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recon-all-rh.log

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Dec 1st, 2021
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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 rh -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 6848232 31485980 114820 27238220 57578848
  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: 2021/12/01-03:45:11-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: 2021/12/01-03:45:11-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: 2021/12/01-03:45:11-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: 2021/12/01-03:45:11-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 rh Wed Dec 1 03:45:11 UTC 2021
  96. /out/freesurfer/sub-003/scripts
  97.  
  98. mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.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+): 2 found - 2 modified | TOTAL: 2
  105. pass 2 (yz+): 0 found - 2 modified | TOTAL: 2
  106. pass 1 (yz-): 1 found - 1 modified | TOTAL: 3
  107. pass 2 (yz-): 0 found - 1 modified | TOTAL: 3
  108. pass 1 (xz+): 1 found - 1 modified | TOTAL: 4
  109. pass 2 (xz+): 0 found - 1 modified | TOTAL: 4
  110. pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
  111. Iteration Number : 1
  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. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  116. Iteration Number : 1
  117. pass 1 (++): 0 found - 0 modified | TOTAL: 0
  118. pass 1 (+-): 0 found - 0 modified | TOTAL: 0
  119. pass 1 (--): 0 found - 0 modified | TOTAL: 0
  120. pass 1 (-+): 0 found - 0 modified | TOTAL: 0
  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 = 4 (out of 342214: 0.001169)
  140. Ambiguous edge configurations...
  141.  
  142. mri_pretess done
  143.  
  144.  
  145. mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.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: 1628 vertices, 1753 faces
  150. slice 40: 7963 vertices, 8198 faces
  151. slice 50: 16289 vertices, 16621 faces
  152. slice 60: 26449 vertices, 26822 faces
  153. slice 70: 37742 vertices, 38153 faces
  154. slice 80: 49276 vertices, 49635 faces
  155. slice 90: 61429 vertices, 61922 faces
  156. slice 100: 75160 vertices, 75617 faces
  157. slice 110: 87796 vertices, 88260 faces
  158. slice 120: 99736 vertices, 100148 faces
  159. slice 130: 111460 vertices, 111901 faces
  160. slice 140: 122828 vertices, 123242 faces
  161. slice 150: 132646 vertices, 132988 faces
  162. slice 160: 141418 vertices, 141717 faces
  163. slice 170: 148820 vertices, 149091 faces
  164. slice 180: 155524 vertices, 155796 faces
  165. slice 190: 161149 vertices, 161363 faces
  166. slice 200: 164019 vertices, 164093 faces
  167. slice 210: 164132 vertices, 164176 faces
  168. slice 220: 164132 vertices, 164176 faces
  169. slice 230: 164132 vertices, 164176 faces
  170. slice 240: 164132 vertices, 164176 faces
  171. slice 250: 164132 vertices, 164176 faces
  172. using the conformed surface RAS to save vertex points...
  173. writing ../surf/rh.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-pretess127.mgz
  181.  
  182.  
  183. mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
  184.  
  185.  
  186. counting number of connected components...
  187. 164132 voxel in cpt #1: X=-44 [v=164132,e=492528,f=328352] located at (27.643436, -19.363033, 34.340668)
  188. For the whole surface: X=-44 [v=164132,e=492528,f=328352]
  189. One single component has been found
  190. nothing to do
  191. done
  192.  
  193. #--------------------------------------------
  194. #@# Smooth1 rh Wed Dec 1 03:45:15 UTC 2021
  195. /out/freesurfer/sub-003/scripts
  196.  
  197. mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.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 rh Wed Dec 1 03:45:19 UTC 2021
  204. /out/freesurfer/sub-003/scripts
  205.  
  206. mris_inflate -no-save-sulc -n 50 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
  207.  
  208. niterations = 50
  209. Not saving sulc
  210. Reading ../surf/rh.smoothwm.nofix
  211. avg radius = 45.4 mm, total surface area = 72300 mm^2
  212. writing inflated surface to ../surf/rh.inflated.nofix
  213. inflation took 1.2 minutes
  214.  
