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fmriprep Crash

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Dec 6th, 2019
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  1. Node: _autorecon_surfs0
  2. Working directory: /flywheel/v0/work/fmriprep_wf/single_subject_TOME3024_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0
  3.  
  4. Node inputs:
  5.  
  6. FLAIR_file = <undefined>
  7. T1_files = <undefined>
  8. T2_file = <undefined>
  9. args = <undefined>
  10. big_ventricles = <undefined>
  11. brainstem = <undefined>
  12. directive = autorecon-hemi
  13. environ = {}
  14. expert = <undefined>
  15. flags = ['-noparcstats', '-noparcstats2', '-noparcstats3', '-nohyporelabel', '-nobalabels']
  16. hemi = lh
  17. hippocampal_subfields_T1 = <undefined>
  18. hippocampal_subfields_T2 = <undefined>
  19. hires = <undefined>
  20. mprage = <undefined>
  21. mri_aparc2aseg = <undefined>
  22. mri_ca_label = <undefined>
  23. mri_ca_normalize = <undefined>
  24. mri_ca_register = <undefined>
  25. mri_edit_wm_with_aseg = <undefined>
  26. mri_em_register = <undefined>
  27. mri_fill = <undefined>
  28. mri_mask = <undefined>
  29. mri_normalize = <undefined>
  30. mri_pretess = <undefined>
  31. mri_remove_neck = <undefined>
  32. mri_segment = <undefined>
  33. mri_segstats = <undefined>
  34. mri_tessellate = <undefined>
  35. mri_watershed = <undefined>
  36. mris_anatomical_stats = <undefined>
  37. mris_ca_label = <undefined>
  38. mris_fix_topology = <undefined>
  39. mris_inflate = <undefined>
  40. mris_make_surfaces = <undefined>
  41. mris_register = <undefined>
  42. mris_smooth = <undefined>
  43. mris_sphere = <undefined>
  44. mris_surf2vol = <undefined>
  45. mrisp_paint = <undefined>
  46. openmp = 3
  47. parallel = <undefined>
  48. steps = <undefined>
  49. subject_id = sub-TOME3024
  50. subjects_dir = /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer
  51. talairach = <undefined>
  52. use_FLAIR = False
  53. use_T2 = True
  54. xopts = <undefined>
  55.  
  56. Traceback (most recent call last):
  57. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
  58. result['result'] = node.run(updatehash=updatehash)
  59. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
  60. result = self._run_interface(execute=True)
  61. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 585, in _run_interface
  62. return self._run_command(execute)
  63. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 678, in _run_command
  64. result = self._interface.run(cwd=outdir)
  65. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 382, in run
  66. runtime = self._run_interface(runtime)
  67. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 767, in _run_interface
  68. self.raise_exception(runtime)
  69. File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 704, in raise_exception
  70. ).format(**runtime.dictcopy()))
  71. RuntimeError: Command:
  72. recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 3 -subjid sub-TOME3024 -sd /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer -T2pial
  73. Standard output:
  74. Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
  75. Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
  76. INFO: SUBJECTS_DIR is /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer
  77. Actual FREESURFER_HOME /opt/freesurfer
  78. Linux runc 4.15.0-1029-gcp #31-Ubuntu SMP Thu Mar 21 09:40:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
  79. '/opt/freesurfer/bin/recon-all' -> '/flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts/recon-all.local-copy'
  80. #--------------------------------------------
  81. #@# Tessellate lh Fri Dec 6 03:47:54 UTC 2019
  82. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  83.  
  84. mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
  85.  
  86.  
  87. Iteration Number : 1
  88. pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
  89. pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
  90. pass 1 (xy-): 0 found - 0 modified | TOTAL: 2
  91. pass 1 (yz+): 2 found - 2 modified | TOTAL: 4
  92. pass 2 (yz+): 0 found - 2 modified | TOTAL: 4
  93. pass 1 (yz-): 1 found - 1 modified | TOTAL: 5
  94. pass 2 (yz-): 0 found - 1 modified | TOTAL: 5
  95. pass 1 (xz+): 1 found - 1 modified | TOTAL: 6
  96. pass 2 (xz+): 0 found - 1 modified | TOTAL: 6
  97. pass 1 (xz-): 0 found - 0 modified | TOTAL: 6
  98. Iteration Number : 1
  99. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  100. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  101. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  102. pass 1 (+++): 0 found - 0 modified | TOTAL: 0
  103. Iteration Number : 1
  104. pass 1 (++): 0 found - 0 modified | TOTAL: 0
  105. pass 1 (+-): 1 found - 1 modified | TOTAL: 1
  106. pass 2 (+-): 0 found - 1 modified | TOTAL: 1
  107. pass 1 (--): 0 found - 0 modified | TOTAL: 1
  108. pass 1 (-+): 0 found - 0 modified | TOTAL: 1
  109. Iteration Number : 2
  110. pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
  111. pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
  112. pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
  113. pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
  114. pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
  115. pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
  116. Iteration Number : 2
  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 (++): 0 found - 0 modified | TOTAL: 0
  123. pass 1 (+-): 0 found - 0 modified | TOTAL: 0
  124. pass 1 (--): 0 found - 0 modified | TOTAL: 0
  125. pass 1 (-+): 0 found - 0 modified | TOTAL: 0
  126.  
  127. Total Number of Modified Voxels = 7 (out of 489677: 0.001430)
  128. Ambiguous edge configurations...
  129.  
  130. mri_pretess done
  131.  
  132.  
  133. mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
  134.  
  135. $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  136. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  137. slice 70: 105 vertices, 128 faces
  138. slice 80: 6377 vertices, 6695 faces
  139. slice 90: 19586 vertices, 20136 faces
  140. slice 100: 34916 vertices, 35474 faces
  141. slice 110: 50224 vertices, 50742 faces
  142. slice 120: 65527 vertices, 66024 faces
  143. slice 130: 80090 vertices, 80552 faces
  144. slice 140: 94748 vertices, 95239 faces
  145. slice 150: 109314 vertices, 109784 faces
  146. slice 160: 123522 vertices, 124030 faces
  147. slice 170: 137273 vertices, 137785 faces
  148. slice 180: 150617 vertices, 151124 faces
  149. slice 190: 164751 vertices, 165255 faces
  150. slice 200: 176402 vertices, 176817 faces
  151. slice 210: 186923 vertices, 187298 faces
  152. slice 220: 195758 vertices, 196053 faces
  153. slice 230: 203782 vertices, 204087 faces
  154. slice 240: 210325 vertices, 210559 faces
  155. slice 250: 214356 vertices, 214448 faces
  156. slice 260: 214630 vertices, 214670 faces
  157. slice 270: 214630 vertices, 214670 faces
  158. slice 280: 214630 vertices, 214670 faces
  159. slice 290: 214630 vertices, 214670 faces
  160. slice 300: 214630 vertices, 214670 faces
  161. slice 310: 214630 vertices, 214670 faces
  162. slice 320: 214630 vertices, 214670 faces
  163. using the conformed surface RAS to save vertex points...
  164. writing ../surf/lh.orig.nofix
  165. using vox2ras matrix:
  166. -0.79993 0.00000 0.00000 127.98951;
  167. 0.00000 0.00000 0.79993 -127.98951;
  168. 0.00000 -0.79993 0.00000 127.98951;
  169. 0.00000 0.00000 0.00000 1.00000;
  170.  
  171. rm -f ../mri/filled-pretess255.mgz
  172.  
  173.  
  174. mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
  175.  
  176.  
  177. counting number of connected components...
  178. 214630 voxel in cpt #1: X=-40 [v=214630,e=644010,f=429340] located at (-26.123610, -7.727585, 1.887897)
  179. For the whole surface: X=-40 [v=214630,e=644010,f=429340]
  180. One single component has been found
  181. nothing to do
  182. done
  183.  
  184. #--------------------------------------------
  185. #@# Smooth1 lh Fri Dec 6 03:48:04 UTC 2019
  186. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  187.  
  188. mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
  189.  
  190. setting seed for random number generator to 1234
  191. smoothing surface tessellation for 10 iterations...
  192. smoothing complete - recomputing first and second fundamental forms...
  193. #--------------------------------------------
  194. #@# Inflation1 lh Fri Dec 6 03:48:12 UTC 2019
  195. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  196.  
  197. mris_inflate -no-save-sulc -n 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
  198.  
  199. niterations = 50
  200. Not saving sulc
  201. Reading ../surf/lh.smoothwm.nofix
  202. avg radius = 45.7 mm, total surface area = 76295 mm^2
  203. writing inflated surface to ../surf/lh.inflated.nofix
  204. inflation took 3.1 minutes
  205.  
  206. step 000: RMS=0.138 (target=0.015)
  207. step 005: RMS=0.106 (target=0.015)
  208. step 010: RMS=0.079 (target=0.015)
  209. step 015: RMS=0.065 (target=0.015)
  210. step 020: RMS=0.056 (target=0.015)
  211. step 025: RMS=0.049 (target=0.015)
  212. step 030: RMS=0.043 (target=0.015)
  213. step 035: RMS=0.039 (target=0.015)
  214. step 040: RMS=0.036 (target=0.015)
  215. step 045: RMS=0.033 (target=0.015)
  216. step 050: RMS=0.032 (target=0.015)
  217. step 055: RMS=0.031 (target=0.015)
  218. step 060: RMS=0.030 (target=0.015)
  219. step 065: RMS=0.029 (target=0.015)
  220. step 070: RMS=0.029 (target=0.015)
  221. step 075: RMS=0.029 (target=0.015)
  222. step 080: RMS=0.028 (target=0.015)
  223. step 085: RMS=0.028 (target=0.015)
  224. step 090: RMS=0.028 (target=0.015)
  225. step 095: RMS=0.028 (target=0.015)
  226. step 100: RMS=0.028 (target=0.015)
  227. step 105: RMS=0.027 (target=0.015)
  228. step 110: RMS=0.027 (target=0.015)
  229. step 115: RMS=0.027 (target=0.015)
  230. step 120: RMS=0.027 (target=0.015)
  231. step 125: RMS=0.027 (target=0.015)
  232. step 130: RMS=0.027 (target=0.015)
  233. step 135: RMS=0.027 (target=0.015)
  234. step 140: RMS=0.027 (target=0.015)
  235. step 145: RMS=0.027 (target=0.015)
  236. step 150: RMS=0.027 (target=0.015)
  237. step 155: RMS=0.027 (target=0.015)
  238. step 160: RMS=0.027 (target=0.015)
  239. step 165: RMS=0.027 (target=0.015)
  240. step 170: RMS=0.027 (target=0.015)
  241. step 175: RMS=0.027 (target=0.015)
  242. step 180: RMS=0.027 (target=0.015)
  243. step 185: RMS=0.027 (target=0.015)
  244. step 190: RMS=0.027 (target=0.015)
  245. step 195: RMS=0.027 (target=0.015)
  246. step 200: RMS=0.027 (target=0.015)
  247. step 205: RMS=0.027 (target=0.015)
  248. step 210: RMS=0.027 (target=0.015)
  249. step 215: RMS=0.027 (target=0.015)
  250. step 220: RMS=0.027 (target=0.015)
  251. step 225: RMS=0.027 (target=0.015)
  252. step 230: RMS=0.027 (target=0.015)
  253. step 235: RMS=0.027 (target=0.015)
  254. step 240: RMS=0.027 (target=0.015)
  255. step 245: RMS=0.027 (target=0.015)
  256. step 250: RMS=0.027 (target=0.015)
  257. step 255: RMS=0.028 (target=0.015)
  258. step 260: RMS=0.028 (target=0.015)
  259. step 265: RMS=0.028 (target=0.015)
  260. step 270: RMS=0.028 (target=0.015)
  261. step 275: RMS=0.028 (target=0.015)
  262. step 280: RMS=0.028 (target=0.015)
  263. step 285: RMS=0.028 (target=0.015)
  264. step 290: RMS=0.028 (target=0.015)
  265. step 295: RMS=0.028 (target=0.015)
  266. step 300: RMS=0.028 (target=0.015)
  267. inflation complete.
