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  1. Wed Dec 1 03:45:10 UTC 2021
  2. /out/freesurfer/sub-003
  3. /opt/freesurfer/bin/recon-all
  4. -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-003 -sd /out/freesurfer
  5. subjid sub-003
  6. setenv SUBJECTS_DIR /out/freesurfer
  7. FREESURFER_HOME /opt/freesurfer
  8. Actual FREESURFER_HOME /opt/freesurfer
  9. build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
  10. Linux eeff23e566a8 5.4.0-91-generic #102~18.04.1-Ubuntu SMP Thu Nov 11 14:46:36 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
  11. cputime unlimited
  12. filesize unlimited
  13. datasize unlimited
  14. stacksize 8192 kbytes
  15. coredumpsize unlimited
  16. memoryuse unlimited
  17. vmemoryuse unlimited
  18. descriptors 1048576
  19. memorylocked 65536 kbytes
  20. maxproc unlimited
  21. maxlocks unlimited
  22. maxsignal 255946
  23. maxmessage 819200
  24. maxnice 0
  25. maxrtprio 0
  26. maxrttime unlimited
  27.  
  28. total used free shared buff/cache available
  29. Mem: 65572432 6846300 31487912 114820 27238220 57580780
  30. Swap: 2097148 1089568 1007580
  31.  
  32. ########################################
  33. program versions used
  34. $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
  35. $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
  36. mri_convert.bin -all-info
  37. ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  38. FLIRT version 5.5
  39. $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
  40. mri_convert.bin --version
  41. stable6
  42. ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  43. Program nu_correct, built from:
  44. Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
  45. ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  46. ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  47. ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  48. ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  49. ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  50. ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  51. ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  52. ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  53. ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  54. ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  55. ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  56. ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  57. ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  58. ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  59. ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  60. ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  61. ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  62. ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  63. ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  64. ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  65. ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  66. ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:10-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  67. ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  68. ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  69. ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  70. ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  71. ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  72. ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  73. ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  74. ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  75. $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
  76.  
  77. ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  78. $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
  79.  
  80. ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  81. ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  82. ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  83. ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  84. ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  85. ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/12/01-03:45:11-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: eeff23e566a8 Platform: Linux PlatformVersion: 5.4.0-91-generic CompilerName: GCC CompilerVersion: 40400
  86. #######################################
  87. GCADIR /opt/freesurfer/average
  88. GCA RB_all_2016-05-10.vc700.gca
  89. GCASkull RB_all_withskull_2016-05-10.vc700.gca
  90. AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
  91. GCSDIR /opt/freesurfer/average
  92. GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
  93. #######################################
  94. #--------------------------------------------
  95. #@# Tessellate lh Wed Dec 1 03:45:11 UTC 2021
  96. /out/freesurfer/sub-003/scripts
  97.  
  98. mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
  99.  
  100.  
  101. Iteration Number : 1
  102. pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
  103. pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
  104. pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
  105. pass 1 (yz-): 2 found - 2 modified | TOTAL: 2
  106. pass 2 (yz-): 0 found - 2 modified | TOTAL: 2
  107. pass 1 (xz+): 3 found - 3 modified | TOTAL: 5
  108. pass 2 (xz+): 0 found - 3 modified | TOTAL: 5
  109. pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
  110. Iteration Number : 1
  111. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  112. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  113. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  114. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  115. Iteration Number : 1
  116. pass 1 (++): 0 found - 0 modified | TOTAL: 0
  117. pass 1 (+-): 1 found - 1 modified | TOTAL: 1
  118. pass 2 (+-): 0 found - 1 modified | TOTAL: 1
  119. pass 1 (--): 0 found - 0 modified | TOTAL: 1
  120. pass 1 (-+): 0 found - 0 modified | TOTAL: 1
  121. Iteration Number : 2
  122. pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
  123. pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
  124. pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
  125. pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
  126. pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
  127. pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
  128. Iteration Number : 2
  129. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  130. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  131. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  132. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  133. Iteration Number : 2
  134. pass 1 (++): 0 found - 0 modified | TOTAL: 0
  135. pass 1 (+-): 0 found - 0 modified | TOTAL: 0
  136. pass 1 (--): 0 found - 0 modified | TOTAL: 0
  137. pass 1 (-+): 0 found - 0 modified | TOTAL: 0
  138.  
  139. Total Number of Modified Voxels = 6 (out of 337380: 0.001778)
  140. Ambiguous edge configurations...
  141.  
  142. mri_pretess done
  143.  
  144.  
  145. mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
  146.  
  147. $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  148. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  149. slice 30: 1379 vertices, 1486 faces
  150. slice 40: 6950 vertices, 7178 faces
  151. slice 50: 14763 vertices, 15062 faces
  152. slice 60: 24747 vertices, 25109 faces
  153. slice 70: 36333 vertices, 36687 faces
  154. slice 80: 47498 vertices, 47929 faces
  155. slice 90: 59465 vertices, 59910 faces
  156. slice 100: 73209 vertices, 73659 faces
  157. slice 110: 86083 vertices, 86545 faces
  158. slice 120: 98545 vertices, 98993 faces
  159. slice 130: 110434 vertices, 110850 faces
  160. slice 140: 122124 vertices, 122509 faces
  161. slice 150: 131918 vertices, 132269 faces
  162. slice 160: 140959 vertices, 141263 faces
  163. slice 170: 148790 vertices, 149084 faces
  164. slice 180: 155611 vertices, 155866 faces
  165. slice 190: 160950 vertices, 161136 faces
  166. slice 200: 163820 vertices, 163909 faces
  167. slice 210: 163928 vertices, 163982 faces
  168. slice 220: 163928 vertices, 163982 faces
  169. slice 230: 163928 vertices, 163982 faces
  170. slice 240: 163928 vertices, 163982 faces
  171. slice 250: 163928 vertices, 163982 faces
  172. using the conformed surface RAS to save vertex points...
  173. writing ../surf/lh.orig.nofix
  174. using vox2ras matrix:
  175. -0.89844 0.00000 0.00000 115.00000;
  176. 0.00000 0.00000 0.89844 -115.00000;
  177. 0.00000 -0.89844 0.00000 115.00000;
  178. 0.00000 0.00000 0.00000 1.00000;
  179.  