  215. step 000: RMS=0.145 (target=0.015)
  216. step 005: RMS=0.110 (target=0.015)
  217. step 010: RMS=0.082 (target=0.015)
  218. step 015: RMS=0.069 (target=0.015)
  219. step 020: RMS=0.060 (target=0.015)
  220. step 025: RMS=0.052 (target=0.015)
  221. step 030: RMS=0.045 (target=0.015)
  222. step 035: RMS=0.041 (target=0.015)
  223. step 040: RMS=0.037 (target=0.015)
  224. step 045: RMS=0.033 (target=0.015)
  225. step 050: RMS=0.032 (target=0.015)
  226. step 055: RMS=0.032 (target=0.015)
  227. step 060: RMS=0.031 (target=0.015)
  228. step 065: RMS=0.030 (target=0.015)
  229. step 070: RMS=0.029 (target=0.015)
  230. step 075: RMS=0.028 (target=0.015)
  231. step 080: RMS=0.028 (target=0.015)
  232. step 085: RMS=0.028 (target=0.015)
  233. step 090: RMS=0.028 (target=0.015)
  234. step 095: RMS=0.028 (target=0.015)
  235. step 100: RMS=0.028 (target=0.015)
  236. step 105: RMS=0.028 (target=0.015)
  237. step 110: RMS=0.028 (target=0.015)
  238. step 115: RMS=0.028 (target=0.015)
  239. step 120: RMS=0.028 (target=0.015)
  240. step 125: RMS=0.027 (target=0.015)
  241. step 130: RMS=0.027 (target=0.015)
  242. step 135: RMS=0.027 (target=0.015)
  243. step 140: RMS=0.027 (target=0.015)
  244. step 145: RMS=0.027 (target=0.015)
  245. step 150: RMS=0.027 (target=0.015)
  246. step 155: RMS=0.027 (target=0.015)
  247. step 160: RMS=0.027 (target=0.015)
  248. step 165: RMS=0.027 (target=0.015)
  249. step 170: RMS=0.027 (target=0.015)
  250. step 175: RMS=0.027 (target=0.015)
  251. step 180: RMS=0.027 (target=0.015)
  252. step 185: RMS=0.027 (target=0.015)
  253. step 190: RMS=0.027 (target=0.015)
  254. step 195: RMS=0.027 (target=0.015)
  255. step 200: RMS=0.027 (target=0.015)
  256. step 205: RMS=0.027 (target=0.015)
  257. step 210: RMS=0.027 (target=0.015)
  258. step 215: RMS=0.027 (target=0.015)
  259. step 220: RMS=0.027 (target=0.015)
  260. step 225: RMS=0.026 (target=0.015)
  261. step 230: RMS=0.026 (target=0.015)
  262. step 235: RMS=0.026 (target=0.015)
  263. step 240: RMS=0.026 (target=0.015)
  264. step 245: RMS=0.026 (target=0.015)
  265. step 250: RMS=0.026 (target=0.015)
  266. step 255: RMS=0.026 (target=0.015)
  267. step 260: RMS=0.026 (target=0.015)
  268. step 265: RMS=0.027 (target=0.015)
  269. step 270: RMS=0.027 (target=0.015)
  270. step 275: RMS=0.027 (target=0.015)
  271. step 280: RMS=0.027 (target=0.015)
  272. step 285: RMS=0.027 (target=0.015)
  273. step 290: RMS=0.027 (target=0.015)
  274. step 295: RMS=0.027 (target=0.015)
  275. step 300: RMS=0.027 (target=0.015)
  276. inflation complete.
  277. Not saving sulc
  278. mris_inflate utimesec 332.993694
  279. mris_inflate stimesec 0.886555
  280. mris_inflate ru_maxrss 264568
  281. mris_inflate ru_ixrss 0
  282. mris_inflate ru_idrss 0
  283. mris_inflate ru_isrss 0
  284. mris_inflate ru_minflt 65032
  285. mris_inflate ru_majflt 0
  286. mris_inflate ru_nswap 0
  287. mris_inflate ru_inblock 0
  288. mris_inflate ru_oublock 11552
  289. mris_inflate ru_msgsnd 0
  290. mris_inflate ru_msgrcv 0
  291. mris_inflate ru_nsignals 0
  292. mris_inflate ru_nvcsw 111147
  293. mris_inflate ru_nivcsw 4712
  294. #--------------------------------------------
  295. #@# QSphere rh Wed Dec 1 03:46:33 UTC 2021
  296. /out/freesurfer/sub-003/scripts
  297.  
  298. mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.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 0.89 +- 0.46 (0.00-->5.79) (max @ vno 125768 --> 126856)
  308. face area 0.02 +- 0.03 (-0.07-->0.61)
  309.  
  310. == Number of threads available to mris_sphere for OpenMP = 8 ==
  311. scaling brain by 0.323...
  312. inflating to sphere (rms error < 2.00)
  313. 000: dt: 0.0000, rms radial error=174.689, avgs=0
  314. 005/300: dt: 0.9000, rms radial error=174.432, avgs=0
  315. 010/300: dt: 0.9000, rms radial error=173.881, avgs=0
  316. 015/300: dt: 0.9000, rms radial error=173.157, avgs=0
  317. 020/300: dt: 0.9000, rms radial error=172.332, avgs=0
  318. 025/300: dt: 0.9000, rms radial error=171.449, avgs=0
  319. 030/300: dt: 0.9000, rms radial error=170.533, avgs=0
  320. 035/300: dt: 0.9000, rms radial error=169.600, avgs=0
  321. 040/300: dt: 0.9000, rms radial error=168.659, avgs=0
  322. 045/300: dt: 0.9000, rms radial error=167.716, avgs=0
  323. 050/300: dt: 0.9000, rms radial error=166.773, avgs=0
  324. 055/300: dt: 0.9000, rms radial error=165.833, avgs=0
  325. 060/300: dt: 0.9000, rms radial error=164.897, avgs=0
  326. 065/300: dt: 0.9000, rms radial error=163.965, avgs=0
  327. 070/300: dt: 0.9000, rms radial error=163.037, avgs=0