  268. Not saving sulc
  269. mris_inflate utimesec 445.850910
  270. mris_inflate stimesec 0.423892
  271. mris_inflate ru_maxrss 326504
  272. mris_inflate ru_ixrss 0
  273. mris_inflate ru_idrss 0
  274. mris_inflate ru_isrss 0
  275. mris_inflate ru_minflt 80198
  276. mris_inflate ru_majflt 5
  277. mris_inflate ru_nswap 0
  278. mris_inflate ru_inblock 1048
  279. mris_inflate ru_oublock 15096
  280. mris_inflate ru_msgsnd 0
  281. mris_inflate ru_msgrcv 0
  282. mris_inflate ru_nsignals 0
  283. mris_inflate ru_nvcsw 16849
  284. mris_inflate ru_nivcsw 5682
  285. #--------------------------------------------
  286. #@# QSphere lh Fri Dec 6 03:51:17 UTC 2019
  287. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  288.  
  289. mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
  290.  
  291. doing quick spherical unfolding.
  292. setting seed for random number genererator to 1234
  293. $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  294. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  295. reading original vertex positions...
  296. unfolding cortex into spherical form...
  297. surface projected - minimizing metric distortion...
  298. vertex spacing 0.79 +- 0.42 (0.00-->6.38) (max @ vno 94376 --> 94398)
  299. face area 0.02 +- 0.02 (-0.24-->0.64)
  300.  
  301. == Number of threads available to mris_sphere for OpenMP = 3 ==
  302. scaling brain by 0.336...
  303. inflating to sphere (rms error < 2.00)
  304. 000: dt: 0.0000, rms radial error=173.273, avgs=0
  305. 005/300: dt: 0.9000, rms radial error=173.018, avgs=0
  306. 010/300: dt: 0.9000, rms radial error=172.470, avgs=0
  307. 015/300: dt: 0.9000, rms radial error=171.750, avgs=0
  308. 020/300: dt: 0.9000, rms radial error=170.929, avgs=0
  309. 025/300: dt: 0.9000, rms radial error=170.051, avgs=0
  310. 030/300: dt: 0.9000, rms radial error=169.139, avgs=0
  311. 035/300: dt: 0.9000, rms radial error=168.210, avgs=0
  312. 040/300: dt: 0.9000, rms radial error=167.274, avgs=0
  313. 045/300: dt: 0.9000, rms radial error=166.336, avgs=0
  314. 050/300: dt: 0.9000, rms radial error=165.398, avgs=0
  315. 055/300: dt: 0.9000, rms radial error=164.464, avgs=0
  316. 060/300: dt: 0.9000, rms radial error=163.533, avgs=0
  317. 065/300: dt: 0.9000, rms radial error=162.607, avgs=0
  318. 070/300: dt: 0.9000, rms radial error=161.685, avgs=0
  319. 075/300: dt: 0.9000, rms radial error=160.768, avgs=0
  320. 080/300: dt: 0.9000, rms radial error=159.857, avgs=0
  321. 085/300: dt: 0.9000, rms radial error=158.951, avgs=0
  322. 090/300: dt: 0.9000, rms radial error=158.050, avgs=0
  323. 095/300: dt: 0.9000, rms radial error=157.154, avgs=0
  324. 100/300: dt: 0.9000, rms radial error=156.263, avgs=0
  325. 105/300: dt: 0.9000, rms radial error=155.377, avgs=0
  326. 110/300: dt: 0.9000, rms radial error=154.497, avgs=0
  327. 115/300: dt: 0.9000, rms radial error=153.621, avgs=0
  328. 120/300: dt: 0.9000, rms radial error=152.751, avgs=0
  329. 125/300: dt: 0.9000, rms radial error=151.885, avgs=0
  330. 130/300: dt: 0.9000, rms radial error=151.024, avgs=0
  331. 135/300: dt: 0.9000, rms radial error=150.169, avgs=0
  332. 140/300: dt: 0.9000, rms radial error=149.318, avgs=0
  333. 145/300: dt: 0.9000, rms radial error=148.472, avgs=0
  334. 150/300: dt: 0.9000, rms radial error=147.631, avgs=0
  335. 155/300: dt: 0.9000, rms radial error=146.796, avgs=0
  336. 160/300: dt: 0.9000, rms radial error=145.965, avgs=0
  337. 165/300: dt: 0.9000, rms radial error=145.139, avgs=0
  338. 170/300: dt: 0.9000, rms radial error=144.318, avgs=0
  339. 175/300: dt: 0.9000, rms radial error=143.502, avgs=0
  340. 180/300: dt: 0.9000, rms radial error=142.690, avgs=0
  341. 185/300: dt: 0.9000, rms radial error=141.883, avgs=0
  342. 190/300: dt: 0.9000, rms radial error=141.081, avgs=0
  343. 195/300: dt: 0.9000, rms radial error=140.283, avgs=0
  344. 200/300: dt: 0.9000, rms radial error=139.489, avgs=0
  345. 205/300: dt: 0.9000, rms radial error=138.700, avgs=0
  346. 210/300: dt: 0.9000, rms radial error=137.916, avgs=0
  347. 215/300: dt: 0.9000, rms radial error=137.136, avgs=0
  348. 220/300: dt: 0.9000, rms radial error=136.360, avgs=0
  349. 225/300: dt: 0.9000, rms radial error=135.589, avgs=0
  350. 230/300: dt: 0.9000, rms radial error=134.822, avgs=0
  351. 235/300: dt: 0.9000, rms radial error=134.060, avgs=0
  352. 240/300: dt: 0.9000, rms radial error=133.301, avgs=0
  353. 245/300: dt: 0.9000, rms radial error=132.548, avgs=0
  354. 250/300: dt: 0.9000, rms radial error=131.798, avgs=0
  355. 255/300: dt: 0.9000, rms radial error=131.052, avgs=0
  356. 260/300: dt: 0.9000, rms radial error=130.311, avgs=0
  357. 265/300: dt: 0.9000, rms radial error=129.574, avgs=0
  358. 270/300: dt: 0.9000, rms radial error=128.841, avgs=0
  359. 275/300: dt: 0.9000, rms radial error=128.113, avgs=0
  360. 280/300: dt: 0.9000, rms radial error=127.389, avgs=0
  361. 285/300: dt: 0.9000, rms radial error=126.669, avgs=0
  362. 290/300: dt: 0.9000, rms radial error=125.953, avgs=0
  363. 295/300: dt: 0.9000, rms radial error=125.241, avgs=0
  364. 300/300: dt: 0.9000, rms radial error=124.533, avgs=0
  365.  
  366. spherical inflation complete.
  367. epoch 1 (K=10.0), pass 1, starting sse = 25915.76
  368. taking momentum steps...
  369. taking momentum steps...
  370. taking momentum steps...
  371. pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
  372. epoch 2 (K=40.0), pass 1, starting sse = 4550.91
  373. taking momentum steps...
  374. taking momentum steps...
  375. taking momentum steps...
  376. pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
  377. epoch 3 (K=160.0), pass 1, starting sse = 471.86
  378. taking momentum steps...
  379. taking momentum steps...
  380. taking momentum steps...
  381. pass 1 complete, delta sse/iter = 0.05/10 = 0.00452
  382. epoch 4 (K=640.0), pass 1, starting sse = 26.64
  383. taking momentum steps...
  384. taking momentum steps...
  385. taking momentum steps...
  386. pass 1 complete, delta sse/iter = 0.07/12 = 0.00620
  387. final distance error %23.70
  388. writing spherical brain to ../surf/lh.qsphere.nofix
  389. spherical transformation took 0.07 hours
  390. mris_sphere utimesec 521.353537
  391. mris_sphere stimesec 0.540005
  392. mris_sphere ru_maxrss 327004
  393. mris_sphere ru_ixrss 0
  394. mris_sphere ru_idrss 0
  395. mris_sphere ru_isrss 0
  396. mris_sphere ru_minflt 80207
  397. mris_sphere ru_majflt 7
  398. mris_sphere ru_nswap 0
  399. mris_sphere ru_inblock 1304
  400. mris_sphere ru_oublock 15104
  401. mris_sphere ru_msgsnd 0
  402. mris_sphere ru_msgrcv 0
  403. mris_sphere ru_nsignals 0
  404. mris_sphere ru_nvcsw 19604
  405. mris_sphere ru_nivcsw 6233
  406. FSRUNTIME@ mris_sphere 0.0667 hours 1 threads
  407. #--------------------------------------------
  408. #@# Fix Topology Copy lh Fri Dec 6 03:55:17 UTC 2019
  409. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  410.  
  411. cp ../surf/lh.orig.nofix ../surf/lh.orig
  412.  
  413.  
  414. cp ../surf/lh.inflated.nofix ../surf/lh.inflated
  415.  