  180. rm -f ../mri/filled-pretess255.mgz
  181.  
  182.  
  183. mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
  184.  
  185.  
  186. counting number of connected components...
  187. 163928 voxel in cpt #1: X=-54 [v=163928,e=491946,f=327964] located at (-27.573355, -18.546221, 34.212749)
  188. For the whole surface: X=-54 [v=163928,e=491946,f=327964]
  189. One single component has been found
  190. nothing to do
  191. done
  192.  
  193. #--------------------------------------------
  194. #@# Smooth1 lh Wed Dec 1 03:45:15 UTC 2021
  195. /out/freesurfer/sub-003/scripts
  196.  
  197. mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
  198.  
  199. setting seed for random number generator to 1234
  200. smoothing surface tessellation for 10 iterations...
  201. smoothing complete - recomputing first and second fundamental forms...
  202. #--------------------------------------------
  203. #@# Inflation1 lh Wed Dec 1 03:45:19 UTC 2021
  204. /out/freesurfer/sub-003/scripts
  205.  
  206. mris_inflate -no-save-sulc -n 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
  207.  
  208. niterations = 50
  209. Not saving sulc
  210. Reading ../surf/lh.smoothwm.nofix
  211. avg radius = 44.9 mm, total surface area = 71202 mm^2
  212. writing inflated surface to ../surf/lh.inflated.nofix
  213. inflation took 1.2 minutes
  214.  
  215. step 000: RMS=0.148 (target=0.015)
  216. step 005: RMS=0.113 (target=0.015)
  217. step 010: RMS=0.084 (target=0.015)
  218. step 015: RMS=0.070 (target=0.015)
  219. step 020: RMS=0.061 (target=0.015)
  220. step 025: RMS=0.053 (target=0.015)
  221. step 030: RMS=0.047 (target=0.015)
  222. step 035: RMS=0.043 (target=0.015)
  223. step 040: RMS=0.040 (target=0.015)
  224. step 045: RMS=0.037 (target=0.015)
  225. step 050: RMS=0.035 (target=0.015)
  226. step 055: RMS=0.034 (target=0.015)
  227. step 060: RMS=0.034 (target=0.015)
  228. step 065: RMS=0.032 (target=0.015)
  229. step 070: RMS=0.032 (target=0.015)
  230. step 075: RMS=0.031 (target=0.015)
  231. step 080: RMS=0.031 (target=0.015)
  232. step 085: RMS=0.031 (target=0.015)
  233. step 090: RMS=0.031 (target=0.015)
  234. step 095: RMS=0.031 (target=0.015)
  235. step 100: RMS=0.031 (target=0.015)
  236. step 105: RMS=0.031 (target=0.015)
  237. step 110: RMS=0.031 (target=0.015)
  238. step 115: RMS=0.031 (target=0.015)
  239. step 120: RMS=0.031 (target=0.015)
  240. step 125: RMS=0.031 (target=0.015)
  241. step 130: RMS=0.031 (target=0.015)
  242. step 135: RMS=0.031 (target=0.015)
  243. step 140: RMS=0.031 (target=0.015)
  244. step 145: RMS=0.030 (target=0.015)
  245. step 150: RMS=0.030 (target=0.015)
  246. step 155: RMS=0.030 (target=0.015)
  247. step 160: RMS=0.030 (target=0.015)
  248. step 165: RMS=0.030 (target=0.015)
  249. step 170: RMS=0.030 (target=0.015)
  250. step 175: RMS=0.030 (target=0.015)
  251. step 180: RMS=0.030 (target=0.015)
  252. step 185: RMS=0.030 (target=0.015)
  253. step 190: RMS=0.030 (target=0.015)
  254. step 195: RMS=0.030 (target=0.015)
  255. step 200: RMS=0.030 (target=0.015)
  256. step 205: RMS=0.030 (target=0.015)
  257. step 210: RMS=0.030 (target=0.015)
  258. step 215: RMS=0.030 (target=0.015)
  259. step 220: RMS=0.030 (target=0.015)
  260. step 225: RMS=0.030 (target=0.015)
  261. step 230: RMS=0.030 (target=0.015)
  262. step 235: RMS=0.030 (target=0.015)
  263. step 240: RMS=0.030 (target=0.015)
  264. step 245: RMS=0.030 (target=0.015)
  265. step 250: RMS=0.030 (target=0.015)
  266. step 255: RMS=0.030 (target=0.015)
  267. step 260: RMS=0.030 (target=0.015)
  268. step 265: RMS=0.031 (target=0.015)
  269. step 270: RMS=0.031 (target=0.015)
  270. step 275: RMS=0.031 (target=0.015)
  271. step 280: RMS=0.031 (target=0.015)
  272. step 285: RMS=0.031 (target=0.015)
  273. step 290: RMS=0.031 (target=0.015)
  274. step 295: RMS=0.031 (target=0.015)
  275. step 300: RMS=0.031 (target=0.015)
  276. inflation complete.
  277. Not saving sulc
  278. mris_inflate utimesec 332.806125
  279. mris_inflate stimesec 0.889608
  280. mris_inflate ru_maxrss 264680
  281. mris_inflate ru_ixrss 0
  282. mris_inflate ru_idrss 0
  283. mris_inflate ru_isrss 0
  284. mris_inflate ru_minflt 65031
  285. mris_inflate ru_majflt 5
  286. mris_inflate ru_nswap 0
  287. mris_inflate ru_inblock 1048
  288. mris_inflate ru_oublock 11536
  289. mris_inflate ru_msgsnd 0
  290. mris_inflate ru_msgrcv 0
  291. mris_inflate ru_nsignals 0
  292. mris_inflate ru_nvcsw 104705
  293. mris_inflate ru_nivcsw 3653
  294. #--------------------------------------------
  295. #@# QSphere lh Wed Dec 1 03:46:34 UTC 2021
  296. /out/freesurfer/sub-003/scripts
  297.  
  298. mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
  299.  
  300. doing quick spherical unfolding.
  301. setting seed for random number genererator to 1234
  302. $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  303. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  304. reading original vertex positions...
  305. unfolding cortex into spherical form...
  306. surface projected - minimizing metric distortion...