  328. 075/300: dt: 0.9000, rms radial error=162.115, avgs=0
  329. 080/300: dt: 0.9000, rms radial error=161.197, avgs=0
  330. 085/300: dt: 0.9000, rms radial error=160.285, avgs=0
  331. 090/300: dt: 0.9000, rms radial error=159.378, avgs=0
  332. 095/300: dt: 0.9000, rms radial error=158.476, 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=154.042, avgs=0
  338. 125/300: dt: 0.9000, rms radial error=153.170, 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=148.883, avgs=0
  344. 155/300: dt: 0.9000, rms radial error=148.040, avgs=0
  345. 160/300: dt: 0.9000, rms radial error=147.202, avgs=0
  346. 165/300: dt: 0.9000, rms radial error=146.369, avgs=0
  347. 170/300: dt: 0.9000, rms radial error=145.540, avgs=0
  348. 175/300: dt: 0.9000, rms radial error=144.716, avgs=0
  349. 180/300: dt: 0.9000, rms radial error=143.897, avgs=0
  350. 185/300: dt: 0.9000, rms radial error=143.082, avgs=0
  351. 190/300: dt: 0.9000, rms radial error=142.272, avgs=0
  352. 195/300: dt: 0.9000, rms radial error=141.467, avgs=0
  353. 200/300: dt: 0.9000, rms radial error=140.666, avgs=0
  354. 205/300: dt: 0.9000, rms radial error=139.869, avgs=0
  355. 210/300: dt: 0.9000, rms radial error=139.077, avgs=0
  356. 215/300: dt: 0.9000, rms radial error=138.290, avgs=0
  357. 220/300: dt: 0.9000, rms radial error=137.507, avgs=0
  358. 225/300: dt: 0.9000, rms radial error=136.728, avgs=0
  359. 230/300: dt: 0.9000, rms radial error=135.954, avgs=0
  360. 235/300: dt: 0.9000, rms radial error=135.184, avgs=0
  361. 240/300: dt: 0.9000, rms radial error=134.419, avgs=0
  362. 245/300: dt: 0.9000, rms radial error=133.658, avgs=0
  363. 250/300: dt: 0.9000, rms radial error=132.901, avgs=0
  364. 255/300: dt: 0.9000, rms radial error=132.149, avgs=0
  365. 260/300: dt: 0.9000, rms radial error=131.400, avgs=0
  366. 265/300: dt: 0.9000, rms radial error=130.657, avgs=0
  367. 270/300: dt: 0.9000, rms radial error=129.917, avgs=0
  368. 275/300: dt: 0.9000, rms radial error=129.181, avgs=0
  369. 280/300: dt: 0.9000, rms radial error=128.450, avgs=0
  370. 285/300: dt: 0.9000, rms radial error=127.723, avgs=0
  371. 290/300: dt: 0.9000, rms radial error=126.999, avgs=0
  372. 295/300: dt: 0.9000, rms radial error=126.280, avgs=0
  373. 300/300: dt: 0.9000, rms radial error=125.565, avgs=0
  374.  
  375. spherical inflation complete.
  376. epoch 1 (K=10.0), pass 1, starting sse = 19433.96
  377. taking momentum steps...
  378. taking momentum steps...
  379. taking momentum steps...
  380. pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
  381. epoch 2 (K=40.0), pass 1, starting sse = 3255.13
  382. taking momentum steps...
  383. taking momentum steps...
  384. taking momentum steps...
  385. pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
  386. epoch 3 (K=160.0), pass 1, starting sse = 329.28
  387. taking momentum steps...
  388. taking momentum steps...
  389. taking momentum steps...
  390. pass 1 complete, delta sse/iter = 0.09/11 = 0.00861
  391. epoch 4 (K=640.0), pass 1, starting sse = 17.39
  392. taking momentum steps...
  393. taking momentum steps...
  394. taking momentum steps...
  395. pass 1 complete, delta sse/iter = 0.28/19 = 0.01478
  396. final distance error %21.97
  397. writing spherical brain to ../surf/rh.qsphere.nofix
  398. spherical transformation took 0.03 hours
  399. mris_sphere utimesec 426.529413
  400. mris_sphere stimesec 0.987669
  401. mris_sphere ru_maxrss 264892
  402. mris_sphere ru_ixrss 0
  403. mris_sphere ru_idrss 0
  404. mris_sphere ru_isrss 0
  405. mris_sphere ru_minflt 65059
  406. mris_sphere ru_majflt 7
  407. mris_sphere ru_nswap 0
  408. mris_sphere ru_inblock 1304
  409. mris_sphere ru_oublock 11552
  410. mris_sphere ru_msgsnd 0
  411. mris_sphere ru_msgrcv 0
  412. mris_sphere ru_nsignals 0
  413. mris_sphere ru_nvcsw 107844
  414. mris_sphere ru_nivcsw 4700
  415. FSRUNTIME@ mris_sphere 0.0304 hours 1 threads
  416. #--------------------------------------------
  417. #@# Fix Topology Copy rh Wed Dec 1 03:48:23 UTC 2021
  418. /out/freesurfer/sub-003/scripts
  419.  
  420. cp ../surf/rh.orig.nofix ../surf/rh.orig
  421.  
  422.  
  423. cp ../surf/rh.inflated.nofix ../surf/rh.inflated
  424.  
  425. #@# Fix Topology rh Wed Dec 1 03:48:23 UTC 2021
  426.  
  427. mris_fix_topology -rusage /out/freesurfer/sub-003/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-003 rh
  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=-44 (nv=164132, nf=328352, ne=492528, g=23)
  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 9 iterations
  462. marking ambiguous vertices...