  416. #@# Fix Topology lh Fri Dec 6 03:55:17 UTC 2019
  417.  
  418. mris_fix_topology -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-TOME3024 lh
  419.  
  420. reading spherical homeomorphism from 'qsphere.nofix'
  421. using genetic algorithm with optimized parameters
  422. setting seed for random number genererator to 1234
  423.  
  424. *************************************************************
  425. Topology Correction Parameters
  426. retessellation mode: genetic search
  427. number of patches/generation : 10
  428. number of generations : 10
  429. surface mri loglikelihood coefficient : 1.0
  430. volume mri loglikelihood coefficient : 10.0
  431. normal dot loglikelihood coefficient : 1.0
  432. quadratic curvature loglikelihood coefficient : 1.0
  433. volume resolution : 2
  434. eliminate vertices during search : 1
  435. initial patch selection : 1
  436. select all defect vertices : 0
  437. ordering dependant retessellation: 0
  438. use precomputed edge table : 0
  439. smooth retessellated patch : 2
  440. match retessellated patch : 1
  441. verbose mode : 0
  442.  
  443. *************************************************************
  444. INFO: assuming .mgz format
  445. $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  446. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  447. before topology correction, eno=-40 (nv=214630, nf=429340, ne=644010, g=21)
  448. using quasi-homeomorphic spherical map to tessellate cortical surface...
  449.  
  450. Correction of the Topology
  451. Finding true center and radius of Spherical Surface...done
  452. Surface centered at (0,0,0) with radius 100.0 in 9 iterations
  453. marking ambiguous vertices...
  454. 4996 ambiguous faces found in tessellation
  455. segmenting defects...
  456. 26 defects found, arbitrating ambiguous regions...
  457. analyzing neighboring defects...
  458. -merging segment 14 into 13
  459. -merging segment 18 into 15
  460. 24 defects to be corrected
  461. 0 vertices coincident
  462. reading input surface /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.qsphere.nofix...
  463. reading brain volume from brain...
  464. reading wm segmentation from wm...
  465. Computing Initial Surface Statistics
  466. -face loglikelihood: -9.0778 (-4.5389)
  467. -vertex loglikelihood: -5.7017 (-2.8509)
  468. -normal dot loglikelihood: -3.6325 (-3.6325)
  469. -quad curv loglikelihood: -6.4609 (-3.2305)
  470. Total Loglikelihood : -24.8729
  471.  
  472. CORRECTING DEFECT 0 (vertices=31, convex hull=73, v0=8625)
  473. After retessellation of defect 0 (v0=8625), euler #=-23 (211792,634674,422859) : difference with theory (-21) = 2
  474.  
  475. CORRECTING DEFECT 1 (vertices=286, convex hull=217, v0=83857)
  476. After retessellation of defect 1 (v0=83857), euler #=-22 (211828,634885,423035) : difference with theory (-20) = 2
  477.  
  478. CORRECTING DEFECT 2 (vertices=24, convex hull=35, v0=89819)
  479. After retessellation of defect 2 (v0=89819), euler #=-21 (211829,634903,423053) : difference with theory (-19) = 2
  480.  
  481. CORRECTING DEFECT 3 (vertices=33, convex hull=33, v0=91403)
  482. After retessellation of defect 3 (v0=91403), euler #=-20 (211832,634920,423068) : difference with theory (-18) = 2
  483.  
  484. CORRECTING DEFECT 4 (vertices=31, convex hull=65, v0=101810)
  485. After retessellation of defect 4 (v0=101810), euler #=-19 (211842,634977,423116) : difference with theory (-17) = 2
  486.  
  487. CORRECTING DEFECT 5 (vertices=36, convex hull=61, v0=110791)
  488. After retessellation of defect 5 (v0=110791), euler #=-18 (211852,635031,423161) : difference with theory (-16) = 2
  489.  
  490. CORRECTING DEFECT 6 (vertices=143, convex hull=46, v0=118861)
  491. After retessellation of defect 6 (v0=118861), euler #=-17 (211861,635076,423198) : difference with theory (-15) = 2
  492.  
  493. CORRECTING DEFECT 7 (vertices=18, convex hull=27, v0=124533)
  494. After retessellation of defect 7 (v0=124533), euler #=-16 (211862,635087,423209) : difference with theory (-14) = 2
  495.  
  496. CORRECTING DEFECT 8 (vertices=35, convex hull=56, v0=129498)
  497. After retessellation of defect 8 (v0=129498), euler #=-15 (211875,635147,423257) : difference with theory (-13) = 2
  498.  
  499. CORRECTING DEFECT 9 (vertices=9, convex hull=14, v0=142271)
  500. After retessellation of defect 9 (v0=142271), euler #=-14 (211876,635154,423264) : difference with theory (-12) = 2
  501.  
  502. CORRECTING DEFECT 10 (vertices=18, convex hull=47, v0=144790)
  503. After retessellation of defect 10 (v0=144790), euler #=-13 (211880,635183,423290) : difference with theory (-11) = 2
  504.  
  505. CORRECTING DEFECT 11 (vertices=98, convex hull=64, v0=145094)
  506. After retessellation of defect 11 (v0=145094), euler #=-12 (211888,635238,423338) : difference with theory (-10) = 2
  507.  
  508. CORRECTING DEFECT 12 (vertices=26, convex hull=34, v0=151354)
  509. After retessellation of defect 12 (v0=151354), euler #=-11 (211891,635258,423356) : difference with theory (-9) = 2
  510.  
  511. CORRECTING DEFECT 13 (vertices=343, convex hull=228, v0=151665)
  512. After retessellation of defect 13 (v0=151665), euler #=-9 (211956,635560,423595) : difference with theory (-8) = 1
  513.  
  514. CORRECTING DEFECT 14 (vertices=198, convex hull=192, v0=154207)
  515. After retessellation of defect 14 (v0=154207), euler #=-7 (211965,635674,423702) : difference with theory (-7) = 0
  516.  
  517. CORRECTING DEFECT 15 (vertices=82, convex hull=68, v0=156952)
  518. After retessellation of defect 15 (v0=156952), euler #=-6 (211982,635753,423765) : difference with theory (-6) = 0
  519.  
  520. CORRECTING DEFECT 16 (vertices=1237, convex hull=98, v0=158308)
  521. After retessellation of defect 16 (v0=158308), euler #=-5 (211993,635833,423835) : difference with theory (-5) = 0
  522.  
  523. CORRECTING DEFECT 17 (vertices=28, convex hull=30, v0=161415)
  524. After retessellation of defect 17 (v0=161415), euler #=-4 (211993,635841,423844) : difference with theory (-4) = 0
  525.  
  526. CORRECTING DEFECT 18 (vertices=5, convex hull=18, v0=168170)
  527. After retessellation of defect 18 (v0=168170), euler #=-3 (211994,635849,423852) : difference with theory (-3) = 0
  528.  
  529. CORRECTING DEFECT 19 (vertices=35, convex hull=56, v0=174914)
  530. After retessellation of defect 19 (v0=174914), euler #=-2 (212003,635898,423893) : difference with theory (-2) = 0
  531.  
  532. CORRECTING DEFECT 20 (vertices=31, convex hull=62, v0=200603)
  533. After retessellation of defect 20 (v0=200603), euler #=-1 (212011,635947,423935) : difference with theory (-1) = 0
  534.  
  535. CORRECTING DEFECT 21 (vertices=32, convex hull=60, v0=202076)
  536. After retessellation of defect 21 (v0=202076), euler #=0 (212017,635993,423976) : difference with theory (0) = 0
  537.  
  538. CORRECTING DEFECT 22 (vertices=20, convex hull=50, v0=209115)
  539. After retessellation of defect 22 (v0=209115), euler #=1 (212020,636022,424003) : difference with theory (1) = 0
  540.  
  541. CORRECTING DEFECT 23 (vertices=47, convex hull=74, v0=213228)
  542. After retessellation of defect 23 (v0=213228), euler #=2 (212031,636087,424058) : difference with theory (2) = 0
  543. computing original vertex metric properties...
  544. storing new metric properties...
  545. computing tessellation statistics...
  546. vertex spacing 0.71 +- 0.18 (0.05-->8.69) (max @ vno 83899 --> 88524)
  547. face area 0.00 +- 0.00 (0.00-->0.00)
  548. performing soap bubble on retessellated vertices for 0 iterations...
  549. vertex spacing 0.71 +- 0.18 (0.05-->8.69) (max @ vno 83899 --> 88524)
  550. face area 0.00 +- 0.00 (0.00-->0.00)
  551. tessellation finished, orienting corrected surface...
  552. 99 mutations (36.9%), 169 crossovers (63.1%), 91 vertices were eliminated
  553. building final representation...
  554. 2599 vertices and 0 faces have been removed from triangulation
  555. after topology correction, eno=2 (nv=212031, nf=424058, ne=636087, g=0)
  556. writing corrected surface to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.orig...
  557.  
  558. 0.000 % of the vertices (0 vertices) exhibit an orientation change
  559. topology fixing took 22.5 minutes
  560. 0 defective edges
  561. removing intersecting faces
  562. 000: 197 intersecting
  563. 001: 8 intersecting
  564. mris_fix_topology utimesec 1360.845325
  565. mris_fix_topology stimesec 1.147923
  566. mris_fix_topology ru_maxrss 697284
  567. mris_fix_topology ru_ixrss 0
  568. mris_fix_topology ru_idrss 0
  569. mris_fix_topology ru_isrss 0
  570. mris_fix_topology ru_minflt 173569
  571. mris_fix_topology ru_majflt 8
  572. mris_fix_topology ru_nswap 0
  573. mris_fix_topology ru_inblock 1464
  574. mris_fix_topology ru_oublock 19952
  575. mris_fix_topology ru_msgsnd 0
  576. mris_fix_topology ru_msgrcv 0
  577. mris_fix_topology ru_nsignals 0
  578. mris_fix_topology ru_nvcsw 4200
  579. mris_fix_topology ru_nivcsw 1390
  580. FSRUNTIME@ mris_fix_topology lh 0.3749 hours 1 threads
  581.  
  582. mris_euler_number ../surf/lh.orig
  583.  
  584. euler # = v-e+f = 2g-2: 212031 - 636087 + 424058 = 2 --> 0 holes
  585. F =2V-4: 424058 = 424062-4 (0)
  586. 2E=3F: 1272174 = 1272174 (0)
  587.  