  307. vertex spacing 0.90 +- 0.48 (0.00-->7.08) (max @ vno 64852 --> 64878)
  308. face area 0.02 +- 0.03 (-0.33-->0.61)
  309.  
  310. == Number of threads available to mris_sphere for OpenMP = 8 ==
  311. scaling brain by 0.326...
  312. inflating to sphere (rms error < 2.00)
  313. 000: dt: 0.0000, rms radial error=174.727, avgs=0
  314. 005/300: dt: 0.9000, rms radial error=174.468, avgs=0
  315. 010/300: dt: 0.9000, rms radial error=173.914, avgs=0
  316. 015/300: dt: 0.9000, rms radial error=173.185, avgs=0
  317. 020/300: dt: 0.9000, rms radial error=172.356, avgs=0
  318. 025/300: dt: 0.9000, rms radial error=171.469, avgs=0
  319. 030/300: dt: 0.9000, rms radial error=170.550, avgs=0
  320. 035/300: dt: 0.9000, rms radial error=169.615, avgs=0
  321. 040/300: dt: 0.9000, rms radial error=168.672, avgs=0
  322. 045/300: dt: 0.9000, rms radial error=167.727, avgs=0
  323. 050/300: dt: 0.9000, rms radial error=166.782, avgs=0
  324. 055/300: dt: 0.9000, rms radial error=165.840, avgs=0
  325. 060/300: dt: 0.9000, rms radial error=164.902, avgs=0
  326. 065/300: dt: 0.9000, rms radial error=163.969, avgs=0
  327. 070/300: dt: 0.9000, rms radial error=163.040, avgs=0
  328. 075/300: dt: 0.9000, rms radial error=162.116, avgs=0
  329. 080/300: dt: 0.9000, rms radial error=161.198, avgs=0
  330. 085/300: dt: 0.9000, rms radial error=160.285, avgs=0
  331. 090/300: dt: 0.9000, rms radial error=159.377, avgs=0
  332. 095/300: dt: 0.9000, rms radial error=158.475, avgs=0
  333. 100/300: dt: 0.9000, rms radial error=157.579, avgs=0
  334. 105/300: dt: 0.9000, rms radial error=156.687, avgs=0
  335. 110/300: dt: 0.9000, rms radial error=155.800, avgs=0
  336. 115/300: dt: 0.9000, rms radial error=154.918, avgs=0
  337. 120/300: dt: 0.9000, rms radial error=154.041, avgs=0
  338. 125/300: dt: 0.9000, rms radial error=153.169, avgs=0
  339. 130/300: dt: 0.9000, rms radial error=152.303, avgs=0
  340. 135/300: dt: 0.9000, rms radial error=151.441, avgs=0
  341. 140/300: dt: 0.9000, rms radial error=150.583, avgs=0
  342. 145/300: dt: 0.9000, rms radial error=149.731, avgs=0
  343. 150/300: dt: 0.9000, rms radial error=148.884, avgs=0
  344. 155/300: dt: 0.9000, rms radial error=148.041, avgs=0
  345. 160/300: dt: 0.9000, rms radial error=147.203, avgs=0
  346. 165/300: dt: 0.9000, rms radial error=146.370, avgs=0
  347. 170/300: dt: 0.9000, rms radial error=145.542, avgs=0
  348. 175/300: dt: 0.9000, rms radial error=144.718, avgs=0
  349. 180/300: dt: 0.9000, rms radial error=143.899, avgs=0
  350. 185/300: dt: 0.9000, rms radial error=143.085, avgs=0
  351. 190/300: dt: 0.9000, rms radial error=142.275, avgs=0
  352. 195/300: dt: 0.9000, rms radial error=141.470, avgs=0
  353. 200/300: dt: 0.9000, rms radial error=140.670, avgs=0
  354. 205/300: dt: 0.9000, rms radial error=139.874, avgs=0
  355. 210/300: dt: 0.9000, rms radial error=139.082, avgs=0
  356. 215/300: dt: 0.9000, rms radial error=138.295, avgs=0
  357. 220/300: dt: 0.9000, rms radial error=137.512, avgs=0
  358. 225/300: dt: 0.9000, rms radial error=136.734, avgs=0
  359. 230/300: dt: 0.9000, rms radial error=135.960, avgs=0
  360. 235/300: dt: 0.9000, rms radial error=135.191, avgs=0
  361. 240/300: dt: 0.9000, rms radial error=134.426, avgs=0
  362. 245/300: dt: 0.9000, rms radial error=133.665, avgs=0
  363. 250/300: dt: 0.9000, rms radial error=132.909, avgs=0
  364. 255/300: dt: 0.9000, rms radial error=132.157, avgs=0
  365. 260/300: dt: 0.9000, rms radial error=131.409, avgs=0
  366. 265/300: dt: 0.9000, rms radial error=130.665, avgs=0
  367. 270/300: dt: 0.9000, rms radial error=129.926, avgs=0
  368. 275/300: dt: 0.9000, rms radial error=129.191, avgs=0
  369. 280/300: dt: 0.9000, rms radial error=128.460, avgs=0
  370. 285/300: dt: 0.9000, rms radial error=127.733, avgs=0
  371. 290/300: dt: 0.9000, rms radial error=127.010, avgs=0
  372. 295/300: dt: 0.9000, rms radial error=126.291, avgs=0
  373. 300/300: dt: 0.9000, rms radial error=125.577, avgs=0
  374.  
  375. spherical inflation complete.
  376. epoch 1 (K=10.0), pass 1, starting sse = 19409.97
  377. taking momentum steps...
  378. taking momentum steps...
  379. taking momentum steps...
  380. pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
  381. epoch 2 (K=40.0), pass 1, starting sse = 3272.87
  382. taking momentum steps...
  383. taking momentum steps...
  384. taking momentum steps...
  385. pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
  386. epoch 3 (K=160.0), pass 1, starting sse = 328.10
  387. taking momentum steps...
  388. taking momentum steps...
  389. taking momentum steps...
  390. pass 1 complete, delta sse/iter = 0.05/10 = 0.00539
  391. epoch 4 (K=640.0), pass 1, starting sse = 18.96
  392. taking momentum steps...
  393. taking momentum steps...
  394. taking momentum steps...