  463. 2348 ambiguous faces found in tessellation
  464. segmenting defects...
  465. 28 defects found, arbitrating ambiguous regions...
  466. analyzing neighboring defects...
  467. -merging segment 9 into 8
  468. 27 defects to be corrected
  469. 0 vertices coincident
  470. reading input surface /out/freesurfer/sub-003/surf/rh.qsphere.nofix...
  471. reading brain volume from brain...
  472. reading wm segmentation from wm...
  473. Computing Initial Surface Statistics
  474. -face loglikelihood: -9.1902 (-4.5951)
  475. -vertex loglikelihood: -5.7064 (-2.8532)
  476. -normal dot loglikelihood: -3.5710 (-3.5710)
  477. -quad curv loglikelihood: -6.2742 (-3.1371)
  478. Total Loglikelihood : -24.7418
  479.  
  480. CORRECTING DEFECT 0 (vertices=32, convex hull=63, v0=9691)
  481. After retessellation of defect 0 (v0=9691), euler #=-24 (162647,487323,324652) : difference with theory (-24) = 0
  482.  
  483. CORRECTING DEFECT 1 (vertices=23, convex hull=67, v0=24662)
  484. After retessellation of defect 1 (v0=24662), euler #=-23 (162659,487383,324701) : difference with theory (-23) = 0
  485.  
  486. CORRECTING DEFECT 2 (vertices=106, convex hull=112, v0=53435)
  487. After retessellation of defect 2 (v0=53435), euler #=-22 (162707,487582,324853) : difference with theory (-22) = 0
  488.  
  489. CORRECTING DEFECT 3 (vertices=7, convex hull=21, v0=55525)
  490. After retessellation of defect 3 (v0=55525), euler #=-21 (162710,487600,324869) : difference with theory (-21) = 0
  491.  
  492. CORRECTING DEFECT 4 (vertices=5, convex hull=26, v0=59439)
  493. After retessellation of defect 4 (v0=59439), euler #=-20 (162712,487614,324882) : difference with theory (-20) = 0
  494.  
  495. CORRECTING DEFECT 5 (vertices=58, convex hull=46, v0=62696)
  496. After retessellation of defect 5 (v0=62696), euler #=-19 (162723,487663,324921) : difference with theory (-19) = 0
  497.  
  498. CORRECTING DEFECT 6 (vertices=46, convex hull=30, v0=66747)
  499. After retessellation of defect 6 (v0=66747), euler #=-18 (162728,487684,324938) : difference with theory (-18) = 0
  500.  
  501. CORRECTING DEFECT 7 (vertices=26, convex hull=20, v0=69295)
  502. After retessellation of defect 7 (v0=69295), euler #=-17 (162730,487698,324951) : difference with theory (-17) = 0
  503.  
  504. CORRECTING DEFECT 8 (vertices=116, convex hull=97, v0=103823)
  505. After retessellation of defect 8 (v0=103823), euler #=-15 (162756,487825,325054) : difference with theory (-16) = -1
  506.  
  507. CORRECTING DEFECT 9 (vertices=199, convex hull=102, v0=113458)
  508. After retessellation of defect 9 (v0=113458), euler #=-14 (162803,488007,325190) : difference with theory (-15) = -1
  509.  
  510. CORRECTING DEFECT 10 (vertices=38, convex hull=44, v0=113539)
  511. After retessellation of defect 10 (v0=113539), euler #=-14 (162809,488049,325226) : difference with theory (-14) = 0
  512.  
  513. CORRECTING DEFECT 11 (vertices=105, convex hull=91, v0=115611)
  514. After retessellation of defect 11 (v0=115611), euler #=-13 (162841,488186,325332) : difference with theory (-13) = 0
  515.  
  516. CORRECTING DEFECT 12 (vertices=5, convex hull=26, v0=121485)
  517. After retessellation of defect 12 (v0=121485), euler #=-12 (162842,488196,325342) : difference with theory (-12) = 0
  518.  
  519. CORRECTING DEFECT 13 (vertices=59, convex hull=88, v0=123891)
  520. After retessellation of defect 13 (v0=123891), euler #=-11 (162867,488310,325432) : difference with theory (-11) = 0
  521.  
  522. CORRECTING DEFECT 14 (vertices=52, convex hull=91, v0=131734)
  523. After retessellation of defect 14 (v0=131734), euler #=-10 (162897,488441,325534) : difference with theory (-10) = 0
  524.  
  525. CORRECTING DEFECT 15 (vertices=7, convex hull=26, v0=134115)
  526. After retessellation of defect 15 (v0=134115), euler #=-9 (162899,488455,325547) : difference with theory (-9) = 0
  527.  
  528. CORRECTING DEFECT 16 (vertices=26, convex hull=28, v0=135011)
  529. After retessellation of defect 16 (v0=135011), euler #=-8 (162902,488472,325562) : difference with theory (-8) = 0
  530.  
  531. CORRECTING DEFECT 17 (vertices=6, convex hull=27, v0=135151)
  532. After retessellation of defect 17 (v0=135151), euler #=-7 (162903,488483,325573) : difference with theory (-7) = 0
  533.  