  588. total defect index = 0
  589. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  590.  
  591. mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
  592.  
  593. intersection removal took 0.00 hours
  594. removing intersecting faces
  595. 000: 27 intersecting
  596. 001: 2 intersecting
  597. writing corrected surface to ../surf/lh.orig
  598.  
  599. rm ../surf/lh.inflated
  600.  
  601. #--------------------------------------------
  602. #@# Make White Surf lh Fri Dec 6 04:17:56 UTC 2019
  603. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  604.  
  605. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-TOME3024 lh
  606.  
  607. using white.preaparc as white matter name...
  608. only generating white matter surface
  609. using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
  610. not using aparc to prevent surfaces crossing the midline
  611. INFO: assuming MGZ format for volumes.
  612. using brain.finalsurfs as T1 volume...
  613. $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
  614. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  615. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/filled.mgz...
  616. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/brain.finalsurfs.mgz...
  617. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/../mri/aseg.presurf.mgz...
  618. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/wm.mgz...
  619. 23343 bright wm thresholded.
  620. 147 bright non-wm voxels segmented.
  621. reading original surface position from /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.orig...
  622. computing class statistics...
  623. border white: 412155 voxels (1.26%)
  624. border gray 444860 voxels (1.36%)
  625. WM (101.0): 101.0 +- 6.5 [70.0 --> 110.0]
  626. GM (82.0) : 80.8 +- 9.2 [30.0 --> 110.0]
  627. setting MIN_GRAY_AT_WHITE_BORDER to 66.8 (was 70)
  628. setting MAX_BORDER_WHITE to 113.5 (was 105)
  629. setting MIN_BORDER_WHITE to 76.0 (was 85)
  630. setting MAX_CSF to 57.7 (was 40)
  631. setting MAX_GRAY to 100.5 (was 95)
  632. setting MAX_GRAY_AT_CSF_BORDER to 66.8 (was 75)
  633. setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40)
  634. repositioning cortical surface to gray/white boundary
  635. smoothing T1 volume with sigma = 2.000
  636. vertex spacing 0.67 +- 0.17 (0.02-->3.93) (max @ vno 158560 --> 159833)
  637. face area 0.19 +- 0.08 (0.00-->2.22)
  638. mean absolute distance = 1.15 +- 1.43
  639. 7376 vertices more than 2 sigmas from mean.
  640. averaging target values for 5 iterations...
  641. spring scale = 1.25
  642. using class modes intead of means, discounting robust sigmas....
  643. intensity peaks found at WM=107+-3.5, GM=76+-6.1
  644. mean inside = 99.1, mean outside = 82.4
  645. smoothing surface for 5 iterations...
  646. inhibiting deformation at non-cortical midline structures...
  647. removing 2 vertex label from ripped group
  648. mean border=91.9, 101 (101) missing vertices, mean dist -0.4 [1.7 (%42.9)->0.6 (%57.1))]
  649. %53 local maxima, %34 large gradients and % 9 min vals, 0 gradients ignored
  650. tol=1.0e-04, sigma=2.0, host= runc, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  651. mom=0.00, dt=0.50
  652. complete_dist_mat 0
  653. rms 0
  654. smooth_averages 0
  655. remove_neg 0
  656. ico_order 0
  657. which_surface 0
  658. target_radius 0.000000
  659. nfields 0
  660. scale 0.000000
  661. desired_rms_height 0.000000
  662. momentum 0.000000
  663. nbhd_size 0
  664. max_nbrs 0
  665. niterations 25
  666. nsurfaces 0
  667. SURFACES 3
  668. flags 0 (0)
  669. use curv 0
  670. no sulc 0
  671. no rigid align 0
  672. mris->nsize 2
  673. mris->hemisphere 0
  674. randomSeed 0
  675.  
  676. smoothing T1 volume with sigma = 1.000
  677. vertex spacing 0.71 +- 0.18 (0.04-->3.66) (max @ vno 158594 --> 159833)
  678. face area 0.19 +- 0.08 (0.00-->1.97)
  679. mean absolute distance = 0.51 +- 0.84
  680. 8222 vertices more than 2 sigmas from mean.
  681. averaging target values for 5 iterations...
  682. 000: dt: 0.0000, sse=3340258.0, rms=7.740
  683. 001: dt: 0.5000, sse=1715287.2, rms=4.523 (41.563%)
  684. 002: dt: 0.5000, sse=1266127.5, rms=3.062 (32.300%)
  685. 003: dt: 0.5000, sse=1190210.1, rms=2.719 (11.220%)
  686. 004: dt: 0.5000, sse=1168926.9, rms=2.657 (2.279%)
  687. rms = 2.65, time step reduction 1 of 3 to 0.250...
  688. 005: dt: 0.5000, sse=1165482.0, rms=2.654 (0.090%)
  689. 006: dt: 0.2500, sse=977750.1, rms=1.370 (48.383%)
  690. 007: dt: 0.2500, sse=947668.6, rms=1.082 (21.050%)
  691. 008: dt: 0.2500, sse=939674.4, rms=0.994 (8.065%)
  692. rms = 0.96, time step reduction 2 of 3 to 0.125...
  693. 009: dt: 0.2500, sse=936116.3, rms=0.956 (3.827%)
  694. rms = 0.94, time step reduction 3 of 3 to 0.062...
  695. 010: dt: 0.1250, sse=932689.5, rms=0.936 (2.166%)
  696. positioning took 1.4 minutes
  697. inhibiting deformation at non-cortical midline structures...
  698. removing 1 vertex label from ripped group
  699. removing 2 vertex label from ripped group
  700. removing 3 vertex label from ripped group
  701. removing 4 vertex label from ripped group
  702. removing 3 vertex label from ripped group
  703. mean border=92.4, 138 (76) missing vertices, mean dist -0.2 [0.8 (%42.3)->0.3 (%57.7))]
  704. %81 local maxima, %13 large gradients and % 2 min vals, 0 gradients ignored
  705. tol=1.0e-04, sigma=1.0, host= runc, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  706. mom=0.00, dt=0.50
  707. smoothing T1 volume with sigma = 0.500
  708. vertex spacing 0.70 +- 0.18 (0.04-->3.87) (max @ vno 159877 --> 161197)
  709. face area 0.21 +- 0.09 (0.00-->2.63)
  710. mean absolute distance = 0.29 +- 0.58
  711. 6737 vertices more than 2 sigmas from mean.
  712. averaging target values for 5 iterations...
  713. 000: dt: 0.0000, sse=1747163.4, rms=4.290
  714. 011: dt: 0.5000, sse=1289145.0, rms=2.675 (37.644%)
  715. 012: dt: 0.5000, sse=1230574.0, rms=2.445 (8.584%)
  716. rms = 2.55, time step reduction 1 of 3 to 0.250...
  717. 013: dt: 0.2500, sse=1094994.8, rms=1.571 (35.744%)
  718. 014: dt: 0.2500, sse=1043141.2, rms=1.030 (34.451%)
  719. 015: dt: 0.2500, sse=1034396.4, rms=0.885 (14.030%)
  720. rms = 0.84, time step reduction 2 of 3 to 0.125...
  721. 016: dt: 0.2500, sse=1028476.4, rms=0.838 (5.318%)
  722. rms = 0.81, time step reduction 3 of 3 to 0.062...
  723. 017: dt: 0.1250, sse=1025300.8, rms=0.811 (3.246%)
  724. positioning took 1.1 minutes
  725. inhibiting deformation at non-cortical midline structures...
  726. removing 4 vertex label from ripped group
  727. mean border=93.1, 101 (57) missing vertices, mean dist -0.1 [0.4 (%44.7)->0.2 (%55.3))]
  728. %89 local maxima, % 6 large gradients and % 1 min vals, 0 gradients ignored
  729. tol=1.0e-04, sigma=0.5, host= runc, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  730. mom=0.00, dt=0.50
  731. smoothing T1 volume with sigma = 0.250
  732. vertex spacing 0.70 +- 0.18 (0.04-->4.23) (max @ vno 148033 --> 146729)
  733. face area 0.20 +- 0.09 (0.00-->2.47)
  734. mean absolute distance = 0.22 +- 0.45
  735. 5109 vertices more than 2 sigmas from mean.
  736. averaging target values for 5 iterations...
  737. 000: dt: 0.0000, sse=1169905.6, rms=2.228
  738. 018: dt: 0.5000, sse=1092670.5, rms=1.712 (23.192%)
  739. rms = 1.97, time step reduction 1 of 3 to 0.250...
  740. 019: dt: 0.2500, sse=1018703.6, rms=1.111 (35.065%)
  741. 020: dt: 0.2500, sse=998473.9, rms=0.840 (24.428%)
  742. 021: dt: 0.2500, sse=992216.9, rms=0.781 (6.959%)
  743. rms = 0.77, time step reduction 2 of 3 to 0.125...
  744. 022: dt: 0.2500, sse=993574.2, rms=0.768 (1.671%)
  745. rms = 0.75, time step reduction 3 of 3 to 0.062...
  746. 023: dt: 0.1250, sse=989574.0, rms=0.750 (2.434%)
  747. positioning took 0.9 minutes
  748. inhibiting deformation at non-cortical midline structures...
  749. removing 3 vertex label from ripped group
  750. mean border=93.2, 95 (54) missing vertices, mean dist -0.0 [0.4 (%34.6)->0.1 (%65.4))]
  751. %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
  752. tol=1.0e-04, sigma=0.2, host= runc, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  753. mom=0.00, dt=0.50
  754. writing white matter surface to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.white.preaparc...
  755. writing smoothed curvature to lh.curv
  756. 000: dt: 0.0000, sse=1039842.3, rms=1.321
  757. 024: dt: 0.5000, sse=1008409.4, rms=1.008 (23.711%)
  758. rms = 1.40, time step reduction 1 of 3 to 0.250...
  759. 025: dt: 0.2500, sse=985581.0, rms=0.693 (31.220%)
  760. 026: dt: 0.2500, sse=984266.3, rms=0.629 (9.168%)
  761. rms = 0.61, time step reduction 2 of 3 to 0.125...
  762. 027: dt: 0.2500, sse=982162.6, rms=0.612 (2.829%)
  763. rms = 0.60, time step reduction 3 of 3 to 0.062...
  764. 028: dt: 0.1250, sse=980170.6, rms=0.602 (1.630%)
  765. positioning took 0.8 minutes
  766. generating cortex label...