  395. pass 1 complete, delta sse/iter = 0.06/13 = 0.00428
  396. final distance error %22.54
  397. writing spherical brain to ../surf/lh.qsphere.nofix
  398. spherical transformation took 0.03 hours
  399. mris_sphere utimesec 389.701493
  400. mris_sphere stimesec 0.912903
  401. mris_sphere ru_maxrss 264788
  402. mris_sphere ru_ixrss 0
  403. mris_sphere ru_idrss 0
  404. mris_sphere ru_isrss 0
  405. mris_sphere ru_minflt 65066
  406. mris_sphere ru_majflt 0
  407. mris_sphere ru_nswap 0
  408. mris_sphere ru_inblock 0
  409. mris_sphere ru_oublock 11536
  410. mris_sphere ru_msgsnd 0
  411. mris_sphere ru_msgrcv 0
  412. mris_sphere ru_nsignals 0
  413. mris_sphere ru_nvcsw 107380
  414. mris_sphere ru_nivcsw 3450
  415. FSRUNTIME@ mris_sphere 0.0281 hours 1 threads
  416. #--------------------------------------------
  417. #@# Fix Topology Copy lh Wed Dec 1 03:48:15 UTC 2021
  418. /out/freesurfer/sub-003/scripts
  419.  
  420. cp ../surf/lh.orig.nofix ../surf/lh.orig
  421.  
  422.  
  423. cp ../surf/lh.inflated.nofix ../surf/lh.inflated
  424.  
  425. #@# Fix Topology lh Wed Dec 1 03:48:15 UTC 2021
  426.  
  427. mris_fix_topology -rusage /out/freesurfer/sub-003/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-003 lh
  428.  
  429. reading spherical homeomorphism from 'qsphere.nofix'
  430. using genetic algorithm with optimized parameters
  431. setting seed for random number genererator to 1234
  432.  
  433. *************************************************************
  434. Topology Correction Parameters
  435. retessellation mode: genetic search
  436. number of patches/generation : 10
  437. number of generations : 10
  438. surface mri loglikelihood coefficient : 1.0
  439. volume mri loglikelihood coefficient : 10.0
  440. normal dot loglikelihood coefficient : 1.0
  441. quadratic curvature loglikelihood coefficient : 1.0
  442. volume resolution : 2
  443. eliminate vertices during search : 1
  444. initial patch selection : 1
  445. select all defect vertices : 0
  446. ordering dependant retessellation: 0
  447. use precomputed edge table : 0
  448. smooth retessellated patch : 2
  449. match retessellated patch : 1
  450. verbose mode : 0
  451.  
  452. *************************************************************
  453. INFO: assuming .mgz format
  454. $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  455. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  456. before topology correction, eno=-54 (nv=163928, nf=327964, ne=491946, g=28)
  457. using quasi-homeomorphic spherical map to tessellate cortical surface...
  458.  
  459. Correction of the Topology
  460. Finding true center and radius of Spherical Surface...done
  461. Surface centered at (0,0,0) with radius 100.0 in 8 iterations
  462. marking ambiguous vertices...
  463. 3198 ambiguous faces found in tessellation
  464. segmenting defects...
  465. 29 defects found, arbitrating ambiguous regions...
  466. analyzing neighboring defects...
  467. 29 defects to be corrected
  468. 0 vertices coincident
  469. reading input surface /out/freesurfer/sub-003/surf/lh.qsphere.nofix...
  470. reading brain volume from brain...
  471. reading wm segmentation from wm...
  472. Computing Initial Surface Statistics
  473. -face loglikelihood: -9.1468 (-4.5734)
  474. -vertex loglikelihood: -5.6958 (-2.8479)
  475. -normal dot loglikelihood: -3.6556 (-3.6556)
  476. -quad curv loglikelihood: -6.2626 (-3.1313)
  477. Total Loglikelihood : -24.7607
  478.  
  479. CORRECTING DEFECT 0 (vertices=33, convex hull=65, v0=8585)
  480. After retessellation of defect 0 (v0=8585), euler #=-24 (161959,485015,323032) : difference with theory (-26) = -2
  481.  
  482. CORRECTING DEFECT 1 (vertices=17, convex hull=53, v0=24240)
  483. After retessellation of defect 1 (v0=24240), euler #=-23 (161970,485068,323075) : difference with theory (-25) = -2
  484.  
  485. CORRECTING DEFECT 2 (vertices=21, convex hull=49, v0=24323)
  486. After retessellation of defect 2 (v0=24323), euler #=-22 (161977,485106,323107) : difference with theory (-24) = -2
  487.  
  488. CORRECTING DEFECT 3 (vertices=35, convex hull=80, v0=31433)
  489. After retessellation of defect 3 (v0=31433), euler #=-21 (161986,485163,323156) : difference with theory (-23) = -2
  490.  
  491. CORRECTING DEFECT 4 (vertices=23, convex hull=60, v0=40876)
  492. After retessellation of defect 4 (v0=40876), euler #=-20 (161996,485217,323201) : difference with theory (-22) = -2
  493.  
  494. CORRECTING DEFECT 5 (vertices=6, convex hull=30, v0=42602)
  495. After retessellation of defect 5 (v0=42602), euler #=-19 (161998,485230,323213) : difference with theory (-21) = -2
  496.  
  497. CORRECTING DEFECT 6 (vertices=58, convex hull=99, v0=50060)
  498. After retessellation of defect 6 (v0=50060), euler #=-18 (162021,485338,323299) : difference with theory (-20) = -2
  499.  
  500. CORRECTING DEFECT 7 (vertices=149, convex hull=151, v0=57784)
  501. normal vector of length zero at vertex 162225 with 3 faces
  502. After retessellation of defect 7 (v0=57784), euler #=-17 (162113,485685,323555) : difference with theory (-19) = -2
  503.  
  504. CORRECTING DEFECT 8 (vertices=12, convex hull=15, v0=58500)
  505. After retessellation of defect 8 (v0=58500), euler #=-16 (162114,485693,323563) : difference with theory (-18) = -2
  506.  
  507. CORRECTING DEFECT 9 (vertices=38, convex hull=32, v0=63322)
  508. After retessellation of defect 9 (v0=63322), euler #=-15 (162119,485719,323585) : difference with theory (-17) = -2
  509.  