  534. CORRECTING DEFECT 18 (vertices=62, convex hull=101, v0=136206)
  535. After retessellation of defect 18 (v0=136206), euler #=-6 (162922,488583,325655) : difference with theory (-6) = 0
  536.  
  537. CORRECTING DEFECT 19 (vertices=28, convex hull=71, v0=143913)
  538. After retessellation of defect 19 (v0=143913), euler #=-5 (162931,488638,325702) : difference with theory (-5) = 0
  539.  
  540. CORRECTING DEFECT 20 (vertices=27, convex hull=55, v0=146921)
  541. After retessellation of defect 20 (v0=146921), euler #=-4 (162941,488688,325743) : difference with theory (-4) = 0
  542.  
  543. CORRECTING DEFECT 21 (vertices=342, convex hull=114, v0=147483)
  544. After retessellation of defect 21 (v0=147483), euler #=-3 (162960,488800,325837) : difference with theory (-3) = 0
  545.  
  546. CORRECTING DEFECT 22 (vertices=32, convex hull=45, v0=160197)
  547. After retessellation of defect 22 (v0=160197), euler #=-2 (162969,488844,325873) : difference with theory (-2) = 0
  548.  
  549. CORRECTING DEFECT 23 (vertices=19, convex hull=27, v0=160766)
  550. After retessellation of defect 23 (v0=160766), euler #=-1 (162973,488862,325888) : difference with theory (-1) = 0
  551.  
  552. CORRECTING DEFECT 24 (vertices=8, convex hull=30, v0=162716)
  553. After retessellation of defect 24 (v0=162716), euler #=0 (162975,488878,325903) : difference with theory (0) = 0
  554.  
  555. CORRECTING DEFECT 25 (vertices=17, convex hull=28, v0=162848)
  556. After retessellation of defect 25 (v0=162848), euler #=1 (162977,488896,325920) : difference with theory (1) = 0
  557.  
  558. CORRECTING DEFECT 26 (vertices=45, convex hull=78, v0=163451)
  559. After retessellation of defect 26 (v0=163451), euler #=2 (163003,489003,326002) : difference with theory (2) = 0
  560. computing original vertex metric properties...
  561. storing new metric properties...
  562. computing tessellation statistics...
  563. vertex spacing 0.80 +- 0.20 (0.09-->9.83) (max @ vno 149176 --> 156050)
  564. face area 0.00 +- 0.00 (0.00-->0.00)
  565. performing soap bubble on retessellated vertices for 0 iterations...
  566. vertex spacing 0.80 +- 0.20 (0.09-->9.83) (max @ vno 149176 --> 156050)
  567. face area 0.00 +- 0.00 (0.00-->0.00)
  568. tessellation finished, orienting corrected surface...
  569. 123 mutations (40.2%), 183 crossovers (59.8%), 89 vertices were eliminated
  570. building final representation...
  571. 1129 vertices and 0 faces have been removed from triangulation
  572. after topology correction, eno=2 (nv=163003, nf=326002, ne=489003, g=0)
  573. writing corrected surface to /out/freesurfer/sub-003/surf/rh.orig...
  574.  
  575. 0.000 % of the vertices (0 vertices) exhibit an orientation change
  576. topology fixing took 9.7 minutes
  577. 0 defective edges
  578. removing intersecting faces
  579. 000: 203 intersecting
  580. mris_fix_topology utimesec 590.444295
  581. mris_fix_topology stimesec 0.216020
  582. mris_fix_topology ru_maxrss 528884
  583. mris_fix_topology ru_ixrss 0
  584. mris_fix_topology ru_idrss 0
  585. mris_fix_topology ru_isrss 0
  586. mris_fix_topology ru_minflt 131662
  587. mris_fix_topology ru_majflt 0
  588. mris_fix_topology ru_nswap 0
  589. mris_fix_topology ru_inblock 0
  590. mris_fix_topology ru_oublock 15328
  591. mris_fix_topology ru_msgsnd 0
  592. mris_fix_topology ru_msgrcv 0
  593. mris_fix_topology ru_nsignals 0
  594. mris_fix_topology ru_nvcsw 838
  595. mris_fix_topology ru_nivcsw 1325
  596. FSRUNTIME@ mris_fix_topology rh 0.1616 hours 1 threads
  597.  
  598. mris_euler_number ../surf/rh.orig
  599.  
  600. euler # = v-e+f = 2g-2: 163003 - 489003 + 326002 = 2 --> 0 holes
  601. F =2V-4: 326002 = 326006-4 (0)
  602. 2E=3F: 978006 = 978006 (0)
  603.  
  604. total defect index = 0
  605. /out/freesurfer/sub-003/scripts
  606.  
  607. mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
  608.  
  609. intersection removal took 0.00 hours
  610. removing intersecting faces
  611. 000: 14 intersecting
  612. writing corrected surface to ../surf/rh.orig
  613.  
  614. rm ../surf/rh.inflated
  615.  
  616. #--------------------------------------------
  617. #@# Make White Surf rh Wed Dec 1 03:58:09 UTC 2021
  618. /out/freesurfer/sub-003/scripts
  619.  
  620. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-003 rh
  621.  
  622. using white.preaparc as white matter name...