  767. 10 non-cortical segments detected
  768. only using segment with 11957 vertices
  769. erasing segment 1 (vno[0] = 128843)
  770. erasing segment 2 (vno[0] = 137121)
  771. erasing segment 3 (vno[0] = 153466)
  772. erasing segment 4 (vno[0] = 154624)
  773. erasing segment 5 (vno[0] = 154781)
  774. erasing segment 6 (vno[0] = 159858)
  775. erasing segment 7 (vno[0] = 161198)
  776. erasing segment 8 (vno[0] = 165058)
  777. erasing segment 9 (vno[0] = 167313)
  778. writing cortex label to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/label/lh.cortex.label...
  779. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.curv
  780. writing smoothed area to lh.area
  781. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.area
  782. vertex spacing 0.70 +- 0.19 (0.02-->4.30) (max @ vno 146729 --> 148033)
  783. face area 0.20 +- 0.09 (0.00-->2.42)
  784. refinement took 6.6 minutes
  785. #--------------------------------------------
  786. #@# Smooth2 lh Fri Dec 6 04:24:29 UTC 2019
  787. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  788.  
  789. mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
  790.  
  791. smoothing for 3 iterations
  792. setting seed for random number generator to 1234
  793. smoothing surface tessellation for 3 iterations...
  794. smoothing complete - recomputing first and second fundamental forms...
  795. #--------------------------------------------
  796. #@# Inflation2 lh Fri Dec 6 04:24:37 UTC 2019
  797. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  798.  
  799. mris_inflate -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated
  800.  
  801. niterations = 50
  802. Reading ../surf/lh.smoothwm
  803. avg radius = 45.9 mm, total surface area = 81237 mm^2
  804. writing inflated surface to ../surf/lh.inflated
  805. writing sulcal depths to ../surf/lh.sulc
  806.  
  807. step 000: RMS=0.152 (target=0.015)
  808. step 005: RMS=0.109 (target=0.015)
  809. step 010: RMS=0.080 (target=0.015)
  810. step 015: RMS=0.066 (target=0.015)
  811. step 020: RMS=0.055 (target=0.015)
  812. step 025: RMS=0.046 (target=0.015)
  813. step 030: RMS=0.040 (target=0.015)
  814. step 035: RMS=0.034 (target=0.015)
  815. step 040: RMS=0.030 (target=0.015)
  816. step 045: RMS=0.026 (target=0.015)
  817. step 050: RMS=0.024 (target=0.015)
  818. step 055: RMS=0.022 (target=0.015)
  819. step 060: RMS=0.021 (target=0.015)
  820. step 065: RMS=0.020 (target=0.015)
  821. step 070: RMS=0.019 (target=0.015)
  822. step 075: RMS=0.018 (target=0.015)
  823. step 080: RMS=0.017 (target=0.015)
  824. step 085: RMS=0.017 (target=0.015)
  825. step 090: RMS=0.016 (target=0.015)
  826. step 095: RMS=0.016 (target=0.015)
  827. step 100: RMS=0.016 (target=0.015)
  828. step 105: RMS=0.016 (target=0.015)
  829. step 110: RMS=0.015 (target=0.015)
  830. step 115: RMS=0.015 (target=0.015)
  831. inflation complete.
  832. inflation took 1.5 minutes
  833. mris_inflate utimesec 234.910936
  834. mris_inflate stimesec 0.528411
  835. mris_inflate ru_maxrss 322776
  836. mris_inflate ru_ixrss 0
  837. mris_inflate ru_idrss 0
  838. mris_inflate ru_isrss 0
  839. mris_inflate ru_minflt 79241
  840. mris_inflate ru_majflt 1
  841. mris_inflate ru_nswap 0
  842. mris_inflate ru_inblock 232
  843. mris_inflate ru_oublock 16584
  844. mris_inflate ru_msgsnd 0
  845. mris_inflate ru_msgrcv 0
  846. mris_inflate ru_nsignals 0
  847. mris_inflate ru_nvcsw 17670
  848. mris_inflate ru_nivcsw 2899
  849. #--------------------------------------------
  850. #@# Curv .H and .K lh Fri Dec 6 04:26:10 UTC 2019
  851. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf
  852.  
  853. mris_curvature -w lh.white.preaparc
  854.  
  855. total integrated curvature = 12.536*4pi (157.527) --> -12 handles
  856. ICI = 189.1, FI = 2140.4, variation=32944.626
  857. writing Gaussian curvature to ./lh.white.preaparc.K...done.
  858. writing mean curvature to ./lh.white.preaparc.H...done.
  859. rm -f lh.white.H
  860. ln -s lh.white.preaparc.H lh.white.H
  861. rm -f lh.white.K
  862. ln -s lh.white.preaparc.K lh.white.K
  863.  
  864. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
  865.  
  866. normalizing curvature values.
  867. averaging curvature patterns 5 times.
  868. sampling 10 neighbors out to a distance of 10 mm
  869. 428 vertices thresholded to be in k1 ~ [-0.16 0.20], k2 ~ [-0.10 0.06]
  870. total integrated curvature = 0.713*4pi (8.955) --> 0 handles
  871. ICI = 1.4, FI = 6.5, variation=117.889
  872. 233 vertices thresholded to be in [-0.01 0.01]
  873. writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
  874. curvature mean = 0.000, std = 0.001
  875. 225 vertices thresholded to be in [-0.11 0.10]
  876. done.
  877. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.018
  878. done.
  879.  
  880. #-----------------------------------------
  881. #@# Curvature Stats lh Fri Dec 6 04:28:06 UTC 2019
  882. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf
  883.  
  884. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-TOME3024 lh curv sulc
  885.  
  886. Toggling save flag on curvature files [ ok ]
  887. Outputting results using filestem [ ../stats/lh.curv.stats ]
  888. Toggling save flag on curvature files [ ok ]
  889. Setting surface [ sub-TOME3024/lh.smoothwm ]
  890. Reading surface... [ ok ]
  891. Setting texture [ curv ]
  892. Reading texture... [ ok ]
  893. Setting texture [ sulc ]
  894. Reading texture...Gb_filter = 0
  895. [ ok ]
  896. Calculating Discrete Principal Curvatures...
  897. Determining geometric order for vertex faces... [####################] [ ok ]
  898. Determining KH curvatures... [####################] [ ok ]
  899. Determining k1k2 curvatures... [####################] [ ok ]
  900. deltaViolations [ 382 ]
  901. Gb_filter = 0
  902.  
  903. WARN: S lookup min: -0.076068
  904. WARN: S explicit min: 0.000000 vertex = 2425
  905. #--------------------------------------------
  906. #@# Sphere lh Fri Dec 6 04:28:13 UTC 2019
  907. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  908.  
  909. mris_sphere -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
  910.  
  911. setting seed for random number genererator to 1234
  912. $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  913. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  914. reading original vertex positions...
  915. unfolding cortex into spherical form...
  916. surface projected - minimizing metric distortion...
  917.  
  918. == Number of threads available to mris_sphere for OpenMP = 3 ==
  919. scaling brain by 0.318...
  920. MRISunfold() max_passes = 1 -------
  921. tol=5.0e-01, sigma=0.0, host= runc, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
  922. using quadratic fit line minimization
  923. complete_dist_mat 0
  924. rms 0
  925. smooth_averages 0
  926. remove_neg 0
  927. ico_order 0
  928. which_surface 0
  929. target_radius 0.000000
  930. nfields 0
  931. scale 1.000000
  932. desired_rms_height -1.000000
  933. momentum 0.900000
  934. nbhd_size 7
  935. max_nbrs 8
  936. niterations 25
  937. nsurfaces 0
  938. SURFACES 3
  939. flags 0 (0)
  940. use curv 0
  941. no sulc 0
  942. no rigid align 0
  943. mris->nsize 2
  944. mris->hemisphere 0
  945. randomSeed 1234
  946.  
  947. singular matrix in quadratic form
  948. singular matrix in quadratic form
  949. --------------------
  950. mrisRemoveNegativeArea()
  951. pass 1: epoch 1 of 3 starting distance error %18.87
  952. pass 1: epoch 2 of 3 starting distance error %18.82
  953. unfolding complete - removing small folds...
  954. starting distance error %18.80
  955. removing remaining folds...