  510. CORRECTING DEFECT 10 (vertices=38, convex hull=31, v0=65940)
  511. After retessellation of defect 10 (v0=65940), euler #=-14 (162122,485740,323604) : difference with theory (-16) = -2
  512.  
  513. CORRECTING DEFECT 11 (vertices=15, convex hull=16, v0=68107)
  514. After retessellation of defect 11 (v0=68107), euler #=-13 (162124,485750,323613) : difference with theory (-15) = -2
  515.  
  516. CORRECTING DEFECT 12 (vertices=23, convex hull=28, v0=74121)
  517. After retessellation of defect 12 (v0=74121), euler #=-12 (162127,485769,323630) : difference with theory (-14) = -2
  518.  
  519. CORRECTING DEFECT 13 (vertices=67, convex hull=78, v0=79224)
  520. After retessellation of defect 13 (v0=79224), euler #=-11 (162160,485906,323735) : difference with theory (-13) = -2
  521.  
  522. CORRECTING DEFECT 14 (vertices=45, convex hull=56, v0=103208)
  523. After retessellation of defect 14 (v0=103208), euler #=-11 (162181,485994,323802) : difference with theory (-12) = -1
  524.  
  525. CORRECTING DEFECT 15 (vertices=316, convex hull=165, v0=110198)
  526. After retessellation of defect 15 (v0=110198), euler #=-10 (162235,486244,323999) : difference with theory (-11) = -1
  527.  
  528. CORRECTING DEFECT 16 (vertices=135, convex hull=142, v0=118227)
  529. After retessellation of defect 16 (v0=118227), euler #=-9 (162274,486430,324147) : difference with theory (-10) = -1
  530.  
  531. CORRECTING DEFECT 17 (vertices=69, convex hull=95, v0=124108)
  532. After retessellation of defect 17 (v0=124108), euler #=-8 (162297,486542,324237) : difference with theory (-9) = -1
  533.  
  534. CORRECTING DEFECT 18 (vertices=379, convex hull=85, v0=125011)
  535. After retessellation of defect 18 (v0=125011), euler #=-8 (162328,486692,324356) : difference with theory (-8) = 0
  536.  
  537. CORRECTING DEFECT 19 (vertices=43, convex hull=75, v0=126244)
  538. After retessellation of defect 19 (v0=126244), euler #=-7 (162349,486784,324428) : difference with theory (-7) = 0
  539.  
  540. CORRECTING DEFECT 20 (vertices=6, convex hull=30, v0=127146)
  541. After retessellation of defect 20 (v0=127146), euler #=-6 (162351,486798,324441) : difference with theory (-6) = 0
  542.  
  543. CORRECTING DEFECT 21 (vertices=35, convex hull=63, v0=132949)
  544. After retessellation of defect 21 (v0=132949), euler #=-5 (162367,486872,324500) : difference with theory (-5) = 0
  545.  
  546. CORRECTING DEFECT 22 (vertices=156, convex hull=134, v0=135767)
  547. After retessellation of defect 22 (v0=135767), euler #=-4 (162416,487086,324666) : difference with theory (-4) = 0
  548.  
  549. CORRECTING DEFECT 23 (vertices=6, convex hull=21, v0=137417)
  550. After retessellation of defect 23 (v0=137417), euler #=-3 (162416,487092,324673) : difference with theory (-3) = 0
  551.  
  552. CORRECTING DEFECT 24 (vertices=48, convex hull=74, v0=146729)
  553. After retessellation of defect 24 (v0=146729), euler #=-2 (162437,487185,324746) : difference with theory (-2) = 0
  554.  
  555. CORRECTING DEFECT 25 (vertices=36, convex hull=78, v0=149826)
  556. After retessellation of defect 25 (v0=149826), euler #=-1 (162460,487284,324823) : difference with theory (-1) = 0
  557.  
  558. CORRECTING DEFECT 26 (vertices=18, convex hull=24, v0=154581)
  559. After retessellation of defect 26 (v0=154581), euler #=0 (162460,487291,324831) : difference with theory (0) = 0
  560.  
  561. CORRECTING DEFECT 27 (vertices=100, convex hull=108, v0=159713)
  562. After retessellation of defect 27 (v0=159713), euler #=1 (162495,487444,324950) : difference with theory (1) = 0
  563.  
  564. CORRECTING DEFECT 28 (vertices=53, convex hull=80, v0=161242)
  565. After retessellation of defect 28 (v0=161242), euler #=2 (162504,487506,325004) : difference with theory (2) = 0
  566. computing original vertex metric properties...
  567. storing new metric properties...
  568. computing tessellation statistics...
  569. vertex spacing 0.79 +- 0.20 (0.07-->7.22) (max @ vno 60122 --> 64354)
  570. face area 0.00 +- 0.00 (0.00-->0.00)
  571. performing soap bubble on retessellated vertices for 0 iterations...
  572. vertex spacing 0.79 +- 0.20 (0.07-->7.22) (max @ vno 60122 --> 64354)
  573. face area 0.00 +- 0.00 (0.00-->0.00)
  574. tessellation finished, orienting corrected surface...
  575. 105 mutations (35.8%), 188 crossovers (64.2%), 125 vertices were eliminated
  576. building final representation...
  577. 1424 vertices and 0 faces have been removed from triangulation
  578. after topology correction, eno=2 (nv=162504, nf=325004, ne=487506, g=0)
  579. writing corrected surface to /out/freesurfer/sub-003/surf/lh.orig...
  580.  
  581. 0.000 % of the vertices (0 vertices) exhibit an orientation change
  582. topology fixing took 12.1 minutes
  583. 0 defective edges
  584. removing intersecting faces
  585. 000: 231 intersecting
  586. 001: 4 intersecting
  587. mris_fix_topology utimesec 734.402801
  588. mris_fix_topology stimesec 0.199976
  589. mris_fix_topology ru_maxrss 528148
  590. mris_fix_topology ru_ixrss 0
  591. mris_fix_topology ru_idrss 0
  592. mris_fix_topology ru_isrss 0
  593. mris_fix_topology ru_minflt 131544
  594. mris_fix_topology ru_majflt 8
  595. mris_fix_topology ru_nswap 0
  596. mris_fix_topology ru_inblock 1464
  597. mris_fix_topology ru_oublock 15296
  598. mris_fix_topology ru_msgsnd 0
  599. mris_fix_topology ru_msgrcv 0
  600. mris_fix_topology ru_nsignals 0
  601. mris_fix_topology ru_nvcsw 796
  602. mris_fix_topology ru_nivcsw 367
  603. FSRUNTIME@ mris_fix_topology lh 0.2017 hours 1 threads
  604.  