  623. only generating white matter surface
  624. using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
  625. not using aparc to prevent surfaces crossing the midline
  626. INFO: assuming MGZ format for volumes.
  627. using brain.finalsurfs as T1 volume...
  628. $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
  629. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  630. reading volume /out/freesurfer/sub-003/mri/filled.mgz...
  631. reading volume /out/freesurfer/sub-003/mri/brain.finalsurfs.mgz...
  632. reading volume /out/freesurfer/sub-003/mri/../mri/aseg.presurf.mgz...
  633. reading volume /out/freesurfer/sub-003/mri/wm.mgz...
  634. 24262 bright wm thresholded.
  635. 58 bright non-wm voxels segmented.
  636. reading original surface position from /out/freesurfer/sub-003/surf/rh.orig...
  637. computing class statistics...
  638. border white: 307435 voxels (1.83%)
  639. border gray 334714 voxels (2.00%)
  640. WM (100.0): 100.4 +- 6.4 [70.0 --> 110.0]
  641. GM (82.0) : 80.9 +- 8.9 [30.0 --> 110.0]
  642. setting MIN_GRAY_AT_WHITE_BORDER to 69.1 (was 70)
  643. setting MAX_BORDER_WHITE to 111.4 (was 105)
  644. setting MIN_BORDER_WHITE to 78.0 (was 85)
  645. setting MAX_CSF to 60.2 (was 40)
  646. setting MAX_GRAY to 98.6 (was 95)
  647. setting MAX_GRAY_AT_CSF_BORDER to 69.1 (was 75)
  648. setting MIN_GRAY_AT_CSF_BORDER to 51.4 (was 40)
  649. repositioning cortical surface to gray/white boundary
  650. smoothing T1 volume with sigma = 2.000
  651. vertex spacing 0.75 +- 0.19 (0.03-->3.81) (max @ vno 155428 --> 162944)
  652. face area 0.23 +- 0.10 (0.00-->1.53)
  653. mean absolute distance = 1.48 +- 1.65
  654. 5183 vertices more than 2 sigmas from mean.
  655. averaging target values for 5 iterations...
  656. spring scale = 1.11
  657. using class modes intead of means, discounting robust sigmas....
  658. intensity peaks found at WM=105+-4.3, GM=78+-7.0
  659. mean inside = 97.7, mean outside = 83.4
  660. smoothing surface for 5 iterations...
  661. inhibiting deformation at non-cortical midline structures...
  662. mean border=94.2, 38 (38) missing vertices, mean dist -0.7 [2.0 (%54.4)->0.7 (%45.6))]
  663. %47 local maxima, %37 large gradients and %11 min vals, 0 gradients ignored
  664. 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
  665. mom=0.00, dt=0.50
  666. complete_dist_mat 0
  667. rms 0
  668. smooth_averages 0
  669. remove_neg 0
  670. ico_order 0
  671. which_surface 0
  672. target_radius 0.000000
  673. nfields 0
  674. scale 0.000000
  675. desired_rms_height 0.000000
  676. momentum 0.000000
  677. nbhd_size 0
  678. max_nbrs 0
  679. niterations 25
  680. nsurfaces 0
  681. SURFACES 3
  682. flags 0 (0)
  683. use curv 0
  684. no sulc 0
  685. no rigid align 0
  686. mris->nsize 2
  687. mris->hemisphere 1
  688. randomSeed 0
  689.  
  690. smoothing T1 volume with sigma = 1.000
  691. vertex spacing 0.79 +- 0.22 (0.03-->3.62) (max @ vno 155428 --> 162944)
  692. face area 0.23 +- 0.11 (0.00-->1.60)
  693. mean absolute distance = 0.70 +- 0.94
  694. 5155 vertices more than 2 sigmas from mean.
  695. averaging target values for 5 iterations...
  696. 000: dt: 0.0000, sse=3079369.0, rms=8.765
  697. 001: dt: 0.5000, sse=1666532.9, rms=5.643 (35.615%)
  698. 002: dt: 0.5000, sse=1070791.8, rms=3.519 (37.639%)
  699. 003: dt: 0.5000, sse=933299.4, rms=2.589 (26.427%)
  700. 004: dt: 0.5000, sse=860460.5, rms=2.310 (10.766%)
  701. 005: dt: 0.5000, sse=845033.0, rms=2.225 (3.694%)
  702. rms = 2.20, time step reduction 1 of 3 to 0.250...
  703. 006: dt: 0.5000, sse=834063.8, rms=2.198 (1.216%)
  704. 007: dt: 0.2500, sse=756494.4, rms=1.309 (40.438%)
  705. 008: dt: 0.2500, sse=734103.6, rms=1.136 (13.233%)
  706. rms = 1.09, time step reduction 2 of 3 to 0.125...
  707. 009: dt: 0.2500, sse=730529.8, rms=1.090 (4.049%)
  708. rms = 1.07, time step reduction 3 of 3 to 0.062...
  709. 010: dt: 0.1250, sse=735056.6, rms=1.072 (1.637%)
  710. positioning took 0.7 minutes
  711. inhibiting deformation at non-cortical midline structures...
