 0.07719 (88) Left_Caudate (11): linear fit = 1.08 x + 0.0 (621 voxels, overlap=1.015) Left_Caudate (11): linear fit = 1.08 x + 0.0 (621 voxels, peak = 94), gca=93.5 gca peak = 0.10475 (83) mri peak = 0.05687 (83) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (20374 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (20374 voxels, peak = 83), gca=82.6 gca peak = 0.08678 (78) mri peak = 0.04162 (79) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (19098 voxels, overlap=0.983) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (19098 voxels, peak = 76), gca=76.1 gca peak = 0.17849 (112) mri peak = 0.06782 (113) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5492 voxels, overlap=0.981) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5492 voxels, peak = 112), gca=112.0 gca peak = 0.19463 (111) mri peak = 0.07640 (111) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5672 voxels, overlap=0.928) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5672 voxels, peak = 112), gca=111.6 gca peak = 0.47468 (81) mri peak = 0.12121 (77) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (117 voxels, overlap=1.040) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (117 voxels, peak = 76), gca=75.7 gca peak = 0.48220 (81) mri peak = 0.09091 (79) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (154 voxels, overlap=1.054) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (154 voxels, peak = 81), gca=81.0 gca peak = 0.14453 (100) mri peak = 0.05975 (100) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3269 voxels, overlap=1.000) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3269 voxels, peak = 100), gca=100.5 gca peak = 0.16039 (104) mri peak = 0.06677 (103) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3304 voxels, overlap=1.001) Right_Thalamus (49): linear fit = 1.00 x + 0.0 (3304 voxels, peak = 105), gca=104.5 gca peak = 0.15155 (88) mri peak = 0.06873 (94) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1199 voxels, overlap=1.001) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1199 voxels, peak = 88), gca=87.6 gca peak = 0.18443 (85) mri peak = 0.07476 (91) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1632 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1632 voxels, peak = 85), gca=84.6 gca peak = 0.27641 (105) mri peak = 0.08591 (106) Brain_Stem (16): linear fit = 1.00 x + 0.0 (5891 voxels, overlap=0.997) Brain_Stem (16): linear fit = 1.00 x + 0.0 (5891 voxels, peak = 106), gca=105.5 gca peak = 0.19540 (107) mri peak = 0.20588 (110) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, overlap=0.881) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1101 voxels, peak = 107), gca=107.0 gca peak = 0.16707 (107) mri peak = 0.18266 (110) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1136 voxels, overlap=0.900) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1136 voxels, peak = 107), gca=107.0 gca peak = 0.44245 (33) mri peak = 0.09604 (30) Third_Ventricle (14): linear fit = 0.88 x + 0.0 (711 voxels, overlap=1.032) Third_Ventricle (14): linear fit = 0.88 x + 0.0 (711 voxels, peak = 29), gca=29.2 gca peak = 0.45471 (27) mri peak = 0.10506 (29) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (419 voxels, overlap=0.949) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (419 voxels, peak = 28), gca=28.5 gca peak Unknown = 1.00000 ( 0) gca peak Left_Inf_Lat_Vent = 0.46711 (48) gca peak CSF = 0.22573 (39) gca peak Left_Accumbens_area = 0.78297 (87) gca peak Left_vessel = 0.92095 (72) gca peak Left_choroid_plexus = 0.16464 (56) gca peak Right_Inf_Lat_Vent = 0.48284 (45) gca peak Right_Accumbens_area = 0.71918 (97) gca peak Right_vessel = 0.81418 (74) gca peak Right_choroid_plexus = 0.17111 (58) gca peak Fifth_Ventricle = 0.98241 (42) gca peak WM_hypointensities = 0.29810 (79) gca peak non_WM_hypointensities = 0.20620 (59) gca peak Optic_Chiasm = 0.77564 (85) gca peak Air = 0.62365 ( 2) gca peak = 0.04778 (23) gca peak = 0.17727 (77) gca peak = 0.19493 (104) gca peak CC_Posterior = 0.70026 (113) gca peak CC_Mid_Posterior = 0.69090 (107) gca peak CC_Central = 0.89754 (108) gca peak CC_Mid_Anterior = 0.58552 (109) gca peak CC_Anterior = 0.23011 (113) gca peak = 0.08560 (44) gca peak = 0.02810 (91) not using caudate to estimate GM means 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 1.02 x + 0.0 Left_Pallidum too bright - rescaling by 0.981 (from 1.015) to 104.5 (was 106.6) Right_Pallidum too bright - rescaling by 0.981 (from 1.015) to 104.5 (was 106.6) saving intensity scales to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.label_intensities.txt saving sequentially combined intensity scales to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.label_intensities.txt 54714 gm and wm labels changed (%42 to gray, %58 to white out of all changed labels) 423 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 299577 changed. image ll: -3.740, PF=1.000 pass 2: 85245 changed. image ll: -3.737, PF=1.000 pass 3: 49537 changed. pass 4: 31533 changed. pass 5: 21566 changed. pass 6: 15553 changed. pass 7: 11635 changed. pass 8: 8941 changed. pass 9: 6937 changed. pass 10: 5590 changed. pass 11: 4764 changed. !!!!!!!!! ventricle segment 1 with volume 28193 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 2438 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 25223 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 1896 above threshold 100 - not erasing !!!!!!!!!! MRItoUCHAR: min=0, max=258 MRItoUCHAR: range too large, not changing type writing labeled volume to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh mri_ca_label utimesec 844.010024 mri_ca_label stimesec 2.782542 mri_ca_label ru_maxrss 1848732 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 3358859 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 71936 mri_ca_label ru_oublock 131128 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 4 mri_ca_label ru_nivcsw 83937 auto-labeling took 14 minutes and 7 seconds. mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh --replace 3 257 --replace 42 257 --replace 2 257 --replace 41 257 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh --replace 3 257 --replace 42 257 --replace 2 257 --replace 41 257 sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 4 1: 3 257 2: 42 257 3: 2 257 4: 41 257 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh Thu Jun 4 14:54:30 CEST 2020 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: mergeseg,v 1.3 2016/02/16 17:17:20 zkaufman Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/not.mergeseg.mgh $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/not.mergeseg.mgh sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/not.mergeseg.mgh Binarizing based on threshold min 0.5 max +infinity binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 1147696 values in range Counting number of voxels in first frame Found 1147695 voxels in final mask Count: 1147695 1147695.000000 16777216 6.840795 mri_binarize done mri_mask /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg2.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/not.mergeseg.