  605. mris_euler_number ../surf/lh.orig
  606.  
  607. euler # = v-e+f = 2g-2: 162504 - 487506 + 325004 = 2 --> 0 holes
  608. F =2V-4: 325004 = 325008-4 (0)
  609. 2E=3F: 975012 = 975012 (0)
  610.  
  611. total defect index = 0
  612. /out/freesurfer/sub-003/scripts
  613.  
  614. mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
  615.  
  616. intersection removal took 0.00 hours
  617. removing intersecting faces
  618. 000: 38 intersecting
  619. writing corrected surface to ../surf/lh.orig
  620.  
  621. rm ../surf/lh.inflated
  622.  
  623. #--------------------------------------------
  624. #@# Make White Surf lh Wed Dec 1 04:00:25 UTC 2021
  625. /out/freesurfer/sub-003/scripts
  626.  
  627. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-003 lh
  628.  
  629. using white.preaparc as white matter name...
  630. only generating white matter surface
  631. using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
  632. not using aparc to prevent surfaces crossing the midline
  633. INFO: assuming MGZ format for volumes.
  634. using brain.finalsurfs as T1 volume...
  635. $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
  636. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  637. reading volume /out/freesurfer/sub-003/mri/filled.mgz...
  638. reading volume /out/freesurfer/sub-003/mri/brain.finalsurfs.mgz...
  639. reading volume /out/freesurfer/sub-003/mri/../mri/aseg.presurf.mgz...
  640. reading volume /out/freesurfer/sub-003/mri/wm.mgz...
  641. 24262 bright wm thresholded.
  642. 58 bright non-wm voxels segmented.
  643. reading original surface position from /out/freesurfer/sub-003/surf/lh.orig...
  644. computing class statistics...
  645. border white: 307435 voxels (1.83%)
  646. border gray 334714 voxels (2.00%)
  647. WM (100.0): 100.4 +- 6.4 [70.0 --> 110.0]
  648. GM (82.0) : 80.9 +- 8.9 [30.0 --> 110.0]
  649. setting MIN_GRAY_AT_WHITE_BORDER to 69.1 (was 70)
  650. setting MAX_BORDER_WHITE to 111.4 (was 105)
  651. setting MIN_BORDER_WHITE to 78.0 (was 85)
  652. setting MAX_CSF to 60.2 (was 40)
  653. setting MAX_GRAY to 98.6 (was 95)
  654. setting MAX_GRAY_AT_CSF_BORDER to 69.1 (was 75)
  655. setting MIN_GRAY_AT_CSF_BORDER to 51.4 (was 40)
  656. repositioning cortical surface to gray/white boundary
  657. smoothing T1 volume with sigma = 2.000
  658. vertex spacing 0.74 +- 0.19 (0.02-->2.97) (max @ vno 162387 --> 162395)
  659. face area 0.23 +- 0.10 (0.00-->2.18)
  660. mean absolute distance = 1.55 +- 1.69
  661. 5234 vertices more than 2 sigmas from mean.
  662. averaging target values for 5 iterations...
  663. spring scale = 1.11
  664. using class modes intead of means, discounting robust sigmas....
  665. intensity peaks found at WM=105+-4.3, GM=78+-6.1
  666. mean inside = 97.8, mean outside = 83.4
  667. smoothing surface for 5 iterations...
  668. inhibiting deformation at non-cortical midline structures...
  669. removing 4 vertex label from ripped group
  670. mean border=94.5, 35 (35) missing vertices, mean dist -0.7 [2.1 (%55.1)->0.7 (%44.9))]
  671. %47 local maxima, %37 large gradients and %12 min vals, 0 gradients ignored
  672. tol=1.0e-04, sigma=2.0, host=eeff2, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.239, l_nspring=0.557, l_intensity=0.200, l_curv=1.000
  673. mom=0.00, dt=0.50
  674. complete_dist_mat 0
  675. rms 0
  676. smooth_averages 0
  677. remove_neg 0
  678. ico_order 0
  679. which_surface 0
  680. target_radius 0.000000
  681. nfields 0
  682. scale 0.000000
  683. desired_rms_height 0.000000
  684. momentum 0.000000
  685. nbhd_size 0
  686. max_nbrs 0
  687. niterations 25
  688. nsurfaces 0
  689. SURFACES 3
  690. flags 0 (0)
  691. use curv 0
  692. no sulc 0
  693. no rigid align 0
  694. mris->nsize 2
  695. mris->hemisphere 0
  696. randomSeed 0
  697.  
  698. smoothing T1 volume with sigma = 1.000
  699. vertex spacing 0.79 +- 0.22 (0.07-->3.47) (max @ vno 162387 --> 162395)
  700. face area 0.23 +- 0.11 (0.00-->2.44)
  701. mean absolute distance = 0.72 +- 0.94
  702. 4996 vertices more than 2 sigmas from mean.
  703. averaging target values for 5 iterations...
  704. 000: dt: 0.0000, sse=3233881.2, rms=9.071
  705. 001: dt: 0.5000, sse=1765713.1, rms=5.940 (34.516%)
  706. 002: dt: 0.5000, sse=1116920.5, rms=3.766 (36.608%)
  707. 003: dt: 0.5000, sse=940558.4, rms=2.803 (25.553%)
  708. 004: dt: 0.5000, sse=890548.4, rms=2.515 (10.288%)
  709. 005: dt: 0.5000, sse=868483.9, rms=2.429 (3.406%)
  710. rms = 2.39, time step reduction 1 of 3 to 0.250...
  711. 006: dt: 0.5000, sse=854074.9, rms=2.391 (1.570%)
  712. 007: dt: 0.2500, sse=752090.0, rms=1.520 (36.444%)
  713. 008: dt: 0.2500, sse=747553.8, rms=1.326 (12.763%)
  714. 009: dt: 0.2500, sse=730620.7, rms=1.268 (4.345%)
  715. rms = 1.23, time step reduction 2 of 3 to 0.125...