  956. final distance error %18.81
  957. MRISunfold() return, current seed 1234
  958. -01: dt=0.0000, 200 negative triangles
  959. 139: dt=0.9900, 200 negative triangles
  960. 140: dt=0.9900, 124 negative triangles
  961. 141: dt=0.9900, 94 negative triangles
  962. 142: dt=0.9900, 86 negative triangles
  963. 143: dt=0.9900, 80 negative triangles
  964. 144: dt=0.9900, 74 negative triangles
  965. 145: dt=0.9900, 65 negative triangles
  966. 146: dt=0.9900, 76 negative triangles
  967. 147: dt=0.9900, 70 negative triangles
  968. 148: dt=0.9900, 65 negative triangles
  969. 149: dt=0.9900, 63 negative triangles
  970. 150: dt=0.9900, 72 negative triangles
  971. 151: dt=0.9900, 60 negative triangles
  972. 152: dt=0.9900, 62 negative triangles
  973. 153: dt=0.9900, 59 negative triangles
  974. 154: dt=0.9900, 51 negative triangles
  975. 155: dt=0.9900, 65 negative triangles
  976. 156: dt=0.9900, 51 negative triangles
  977. 157: dt=0.9900, 48 negative triangles
  978. 158: dt=0.9900, 55 negative triangles
  979. 159: dt=0.9900, 51 negative triangles
  980. 160: dt=0.9900, 55 negative triangles
  981. 161: dt=0.9900, 50 negative triangles
  982. 162: dt=0.9900, 46 negative triangles
  983. 163: dt=0.9900, 45 negative triangles
  984. 164: dt=0.9900, 44 negative triangles
  985. 165: dt=0.9900, 43 negative triangles
  986. 166: dt=0.9900, 44 negative triangles
  987. 167: dt=0.9900, 37 negative triangles
  988. 168: dt=0.9900, 36 negative triangles
  989. 169: dt=0.9900, 31 negative triangles
  990. 170: dt=0.9900, 33 negative triangles
  991. 171: dt=0.9900, 24 negative triangles
  992. 172: dt=0.9900, 29 negative triangles
  993. 173: dt=0.9900, 22 negative triangles
  994. 174: dt=0.9900, 21 negative triangles
  995. 175: dt=0.9900, 21 negative triangles
  996. 176: dt=0.9900, 16 negative triangles
  997. 177: dt=0.9900, 12 negative triangles
  998. 178: dt=0.9900, 12 negative triangles
  999. 179: dt=0.9900, 6 negative triangles
  1000. 180: dt=0.9900, 3 negative triangles
  1001. 181: dt=0.9900, 3 negative triangles
  1002. 182: dt=0.9900, 7 negative triangles
  1003. 183: dt=0.9900, 6 negative triangles
  1004. 184: dt=0.9900, 6 negative triangles
  1005. 185: dt=0.9900, 2 negative triangles
  1006. 186: dt=0.9900, 2 negative triangles
  1007. 187: dt=0.9900, 3 negative triangles
  1008. 188: dt=0.9900, 7 negative triangles
  1009. 189: dt=0.9900, 5 negative triangles
  1010. 190: dt=0.9900, 3 negative triangles
  1011. 191: dt=0.9900, 1 negative triangles
  1012. 192: dt=0.9900, 4 negative triangles
  1013. 193: dt=0.9900, 2 negative triangles
  1014. 194: dt=0.9900, 2 negative triangles
  1015. 195: dt=0.9900, 1 negative triangles
  1016. 196: dt=0.9900, 2 negative triangles
  1017. writing spherical brain to ../surf/lh.sphere
  1018. spherical transformation took 0.56 hours
  1019. mris_sphere utimesec 5642.873979
  1020. mris_sphere stimesec 1.471747
  1021. mris_sphere ru_maxrss 451688
  1022. mris_sphere ru_ixrss 0
  1023. mris_sphere ru_idrss 0
  1024. mris_sphere ru_isrss 0
  1025. mris_sphere ru_minflt 111373
  1026. mris_sphere ru_majflt 0
  1027. mris_sphere ru_nswap 0
  1028. mris_sphere ru_inblock 0
  1029. mris_sphere ru_oublock 14920
  1030. mris_sphere ru_msgsnd 0
  1031. mris_sphere ru_msgrcv 0
  1032. mris_sphere ru_nsignals 0
  1033. mris_sphere ru_nvcsw 24971
  1034. mris_sphere ru_nivcsw 36444
  1035. FSRUNTIME@ mris_sphere 0.5643 hours 1 threads
  1036. #--------------------------------------------
  1037. #@# Surf Reg lh Fri Dec 6 05:02:05 UTC 2019
  1038. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1039.  
  1040. mris_register -curv -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
  1041.  
  1042. using smoothwm curvature for final alignment
  1043.  
  1044. cwd /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1045. cmdline mris_register -curv -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
  1046.  
  1047. 0 inflated.H
  1048. 1 sulc
  1049. 2 smoothwm (computed)
  1050. $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $
  1051. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  1052. reading surface from ../surf/lh.sphere...
  1053. reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
  1054. MRISregister() -------
  1055. max_passes = 4
  1056. min_degrees = 0.500000
  1057. max_degrees = 64.000000
  1058. nangles = 8
  1059. tol=5.0e-01, sigma=0.0, host= runc, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
  1060. using quadratic fit line minimization
  1061. complete_dist_mat 0
  1062. rms 0
  1063. smooth_averages 0
  1064. remove_neg 0
  1065. ico_order 0
  1066. which_surface 0
  1067. target_radius 0.000000
  1068. nfields 0
  1069. scale 0.000000
  1070. desired_rms_height -1.000000
  1071. momentum 0.950000
  1072. nbhd_size -10
  1073. max_nbrs 10
  1074. niterations 25
  1075. nsurfaces 0
  1076. SURFACES 3
  1077. flags 16 (10)
  1078. use curv 16
  1079. no sulc 0
  1080. no rigid align 0
  1081. mris->nsize 1
  1082. mris->hemisphere 0
  1083. randomSeed 0
  1084.  
  1085. tol=5.0e-01, sigma=0.0, host= runc, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
  1086. using quadratic fit line minimization
  1087. --------------------
  1088. 1 Reading lh.sulc
  1089. curvature mean = 0.000, std = 5.797
  1090. curvature mean = 0.021, std = 0.817
  1091. curvature mean = 0.017, std = 0.881
  1092. Starting MRISrigidBodyAlignGlobal()
  1093. d=64.00 min @ (0.00, 0.00, -16.00) sse = 479896.0, tmin=1.4497
  1094. d=32.00 min @ (0.00, -8.00, 8.00) sse = 338893.7, tmin=2.9093
  1095. d=16.00 min @ (0.00, 4.00, 0.00) sse = 289384.6, tmin=4.3801
  1096. d=8.00 min @ (-2.00, -2.00, 0.00) sse = 281435.9, tmin=5.8620
  1097. d=4.00 min @ (1.00, 1.00, 0.00) sse = 279953.2, tmin=7.3423
  1098. d=2.00 min @ (-0.50, 0.00, 0.00) sse = 279332.2, tmin=8.8312
  1099. d=1.00 min @ (0.00, -0.25, 0.00) sse = 279031.8, tmin=10.3124
  1100. tol=1.0e+00, sigma=0.5, host= runc, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
  1101. using quadratic fit line minimization
  1102. MRISrigidBodyAlignGlobal() done 11.79 min
  1103. curvature mean = 0.010, std = 0.845
  1104. curvature mean = 0.005, std = 0.954
  1105. curvature mean = 0.008, std = 0.855
  1106. curvature mean = 0.002, std = 0.981
  1107. curvature mean = 0.007, std = 0.855
  1108. curvature mean = 0.000, std = 0.992
  1109. 2 Reading smoothwm
  1110. curvature mean = -0.033, std = 0.304
  1111. curvature mean = 0.040, std = 0.243
  1112. curvature mean = 0.045, std = 0.362
  1113. curvature mean = 0.038, std = 0.299
  1114. curvature mean = 0.019, std = 0.562
  1115. curvature mean = 0.037, std = 0.324
  1116. curvature mean = 0.009, std = 0.714
  1117. curvature mean = 0.038, std = 0.334
  1118. curvature mean = 0.002, std = 0.822
  1119. MRISregister() return, current seed 0
  1120. -01: dt=0.0000, 54 negative triangles
  1121. 112: dt=0.9900, 54 negative triangles
  1122. expanding nbhd size to 1
  1123. 113: dt=0.9900, 65 negative triangles
  1124. 114: dt=0.9900, 51 negative triangles
  1125. 115: dt=0.9900, 51 negative triangles
  1126. 116: dt=0.9900, 48 negative triangles
  1127. 117: dt=0.9900, 47 negative triangles
  1128. 118: dt=0.9900, 48 negative triangles
  1129. 119: dt=0.9900, 47 negative triangles
  1130. 120: dt=0.9900, 42 negative triangles
  1131. 121: dt=0.9900, 39 negative triangles
  1132. 122: dt=0.9900, 39 negative triangles
  1133. 123: dt=0.9900, 40 negative triangles
  1134. 124: dt=0.9900, 36 negative triangles
  1135. 125: dt=0.9900, 37 negative triangles
  1136. 126: dt=0.9900, 32 negative triangles
  1137. 127: dt=0.9900, 30 negative triangles
  1138. 128: dt=0.9900, 26 negative triangles
  1139. 129: dt=0.9900, 26 negative triangles
  1140. 130: dt=0.9900, 26 negative triangles
  1141. 131: dt=0.9900, 20 negative triangles
  1142. 132: dt=0.9900, 17 negative triangles
  1143. 133: dt=0.9900, 16 negative triangles
  1144. 134: dt=0.9900, 15 negative triangles
  1145. 135: dt=0.9900, 16 negative triangles
  1146. 136: dt=0.9900, 13 negative triangles
  1147. 137: dt=0.9900, 11 negative triangles
  1148. 138: dt=0.9900, 11 negative triangles
  1149. 139: dt=0.9900, 10 negative triangles
  1150. 140: dt=0.9900, 8 negative triangles
  1151. 141: dt=0.9900, 13 negative triangles
  1152. 142: dt=0.9900, 6 negative triangles
  1153. 143: dt=0.9900, 6 negative triangles
  1154. 144: dt=0.9900, 4 negative triangles
  1155. 145: dt=0.9900, 4 negative triangles
  1156. 146: dt=0.9900, 4 negative triangles
  1157. 147: dt=0.9900, 3 negative triangles
  1158. 148: dt=0.9900, 2 negative triangles
  1159. 149: dt=0.9900, 2 negative triangles
  1160. 150: dt=0.9900, 1 negative triangles
  1161. writing registered surface to ../surf/lh.sphere.reg...
  1162. registration took 0.82 hours
  1163. mris_register utimesec 6691.444464
  1164. mris_register stimesec 1.535710
  1165. mris_register ru_maxrss 376424
  1166. mris_register ru_ixrss 0
  1167. mris_register ru_idrss 0
  1168. mris_register ru_isrss 0
  1169. mris_register ru_minflt 92445
  1170. mris_register ru_majflt 11
  1171. mris_register ru_nswap 0
  1172. mris_register ru_inblock 7208
  1173. mris_register ru_oublock 14920
  1174. mris_register ru_msgsnd 0
  1175. mris_register ru_msgrcv 0
  1176. mris_register ru_nsignals 0
  1177. mris_register ru_nvcsw 21680
  1178. mris_register ru_nivcsw 22412
  1179. FSRUNTIME@ mris_register 0.8247 hours 1 threads
  1180. #--------------------------------------------
  1181. #@# Jacobian white lh Fri Dec 6 05:51:33 UTC 2019
  1182. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1183.  
  1184. mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
  1185.  
  1186. reading surface from ../surf/lh.white.preaparc...
  1187. writing curvature file ../surf/lh.jacobian_white
  1188. #--------------------------------------------
  1189. #@# AvgCurv lh Fri Dec 6 05:51:36 UTC 2019
  1190. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1191.  
  1192. mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
  1193.  
  1194. averaging curvature patterns 5 times...
  1195. reading surface from ../surf/lh.sphere.reg...
  1196. reading template parameterization from /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
  1197. writing curvature file to ../surf/lh.avg_curv...
  1198. #-----------------------------------------
  1199. #@# Cortical Parc lh Fri Dec 6 05:51:38 UTC 2019
  1200. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1201.  
  1202. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-TOME3024 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
  1203.  
  1204. setting seed for random number generator to 1234
  1205. using ../mri/aseg.presurf.mgz aseg volume to correct midline
  1206. $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  1207. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  1208. reading atlas from /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
  1209. reading color table from GCSA file....