  712. removing 1 vertex label from ripped group
  713. removing 4 vertex label from ripped group
  714. mean border=93.2, 46 (0) missing vertices, mean dist -0.1 [1.1 (%38.4)->0.4 (%61.6))]
  715. %73 local maxima, %19 large gradients and % 3 min vals, 0 gradients ignored
  716. 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
  717. mom=0.00, dt=0.50
  718. smoothing T1 volume with sigma = 0.500
  719. vertex spacing 0.78 +- 0.21 (0.04-->3.77) (max @ vno 113046 --> 113073)
  720. face area 0.26 +- 0.12 (0.00-->2.09)
  721. mean absolute distance = 0.42 +- 0.70
  722. 6266 vertices more than 2 sigmas from mean.
  723. averaging target values for 5 iterations...
  724. 000: dt: 0.0000, sse=1296502.2, rms=4.079
  725. 011: dt: 0.5000, sse=944641.7, rms=2.380 (41.667%)
  726. 012: dt: 0.5000, sse=872233.3, rms=1.898 (20.238%)
  727. rms = 1.91, time step reduction 1 of 3 to 0.250...
  728. 013: dt: 0.2500, sse=819433.6, rms=1.382 (27.181%)
  729. 014: dt: 0.2500, sse=804438.8, rms=1.052 (23.906%)
  730. 015: dt: 0.2500, sse=788628.7, rms=0.957 (8.967%)
  731. rms = 0.92, time step reduction 2 of 3 to 0.125...
  732. 016: dt: 0.2500, sse=786468.2, rms=0.923 (3.559%)
  733. rms = 0.90, time step reduction 3 of 3 to 0.062...
  734. 017: dt: 0.1250, sse=782799.9, rms=0.904 (2.075%)
  735. positioning took 0.5 minutes
  736. inhibiting deformation at non-cortical midline structures...
  737. removing 2 vertex label from ripped group
  738. mean border=93.9, 40 (0) missing vertices, mean dist -0.2 [0.5 (%52.7)->0.3 (%47.3))]
  739. %85 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored
  740. 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
  741. mom=0.00, dt=0.50
  742. smoothing T1 volume with sigma = 0.250
  743. vertex spacing 0.78 +- 0.21 (0.06-->4.13) (max @ vno 113046 --> 113073)
  744. face area 0.25 +- 0.12 (0.00-->2.51)
  745. mean absolute distance = 0.32 +- 0.54
  746. 5114 vertices more than 2 sigmas from mean.
  747. averaging target values for 5 iterations...
  748. 000: dt: 0.0000, sse=909782.3, rms=2.350
  749. 018: dt: 0.5000, sse=815063.1, rms=1.507 (35.849%)
  750. rms = 1.49, time step reduction 1 of 3 to 0.250...
  751. 019: dt: 0.5000, sse=811523.0, rms=1.486 (1.391%)
  752. 020: dt: 0.2500, sse=764868.1, rms=0.931 (37.393%)
  753. 021: dt: 0.2500, sse=760351.4, rms=0.849 (8.731%)
  754. rms = 0.84, time step reduction 2 of 3 to 0.125...
  755. 022: dt: 0.2500, sse=760507.2, rms=0.839 (1.168%)
  756. rms = 0.82, time step reduction 3 of 3 to 0.062...
  757. 023: dt: 0.1250, sse=757506.9, rms=0.824 (1.845%)
  758. positioning took 0.4 minutes
  759. inhibiting deformation at non-cortical midline structures...
  760. removing 1 vertex label from ripped group
  761. removing 3 vertex label from ripped group
  762. mean border=93.9, 42 (0) missing vertices, mean dist -0.1 [0.4 (%47.9)->0.2 (%52.1))]
  763. %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
  764. 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
  765. mom=0.00, dt=0.50
  766. writing white matter surface to /out/freesurfer/sub-003/surf/rh.white.preaparc...
  767. writing smoothed curvature to rh.curv
  768. 000: dt: 0.0000, sse=810153.2, rms=1.548
  769. 024: dt: 0.5000, sse=768173.2, rms=1.036 (33.091%)
  770. rms = 1.25, time step reduction 1 of 3 to 0.250...
  771. 025: dt: 0.2500, sse=751636.4, rms=0.780 (24.652%)
  772. 026: dt: 0.2500, sse=751991.6, rms=0.707 (9.389%)
  773. rms = 0.69, time step reduction 2 of 3 to 0.125...
  774. 027: dt: 0.2500, sse=754413.4, rms=0.688 (2.731%)
  775. rms = 0.69, time step reduction 3 of 3 to 0.062...
  776. 028: dt: 0.1250, sse=750438.5, rms=0.686 (0.234%)
  777. positioning took 0.4 minutes
  778. generating cortex label...
  779. 14 non-cortical segments detected
  780. only using segment with 9103 vertices
  781. erasing segment 1 (vno[0] = 65180)
  782. erasing segment 2 (vno[0] = 113001)
  783. erasing segment 3 (vno[0] = 114216)
  784. erasing segment 4 (vno[0] = 115230)
  785. erasing segment 5 (vno[0] = 120631)
  786. erasing segment 6 (vno[0] = 120694)
  787. erasing segment 7 (vno[0] = 122698)
  788. erasing segment 8 (vno[0] = 124916)
  789. erasing segment 9 (vno[0] = 124918)
  790. erasing segment 10 (vno[0] = 125911)
  791. erasing segment 11 (vno[0] = 126962)
  792. erasing segment 12 (vno[0] = 126965)
  793. erasing segment 13 (vno[0] = 126966)
  794. writing cortex label to /out/freesurfer/sub-003/label/rh.cortex.label...