  716. 010: dt: 0.2500, sse=743946.1, rms=1.225 (3.402%)
  717. rms = 1.21, time step reduction 3 of 3 to 0.062...
  718. 011: dt: 0.1250, sse=723482.1, rms=1.209 (1.332%)
  719. positioning took 0.8 minutes
  720. inhibiting deformation at non-cortical midline structures...
  721. removing 1 vertex label from ripped group
  722. removing 2 vertex label from ripped group
  723. mean border=93.3, 82 (12) missing vertices, mean dist -0.1 [1.1 (%36.9)->0.4 (%63.1))]
  724. %75 local maxima, %17 large gradients and % 3 min vals, 0 gradients ignored
  725. tol=1.0e-04, sigma=1.0, host=eeff2, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.239, l_nspring=0.557, l_intensity=0.200, l_curv=1.000
  726. mom=0.00, dt=0.50
  727. smoothing T1 volume with sigma = 0.500
  728. vertex spacing 0.78 +- 0.21 (0.06-->3.78) (max @ vno 113939 --> 112739)
  729. face area 0.26 +- 0.12 (0.00-->3.07)
  730. mean absolute distance = 0.43 +- 0.70
  731. 6659 vertices more than 2 sigmas from mean.
  732. averaging target values for 5 iterations...
  733. 000: dt: 0.0000, sse=1292450.1, rms=4.127
  734. 012: dt: 0.5000, sse=940380.9, rms=2.407 (41.670%)
  735. 013: dt: 0.5000, sse=879051.8, rms=1.980 (17.774%)
  736. rms = 2.03, time step reduction 1 of 3 to 0.250...
  737. 014: dt: 0.2500, sse=818777.9, rms=1.439 (27.284%)
  738. 015: dt: 0.2500, sse=796150.8, rms=1.108 (23.052%)
  739. 016: dt: 0.2500, sse=787752.4, rms=1.025 (7.453%)
  740. rms = 0.99, time step reduction 2 of 3 to 0.125...
  741. 017: dt: 0.2500, sse=787102.1, rms=0.988 (3.628%)
  742. rms = 0.98, time step reduction 3 of 3 to 0.062...
  743. 018: dt: 0.1250, sse=786545.9, rms=0.977 (1.055%)
  744. positioning took 0.5 minutes
  745. inhibiting deformation at non-cortical midline structures...
  746. mean border=93.6, 67 (5) missing vertices, mean dist -0.1 [0.6 (%49.1)->0.3 (%50.9))]
  747. %86 local maxima, % 8 large gradients and % 1 min vals, 0 gradients ignored
  748. tol=1.0e-04, sigma=0.5, host=eeff2, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.239, l_nspring=0.557, l_intensity=0.200, l_curv=1.000
  749. mom=0.00, dt=0.50
  750. smoothing T1 volume with sigma = 0.250
  751. vertex spacing 0.78 +- 0.21 (0.02-->3.68) (max @ vno 34941 --> 34963)
  752. face area 0.25 +- 0.12 (0.00-->3.12)
  753. mean absolute distance = 0.32 +- 0.54
  754. 5455 vertices more than 2 sigmas from mean.
  755. averaging target values for 5 iterations...
  756. 000: dt: 0.0000, sse=896520.8, rms=2.268
  757. 019: dt: 0.5000, sse=815495.4, rms=1.572 (30.708%)
  758. rms = 1.58, time step reduction 1 of 3 to 0.250...
  759. 020: dt: 0.2500, sse=776513.4, rms=1.187 (24.461%)
  760. 021: dt: 0.2500, sse=764058.2, rms=0.970 (18.314%)
  761. rms = 0.92, time step reduction 2 of 3 to 0.125...
  762. 022: dt: 0.2500, sse=761770.1, rms=0.921 (5.083%)
  763. rms = 0.90, time step reduction 3 of 3 to 0.062...
  764. 023: dt: 0.1250, sse=773591.0, rms=0.902 (2.057%)
  765. positioning took 0.4 minutes
  766. inhibiting deformation at non-cortical midline structures...
  767. removing 4 vertex label from ripped group
  768. removing 4 vertex label from ripped group
  769. mean border=93.5, 47 (4) missing vertices, mean dist -0.1 [0.4 (%46.5)->0.3 (%53.5))]
  770. %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
  771. tol=1.0e-04, sigma=0.2, host=eeff2, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.239, l_nspring=0.557, l_intensity=0.200, l_curv=1.000
  772. mom=0.00, dt=0.50
  773. writing white matter surface to /out/freesurfer/sub-003/surf/lh.white.preaparc...
  774. writing smoothed curvature to lh.curv
  775. 000: dt: 0.0000, sse=825156.3, rms=1.591
  776. 024: dt: 0.5000, sse=768712.9, rms=1.100 (30.863%)
  777. rms = 1.34, time step reduction 1 of 3 to 0.250...
  778. 025: dt: 0.2500, sse=750135.9, rms=0.842 (23.491%)
  779. 026: dt: 0.2500, sse=748694.1, rms=0.776 (7.770%)
  780. rms = 0.75, time step reduction 2 of 3 to 0.125...
  781. 027: dt: 0.2500, sse=743344.0, rms=0.745 (4.024%)
  782. rms = 0.76, time step reduction 3 of 3 to 0.062...
  783. 028: dt: 0.1250, sse=743854.0, rms=0.759 (-1.837%)
  784. positioning took 0.4 minutes
  785. generating cortex label...
  786. 5 non-cortical segments detected
  787. only using segment with 9085 vertices
  788. erasing segment 0 (vno[0] = 33837)
  789. erasing segment 2 (vno[0] = 113824)
  790. erasing segment 3 (vno[0] = 116242)
  791. erasing segment 4 (vno[0] = 121794)
  792. writing cortex label to /out/freesurfer/sub-003/label/lh.cortex.label...
  793. writing curvature file /out/freesurfer/sub-003/surf/lh.curv
  794. writing smoothed area to lh.area
  795. writing curvature file /out/freesurfer/sub-003/surf/lh.area
  796. vertex spacing 0.78 +- 0.21 (0.01-->3.78) (max @ vno 112739 --> 113939)
  797. face area 0.25 +- 0.12 (0.00-->3.20)
  798. refinement took 3.1 minutes
  799. #--------------------------------------------
  800. #@# Smooth2 lh Wed Dec 1 04:03:32 UTC 2021
  801. /out/freesurfer/sub-003/scripts
  802.  