  1210. average std = 0.8 using min determinant for regularization = 0.006
  1211. 0 singular and 342 ill-conditioned covariance matrices regularized
  1212. input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
  1213. labeling surface...
  1214. 2181 labels changed using aseg
  1215. relabeling using gibbs priors...
  1216. 000: 4323 changed, 212031 examined...
  1217. 001: 1062 changed, 18022 examined...
  1218. 002: 260 changed, 5805 examined...
  1219. 003: 94 changed, 1527 examined...
  1220. 004: 42 changed, 543 examined...
  1221. 005: 22 changed, 231 examined...
  1222. 006: 9 changed, 129 examined...
  1223. 007: 2 changed, 45 examined...
  1224. 008: 3 changed, 16 examined...
  1225. 009: 0 changed, 16 examined...
  1226. 316 labels changed using aseg
  1227. 000: 160 total segments, 114 labels (478 vertices) changed
  1228. 001: 45 total segments, 6 labels (20 vertices) changed
  1229. 002: 39 total segments, 0 labels (0 vertices) changed
  1230. 10 filter iterations complete (10 requested, 7 changed)
  1231. rationalizing unknown annotations with cortex label
  1232. relabeling unknown label...
  1233. relabeling corpuscallosum label...
  1234. 2824 vertices marked for relabeling...
  1235. 2824 labels changed in reclassification.
  1236. writing output to ../label/lh.aparc.annot...
  1237. classification took 0 minutes and 21 seconds.
  1238. #--------------------------------------------
  1239. #@# Make Pial Surf lh Fri Dec 6 05:52:00 UTC 2019
  1240. /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1241.  
  1242. mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-TOME3024 lh
  1243.  
  1244. using white.preaparc starting white location...
  1245. using white.preaparc starting pial locations...
  1246. using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
  1247. INFO: assuming MGZ format for volumes.
  1248. using brain.finalsurfs as T1 volume...
  1249. $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
  1250. $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  1251. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/filled.mgz...
  1252. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/brain.finalsurfs.mgz...
  1253. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/../mri/aseg.presurf.mgz...
  1254. reading volume /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/wm.mgz...
  1255. 23343 bright wm thresholded.
  1256. 147 bright non-wm voxels segmented.
  1257. reading original surface position from /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.orig...
  1258. computing class statistics...
  1259. border white: 412155 voxels (1.26%)
  1260. border gray 444860 voxels (1.36%)
  1261. WM (101.0): 101.0 +- 6.5 [70.0 --> 110.0]
  1262. GM (82.0) : 80.8 +- 9.2 [30.0 --> 110.0]
  1263. setting MIN_GRAY_AT_WHITE_BORDER to 66.8 (was 70)
  1264. setting MAX_BORDER_WHITE to 113.5 (was 105)
  1265. setting MIN_BORDER_WHITE to 76.0 (was 85)
  1266. setting MAX_CSF to 57.7 (was 40)
  1267. setting MAX_GRAY to 100.5 (was 95)
  1268. setting MAX_GRAY_AT_CSF_BORDER to 66.8 (was 75)
  1269. setting MIN_GRAY_AT_CSF_BORDER to 48.5 (was 40)
  1270. spring scale = 1.25
  1271. using class modes intead of means, discounting robust sigmas....
  1272. intensity peaks found at WM=107+-3.5, GM=76+-6.1
  1273. mean inside = 99.1, mean outside = 82.4
  1274. smoothing surface for 5 iterations...
  1275. reading initial white vertex positions from white.preaparc...
  1276. reading colortable from annotation file...
  1277. colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
  1278. repositioning cortical surface to gray/white boundary
  1279. smoothing T1 volume with sigma = 2.000
  1280. vertex spacing 0.70 +- 0.19 (0.02-->4.30) (max @ vno 146729 --> 148033)
  1281. face area 0.21 +- 0.09 (0.00-->2.43)
  1282. mean absolute distance = 1.07 +- 1.28
  1283. 6735 vertices more than 2 sigmas from mean.
  1284. averaging target values for 5 iterations...
  1285. inhibiting deformation at non-cortical midline structures...
  1286. removing 2 vertex label from ripped group
  1287. deleting segment 3 with 445 points - only 0.00% unknown
  1288. deleting segment 4 with 10 points - only 0.00% unknown
  1289. deleting segment 5 with 66 points - only 0.00% unknown
  1290. deleting segment 6 with 42 points - only 0.00% unknown
  1291. deleting segment 7 with 28 points - only 0.00% unknown
  1292. mean border=91.8, 87 (85) missing vertices, mean dist -0.2 [2.5 (%24.3)->0.5 (%75.7))]
  1293. %52 local maxima, %34 large gradients and % 9 min vals, 0 gradients ignored
  1294. tol=1.0e-04, sigma=2.0, host= runc, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1295. mom=0.00, dt=0.50
  1296. complete_dist_mat 0
  1297. rms 0
  1298. smooth_averages 0
  1299. remove_neg 0
  1300. ico_order 0
  1301. which_surface 0
  1302. target_radius 0.000000
  1303. nfields 0
  1304. scale 0.000000
  1305. desired_rms_height 0.000000
  1306. momentum 0.000000
  1307. nbhd_size 0
  1308. max_nbrs 0
  1309. niterations 25
  1310. nsurfaces 0
  1311. SURFACES 3
  1312. flags 0 (0)
  1313. use curv 0
  1314. no sulc 0
  1315. no rigid align 0
  1316. mris->nsize 2
  1317. mris->hemisphere 0
  1318. randomSeed 0
  1319.  
  1320. smoothing T1 volume with sigma = 1.000
  1321. vertex spacing 0.71 +- 0.18 (0.04-->4.54) (max @ vno 148032 --> 146728)
  1322. face area 0.21 +- 0.09 (0.00-->2.80)
  1323. mean absolute distance = 0.49 +- 0.82
  1324. 7527 vertices more than 2 sigmas from mean.
  1325. averaging target values for 5 iterations...
  1326. 000: dt: 0.0000, sse=2087113.5, rms=5.245
  1327. 001: dt: 0.5000, sse=1323552.2, rms=2.953 (43.698%)
  1328. 002: dt: 0.5000, sse=1210038.2, rms=2.448 (17.103%)
  1329. rms = 2.44, time step reduction 1 of 3 to 0.250...
  1330. 003: dt: 0.5000, sse=1206172.9, rms=2.438 (0.400%)
  1331. 004: dt: 0.2500, sse=1038144.5, rms=1.210 (50.352%)
  1332. 005: dt: 0.2500, sse=1018199.0, rms=0.987 (18.447%)
  1333. rms = 0.94, time step reduction 2 of 3 to 0.125...
  1334. 006: dt: 0.2500, sse=1015427.9, rms=0.940 (4.819%)
  1335. rms = 0.91, time step reduction 3 of 3 to 0.062...
  1336. 007: dt: 0.1250, sse=1012586.1, rms=0.909 (3.242%)
  1337. positioning took 1.0 minutes
  1338. inhibiting deformation at non-cortical midline structures...
  1339. removing 1 vertex label from ripped group
  1340. removing 4 vertex label from ripped group
  1341. deleting segment 3 with 419 points - only 0.00% unknown
  1342. deleting segment 4 with 21 points - only 0.00% unknown
  1343. deleting segment 5 with 71 points - only 0.00% unknown
  1344. deleting segment 6 with 46 points - only 0.00% unknown
  1345. deleting segment 7 with 11 points - only 0.00% unknown
  1346. mean border=92.3, 84 (59) missing vertices, mean dist -0.2 [0.8 (%42.0)->0.2 (%58.0))]
  1347. %81 local maxima, %13 large gradients and % 2 min vals, 0 gradients ignored
  1348. tol=1.0e-04, sigma=1.0, host= runc, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1349. mom=0.00, dt=0.50
  1350. smoothing T1 volume with sigma = 0.500
  1351. vertex spacing 0.70 +- 0.18 (0.03-->4.63) (max @ vno 148032 --> 146728)
  1352. face area 0.21 +- 0.10 (0.00-->2.90)
  1353. mean absolute distance = 0.28 +- 0.58
  1354. 6740 vertices more than 2 sigmas from mean.
  1355. averaging target values for 5 iterations...
  1356. 000: dt: 0.0000, sse=1681126.0, rms=4.086
  1357. 008: dt: 0.5000, sse=1259505.2, rms=2.528 (38.126%)
  1358. 009: dt: 0.5000, sse=1217506.8, rms=2.351 (6.986%)
  1359. rms = 2.50, time step reduction 1 of 3 to 0.250...
  1360. 010: dt: 0.2500, sse=1088695.2, rms=1.464 (37.739%)
  1361. 011: dt: 0.2500, sse=1041798.2, rms=0.941 (35.718%)
  1362. 012: dt: 0.2500, sse=1031717.4, rms=0.824 (12.402%)
  1363. rms = 0.79, time step reduction 2 of 3 to 0.125...
  1364. 013: dt: 0.2500, sse=1030041.1, rms=0.791 (4.005%)
  1365. rms = 0.77, time step reduction 3 of 3 to 0.062...
  1366. 014: dt: 0.1250, sse=1027704.6, rms=0.767 (3.012%)
  1367. positioning took 1.0 minutes
  1368. inhibiting deformation at non-cortical midline structures...
  1369. removing 1 vertex label from ripped group
  1370. deleting segment 1 with 16 points - only 0.00% unknown
  1371. deleting segment 2 with 360 points - only 0.00% unknown
  1372. deleting segment 3 with 40 points - only 0.00% unknown
  1373. deleting segment 5 with 46 points - only 0.00% unknown
  1374. deleting segment 6 with 14 points - only 0.00% unknown
  1375. mean border=93.1, 80 (50) missing vertices, mean dist -0.1 [0.4 (%45.2)->0.1 (%54.8))]
  1376. %89 local maxima, % 6 large gradients and % 1 min vals, 0 gradients ignored
  1377. tol=1.0e-04, sigma=0.5, host= runc, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1378. mom=0.00, dt=0.50
  1379. smoothing T1 volume with sigma = 0.250
  1380. vertex spacing 0.70 +- 0.18 (0.04-->4.82) (max @ vno 148032 --> 146728)
  1381. face area 0.20 +- 0.09 (0.00-->2.93)
  1382. mean absolute distance = 0.22 +- 0.45
  1383. 4959 vertices more than 2 sigmas from mean.