  795. writing curvature file /out/freesurfer/sub-003/surf/rh.curv
  796. writing smoothed area to rh.area
  797. writing curvature file /out/freesurfer/sub-003/surf/rh.area
  798. vertex spacing 0.78 +- 0.22 (0.03-->4.20) (max @ vno 113046 --> 113073)
  799. face area 0.25 +- 0.12 (0.00-->2.82)
  800. refinement took 3.1 minutes
  801. #--------------------------------------------
  802. #@# Smooth2 rh Wed Dec 1 04:01:14 UTC 2021
  803. /out/freesurfer/sub-003/scripts
  804.  
  805. mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
  806.  
  807. smoothing for 3 iterations
  808. setting seed for random number generator to 1234
  809. smoothing surface tessellation for 3 iterations...
  810. smoothing complete - recomputing first and second fundamental forms...
  811. #--------------------------------------------
  812. #@# Inflation2 rh Wed Dec 1 04:01:18 UTC 2021
  813. /out/freesurfer/sub-003/scripts
  814.  
  815. mris_inflate -rusage /out/freesurfer/sub-003/touch/rusage.mris_inflate.rh.dat -n 50 ../surf/rh.smoothwm ../surf/rh.inflated
  816.  
  817. niterations = 50
  818. Reading ../surf/rh.smoothwm
  819. avg radius = 45.4 mm, total surface area = 76662 mm^2
  820. writing inflated surface to ../surf/rh.inflated
  821. writing sulcal depths to ../surf/rh.sulc
  822.  
  823. step 000: RMS=0.159 (target=0.015)
  824. step 005: RMS=0.113 (target=0.015)
  825. step 010: RMS=0.084 (target=0.015)
  826. step 015: RMS=0.069 (target=0.015)
  827. step 020: RMS=0.057 (target=0.015)
  828. step 025: RMS=0.048 (target=0.015)
  829. step 030: RMS=0.040 (target=0.015)
  830. step 035: RMS=0.034 (target=0.015)
  831. step 040: RMS=0.029 (target=0.015)
  832. step 045: RMS=0.026 (target=0.015)
  833. step 050: RMS=0.023 (target=0.015)
  834. step 055: RMS=0.022 (target=0.015)
  835. step 060: RMS=0.021 (target=0.015)
  836. step 065: RMS=0.020 (target=0.015)
  837. step 070: RMS=0.019 (target=0.015)
  838. step 075: RMS=0.018 (target=0.015)
  839. step 080: RMS=0.017 (target=0.015)
  840. step 085: RMS=0.017 (target=0.015)
  841. step 090: RMS=0.017 (target=0.015)
  842. step 095: RMS=0.017 (target=0.015)
  843. step 100: RMS=0.016 (target=0.015)
  844. step 105: RMS=0.016 (target=0.015)
  845. step 110: RMS=0.016 (target=0.015)
  846. step 115: RMS=0.016 (target=0.015)
  847. step 120: RMS=0.016 (target=0.015)
  848. step 125: RMS=0.016 (target=0.015)
  849. step 130: RMS=0.015 (target=0.015)
  850. step 135: RMS=0.015 (target=0.015)
  851. step 140: RMS=0.015 (target=0.015)
  852. step 145: RMS=0.015 (target=0.015)
  853. step 150: RMS=0.015 (target=0.015)
  854. inflation complete.
  855. inflation took 0.6 minutes
  856. mris_inflate utimesec 176.692003
  857. mris_inflate stimesec 0.798914
  858. mris_inflate ru_maxrss 262672
  859. mris_inflate ru_ixrss 0
  860. mris_inflate ru_idrss 0
  861. mris_inflate ru_isrss 0
  862. mris_inflate ru_minflt 64574
  863. mris_inflate ru_majflt 1
  864. mris_inflate ru_nswap 0
  865. mris_inflate ru_inblock 232
  866. mris_inflate ru_oublock 12752
  867. mris_inflate ru_msgsnd 0
  868. mris_inflate ru_msgrcv 0
  869. mris_inflate ru_nsignals 0
  870. mris_inflate ru_nvcsw 99027
  871. mris_inflate ru_nivcsw 791
  872. #--------------------------------------------
  873. #@# Curv .H and .K rh Wed Dec 1 04:01:54 UTC 2021
  874. /out/freesurfer/sub-003/surf
  875.  
  876. mris_curvature -w rh.white.preaparc
  877.  
  878. total integrated curvature = 21.119*4pi (265.393) --> -20 handles
  879. ICI = 183.5, FI = 1836.1, variation=28848.006
  880. writing Gaussian curvature to ./rh.white.preaparc.K...done.
  881. writing mean curvature to ./rh.white.preaparc.H...done.
  882. rm -f rh.white.H
  883. ln -s rh.white.preaparc.H rh.white.H
  884. 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
  885.  
  886. recon-all -s sub-003 exited with ERRORS at Wed Dec 1 04:01:57 UTC 2021
  887.  
  888. To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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