  803. mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
  804.  
  805. smoothing for 3 iterations
  806. setting seed for random number generator to 1234
  807. smoothing surface tessellation for 3 iterations...
  808. smoothing complete - recomputing first and second fundamental forms...
  809. #--------------------------------------------
  810. #@# Inflation2 lh Wed Dec 1 04:03:36 UTC 2021
  811. /out/freesurfer/sub-003/scripts
  812.  
  813. mris_inflate -rusage /out/freesurfer/sub-003/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated
  814.  
  815. niterations = 50
  816. Reading ../surf/lh.smoothwm
  817. avg radius = 44.9 mm, total surface area = 76046 mm^2
  818. writing inflated surface to ../surf/lh.inflated
  819. writing sulcal depths to ../surf/lh.sulc
  820.  
  821. step 000: RMS=0.162 (target=0.015)
  822. step 005: RMS=0.116 (target=0.015)
  823. step 010: RMS=0.086 (target=0.015)
  824. step 015: RMS=0.071 (target=0.015)
  825. step 020: RMS=0.059 (target=0.015)
  826. step 025: RMS=0.050 (target=0.015)
  827. step 030: RMS=0.042 (target=0.015)
  828. step 035: RMS=0.036 (target=0.015)
  829. step 040: RMS=0.032 (target=0.015)
  830. step 045: RMS=0.028 (target=0.015)
  831. step 050: RMS=0.025 (target=0.015)
  832. step 055: RMS=0.024 (target=0.015)
  833. step 060: RMS=0.022 (target=0.015)
  834. step 065: RMS=0.021 (target=0.015)
  835. step 070: RMS=0.020 (target=0.015)
  836. step 075: RMS=0.019 (target=0.015)
  837. step 080: RMS=0.019 (target=0.015)
  838. step 085: RMS=0.018 (target=0.015)
  839. step 090: RMS=0.018 (target=0.015)
  840. step 095: RMS=0.018 (target=0.015)
  841. step 100: RMS=0.017 (target=0.015)
  842. step 105: RMS=0.017 (target=0.015)
  843. step 110: RMS=0.017 (target=0.015)
  844. step 115: RMS=0.017 (target=0.015)
  845. step 120: RMS=0.017 (target=0.015)
  846. step 125: RMS=0.017 (target=0.015)
  847. step 130: RMS=0.016 (target=0.015)
  848. step 135: RMS=0.016 (target=0.015)
  849. step 140: RMS=0.016 (target=0.015)
  850. step 145: RMS=0.016 (target=0.015)
  851. step 150: RMS=0.016 (target=0.015)
  852. step 155: RMS=0.016 (target=0.015)
  853. step 160: RMS=0.016 (target=0.015)
  854. step 165: RMS=0.016 (target=0.015)
  855. step 170: RMS=0.016 (target=0.015)
  856. step 175: RMS=0.016 (target=0.015)
  857. step 180: RMS=0.016 (target=0.015)
  858. step 185: RMS=0.016 (target=0.015)
  859. step 190: RMS=0.016 (target=0.015)
  860. step 195: RMS=0.015 (target=0.015)
  861. step 200: RMS=0.015 (target=0.015)
  862. step 205: RMS=0.015 (target=0.015)
  863. step 210: RMS=0.015 (target=0.015)
  864. step 215: RMS=0.015 (target=0.015)
  865. step 220: RMS=0.015 (target=0.015)
  866. step 225: RMS=0.015 (target=0.015)
  867. step 230: RMS=0.015 (target=0.015)
  868. step 235: RMS=0.015 (target=0.015)
  869. step 240: RMS=0.015 (target=0.015)
  870. step 245: RMS=0.015 (target=0.015)
  871. step 250: RMS=0.015 (target=0.015)
  872. step 255: RMS=0.015 (target=0.015)
  873. step 260: RMS=0.015 (target=0.015)
  874. step 265: RMS=0.015 (target=0.015)
  875. step 270: RMS=0.015 (target=0.015)
  876. step 275: RMS=0.015 (target=0.015)
  877. step 280: RMS=0.015 (target=0.015)
  878. step 285: RMS=0.015 (target=0.015)
  879. step 290: RMS=0.015 (target=0.015)
  880. step 295: RMS=0.015 (target=0.015)
  881. step 300: RMS=0.015 (target=0.015)
  882. inflation complete.
  883. inflation took 1.0 minutes
  884. mris_inflate utimesec 280.498084
  885. mris_inflate stimesec 0.873651
  886. mris_inflate ru_maxrss 262516
  887. mris_inflate ru_ixrss 0
  888. mris_inflate ru_idrss 0
  889. mris_inflate ru_isrss 0
  890. mris_inflate ru_minflt 64466
  891. mris_inflate ru_majflt 0
  892. mris_inflate ru_nswap 0
  893. mris_inflate ru_inblock 0
  894. mris_inflate ru_oublock 12704
  895. mris_inflate ru_msgsnd 0
  896. mris_inflate ru_msgrcv 0
  897. mris_inflate ru_nsignals 0
  898. mris_inflate ru_nvcsw 105838
  899. mris_inflate ru_nivcsw 945
  900. #--------------------------------------------
  901. #@# Curv .H and .K lh Wed Dec 1 04:04:38 UTC 2021
  902. /out/freesurfer/sub-003/surf
  903.  
  904. mris_curvature -w lh.white.preaparc
  905.  
  906. total integrated curvature = 18.848*4pi (236.849) --> -18 handles
  907. ICI = 190.6, FI = 1869.5, variation=29563.506
  908. writing Gaussian curvature to ./lh.white.preaparc.K...done.
  909. writing mean curvature to ./lh.white.preaparc.H...done.
  910. rm -f lh.white.H
  911. ln -s lh.white.preaparc.H lh.white.H
  912. Linux eeff23e566a8 5.4.0-91-generic #102~18.04.1-Ubuntu SMP Thu Nov 11 14:46:36 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
  913.  
  914. recon-all -s sub-003 exited with ERRORS at Wed Dec 1 04:04:41 UTC 2021
  915.  
  916. To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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