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/srcsegnotmerge.mgh DoAbs = 0 Writing masked volume to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/srcsegnotmerge.mgh...done. fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh Thu Jun 4 14:54:35 CEST 2020 cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/aparc+aseg.mgz... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh... ---------------------- mris_calc -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh add /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.36780/srcsegnotmerge.mgh ---------------------- mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37080/tmp.mgh... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh... Started at Thu Jun 4 14:54:30 CEST 2020 Ended at Thu Jun 4 14:54:40 CEST 2020 Mergeseg-Run-Time-Sec 10 Mergeseg-Run-Time-Hours 0.00 mergeseg Done mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --match 174 --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --binval 174 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --match 174 --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --binval 174 sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh Binarizing based on matching values nMatch 1 0 174 binval 174 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 11932 values in range Counting number of voxels in first frame Found 11931 voxels in final mask Count: 11931 11931.000000 16777216 0.071114 mri_binarize done mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh Thu Jun 4 14:54:44 CEST 2020 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: mergeseg,v 1.3 2016/02/16 17:17:20 zkaufman Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/not.mergeseg.mgh $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/not.mergeseg.mgh sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/not.mergeseg.mgh Binarizing based on threshold min 0.5 max +infinity binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 11932 values in range Counting number of voxels in first frame Found 11931 voxels in final mask Count: 11931 11931.000000 16777216 0.071114 mri_binarize done mri_mask /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/not.mergeseg.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/srcsegnotmerge.mgh DoAbs = 0 Writing masked volume to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/srcsegnotmerge.mgh...done. fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh Thu Jun 4 14:54:48 CEST 2020 cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/pons.mgh... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh... ---------------------- mris_calc -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh add /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37211/srcsegnotmerge.mgh ---------------------- mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37312/tmp.mgh... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh... Started at Thu Jun 4 14:54:44 CEST 2020 Ended at Thu Jun 4 14:54:54 CEST 2020 Mergeseg-Run-Time-Sec 10 Mergeseg-Run-Time-Hours 0.00 mergeseg Done mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --match 172 --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --binval 172 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh --match 172 --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --binval 172 sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh Binarizing based on matching values nMatch 1 0 172 binval 172 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 4010 values in range Counting number of voxels in first frame Found 4009 voxels in final mask Count: 4009 4009.000000 16777216 0.023896 mri_binarize done mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh Thu Jun 4 14:54:57 CEST 2020 setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/mergeseg --src /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh --merge /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 $Id: mergeseg,v 1.3 2016/02/16 17:17:20 zkaufman Exp $ Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/not.mergeseg.mgh $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS cmdline mri_binarize --min 0.5 --i /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh --inv --o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/not.mergeseg.mgh sysname Linux hostname linuxrechner2 machine x86_64 user demenzbild input /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh frame 0 nErode3d 0 nErode2d 0 output /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/not.mergeseg.mgh Binarizing based on threshold min 0.5 max +infinity binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 4010 values in range Counting number of voxels in first frame Found 4009 voxels in final mask Count: 4009 4009.000000 16777216 0.023896 mri_binarize done mri_mask /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3b.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/not.mergeseg.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/srcsegnotmerge.mgh DoAbs = 0 Writing masked volume to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/srcsegnotmerge.mgh...done. fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh Thu Jun 4 14:55:02 CEST 2020 cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS /usr/local/freesurfer/bin/fscalc /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh sum /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/srcsegnotmerge.mgh -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh freesurfer-linux-centos6_x86_64-dev-20180911-69aa645 Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/vermis.mgh... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh... ---------------------- mris_calc -o /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh add /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.mergeseg.37627/srcsegnotmerge.mgh ---------------------- mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh mri_convert /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/tmpdir.fscalc.37779/tmp.mgh... TR=7.24, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg3c.mgh... Started at Thu Jun 4 14:54:57 CEST 2020 Ended at Thu Jun 4 14:55:09 CEST 2020 Mergeseg-Run-Time-Sec 12 Mergeseg-Run-Time-Hours 0.00 mergeseg Done mri_seghead --invol /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz --outvol /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seghead.mgz --fill 1 --thresh1 20 --thresh2 20 --nhitsmin 2 input volume: /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz output volume: /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seghead.mgz threshold1: 20 threshold2: 20 nhitsmin: 2 fill value: 1 Loading input volume Filling Columns Filling Rows Filling Slices Merging and Inverting Growing Counting MRIreorder() ----------- xdim=1 ydim=2 zdim=3 src 256 256 256, 1.000000 1.000000 1.000000 dst 256 256 256, 1.000000 1.000000 1.000000 MRIreorder() ----------- xdim=1 ydim=2 zdim=3 src 256 256 256, 1.000000 1.000000 1.000000 dst 256 256 256, 1.000000 1.000000 1.000000 found head voxel at 118 133 0 head slice 0 WARNING: only 0 < 7 slices behind head! ERROR: xcerebralseg --s 098_S_6655_20190107 gtmseg exited with errors
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