  1384. averaging target values for 5 iterations...
  1385. 000: dt: 0.0000, sse=1165240.4, rms=2.186
  1386. 015: dt: 0.5000, sse=1093222.4, rms=1.684 (22.976%)
  1387. rms = 1.95, time step reduction 1 of 3 to 0.250...
  1388. 016: dt: 0.2500, sse=1019831.1, rms=1.073 (36.287%)
  1389. 017: dt: 0.2500, sse=999890.8, rms=0.789 (26.503%)
  1390. 018: dt: 0.2500, sse=993041.3, rms=0.737 (6.519%)
  1391. rms = 0.73, time step reduction 2 of 3 to 0.125...
  1392. 019: dt: 0.2500, sse=993297.1, rms=0.728 (1.300%)
  1393. rms = 0.71, time step reduction 3 of 3 to 0.062...
  1394. 020: dt: 0.1250, sse=990727.4, rms=0.711 (2.282%)
  1395. positioning took 0.9 minutes
  1396. inhibiting deformation at non-cortical midline structures...
  1397. removing 1 vertex label from ripped group
  1398. deleting segment 1 with 14 points - only 0.00% unknown
  1399. deleting segment 2 with 335 points - only 0.00% unknown
  1400. deleting segment 3 with 27 points - only 0.00% unknown
  1401. deleting segment 4 with 46 points - only 0.00% unknown
  1402. deleting segment 5 with 30 points - only 0.00% unknown
  1403. mean border=93.1, 92 (48) missing vertices, mean dist -0.0 [0.4 (%34.6)->0.1 (%65.4))]
  1404. %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
  1405. tol=1.0e-04, sigma=0.2, host= runc, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1406. mom=0.00, dt=0.50
  1407. writing white matter surface to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.white...
  1408. writing smoothed curvature to lh.curv
  1409. 000: dt: 0.0000, sse=1039577.4, rms=1.288
  1410. 021: dt: 0.5000, sse=1011219.5, rms=0.992 (22.960%)
  1411. rms = 1.40, time step reduction 1 of 3 to 0.250...
  1412. 022: dt: 0.2500, sse=988475.0, rms=0.676 (31.821%)
  1413. 023: dt: 0.2500, sse=986614.6, rms=0.619 (8.479%)
  1414. rms = 0.60, time step reduction 2 of 3 to 0.125...
  1415. 024: dt: 0.2500, sse=985252.1, rms=0.603 (2.643%)
  1416. rms = 0.59, time step reduction 3 of 3 to 0.062...
  1417. 025: dt: 0.1250, sse=984217.6, rms=0.595 (1.306%)
  1418. positioning took 0.8 minutes
  1419. generating cortex label...
  1420. 10 non-cortical segments detected
  1421. only using segment with 11986 vertices
  1422. erasing segment 1 (vno[0] = 130208)
  1423. erasing segment 2 (vno[0] = 136132)
  1424. erasing segment 3 (vno[0] = 149416)
  1425. erasing segment 4 (vno[0] = 154624)
  1426. erasing segment 5 (vno[0] = 154781)
  1427. erasing segment 6 (vno[0] = 159858)
  1428. erasing segment 7 (vno[0] = 161198)
  1429. erasing segment 8 (vno[0] = 165058)
  1430. erasing segment 9 (vno[0] = 167305)
  1431. writing cortex label to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/label/lh.cortex.label...
  1432. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.curv
  1433. writing smoothed area to lh.area
  1434. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.area
  1435. vertex spacing 0.70 +- 0.19 (0.02-->4.79) (max @ vno 146728 --> 148032)
  1436. face area 0.21 +- 0.09 (0.00-->3.12)
  1437. repositioning cortical surface to gray/csf boundary.
  1438. smoothing T1 volume with sigma = 2.000
  1439. averaging target values for 5 iterations...
  1440. inhibiting deformation at non-cortical midline structures...
  1441. deleting segment 1 with 6 points - only 0.00% unknown
  1442. removing 1 vertex label from ripped group
  1443. deleting segment 6 with 8 points - only 0.00% unknown
  1444. deleting segment 8 with 61 points - only 0.00% unknown
  1445. smoothing surface for 5 iterations...
  1446. reading initial pial vertex positions from white.preaparc...
  1447. mean border=71.0, 112 (112) missing vertices, mean dist 1.1 [0.2 (%0.0)->1.7 (%100.0))]
  1448. %14 local maxima, %48 large gradients and %34 min vals, 143 gradients ignored
  1449. perforing initial smooth deformation to move away from white surface
  1450. tol=1.0e-04, sigma=2.0, host= runc, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1451. mom=0.00, dt=0.05
  1452. 000: dt: 0.0000, sse=22321926.0, rms=22.981
  1453. 001: dt: 0.0500, sse=18070204.0, rms=20.566 (10.506%)
  1454. 002: dt: 0.0500, sse=15741809.0, rms=19.115 (7.057%)
  1455. 003: dt: 0.0500, sse=14176530.0, rms=18.074 (5.447%)
  1456. 004: dt: 0.0500, sse=13001107.0, rms=17.250 (4.556%)
  1457. 005: dt: 0.0500, sse=12057984.0, rms=16.560 (4.002%)
  1458. 006: dt: 0.0500, sse=11266631.0, rms=15.958 (3.638%)
  1459. 007: dt: 0.0500, sse=10582380.0, rms=15.418 (3.384%)
  1460. 008: dt: 0.0500, sse=9978156.0, rms=14.924 (3.199%)
  1461. 009: dt: 0.0500, sse=9436283.0, rms=14.468 (3.061%)
  1462. 010: dt: 0.0500, sse=8945184.0, rms=14.041 (2.951%)
  1463. positioning took 1.3 minutes
  1464. mean border=68.2, 82 (63) missing vertices, mean dist 0.9 [0.1 (%0.0)->1.3 (%100.0))]
  1465. %15 local maxima, %48 large gradients and %33 min vals, 169 gradients ignored
  1466. tol=1.0e-04, sigma=2.0, host= runc, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1467. mom=0.00, dt=0.05
  1468. 000: dt: 0.0000, sse=13241497.0, rms=17.417
  1469. 011: dt: 0.0500, sse=12683541.0, rms=17.016 (2.305%)
  1470. 012: dt: 0.0500, sse=12176472.0, rms=16.642 (2.195%)
  1471. 013: dt: 0.0500, sse=11713340.0, rms=16.294 (2.095%)
  1472. 014: dt: 0.0500, sse=11289092.0, rms=15.968 (2.002%)
  1473. 015: dt: 0.0500, sse=10898844.0, rms=15.661 (1.918%)
  1474. 016: dt: 0.0500, sse=10538530.0, rms=15.373 (1.840%)
  1475. 017: dt: 0.0500, sse=10204400.0, rms=15.101 (1.771%)
  1476. 018: dt: 0.0500, sse=9891938.0, rms=14.841 (1.717%)
  1477. 019: dt: 0.0500, sse=9594252.0, rms=14.590 (1.693%)
  1478. 020: dt: 0.0500, sse=9308206.0, rms=14.345 (1.683%)
  1479. positioning took 1.3 minutes
  1480. mean border=66.9, 78 (49) missing vertices, mean dist 0.8 [0.1 (%0.1)->1.2 (%99.9))]
  1481. %15 local maxima, %47 large gradients and %33 min vals, 206 gradients ignored
  1482. tol=1.0e-04, sigma=2.0, host= runc, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1483. mom=0.00, dt=0.05
  1484. 000: dt: 0.0000, sse=10284133.0, rms=15.169
  1485. 021: dt: 0.0500, sse=9963087.0, rms=14.904 (1.751%)
  1486. 022: dt: 0.0500, sse=9659105.0, rms=14.648 (1.718%)
  1487. 023: dt: 0.0500, sse=9374487.0, rms=14.404 (1.665%)
  1488. 024: dt: 0.0500, sse=9107295.0, rms=14.171 (1.617%)
  1489. 025: dt: 0.0500, sse=8855494.0, rms=13.948 (1.575%)
  1490. 026: dt: 0.0500, sse=8616281.0, rms=13.732 (1.545%)
  1491. 027: dt: 0.0500, sse=8387187.0, rms=13.523 (1.527%)
  1492. 028: dt: 0.0500, sse=8167326.0, rms=13.318 (1.512%)
  1493. 029: dt: 0.0500, sse=7955072.5, rms=13.118 (1.505%)
  1494. 030: dt: 0.0500, sse=7749272.0, rms=12.920 (1.504%)
  1495. positioning took 1.3 minutes
  1496. mean border=66.1, 94 (39) missing vertices, mean dist 0.7 [0.1 (%3.2)->1.1 (%96.8))]
  1497. %15 local maxima, %47 large gradients and %33 min vals, 245 gradients ignored
  1498. tol=1.0e-04, sigma=2.0, host= runc, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1499. mom=0.00, dt=0.50
  1500. smoothing T1 volume with sigma = 1.000
  1501. averaging target values for 5 iterations...
  1502. 000: dt: 0.0000, sse=8330991.0, rms=13.464
  1503. 031: dt: 0.5000, sse=6840926.0, rms=12.001 (10.869%)
  1504. 032: dt: 0.5000, sse=5633024.5, rms=10.670 (11.086%)
  1505. 033: dt: 0.5000, sse=4582733.0, rms=9.372 (12.164%)
  1506. 034: dt: 0.5000, sse=3755103.2, rms=8.195 (12.561%)
  1507. 035: dt: 0.5000, sse=3107235.0, rms=7.145 (12.809%)
  1508. 036: dt: 0.5000, sse=2678561.5, rms=6.354 (11.077%)
  1509. 037: dt: 0.5000, sse=2420107.2, rms=5.829 (8.259%)
  1510. 038: dt: 0.5000, sse=2288904.5, rms=5.542 (4.924%)
  1511. 039: dt: 0.5000, sse=2215107.0, rms=5.376 (2.992%)
  1512. 040: dt: 0.5000, sse=2173792.2, rms=5.278 (1.829%)
  1513. 041: dt: 0.5000, sse=2141282.0, rms=5.203 (1.425%)
  1514. rms = 5.16, time step reduction 1 of 3 to 0.250...
  1515. 042: dt: 0.5000, sse=2123470.2, rms=5.159 (0.847%)
  1516. 043: dt: 0.2500, sse=1944526.2, rms=4.650 (9.865%)
  1517. 044: dt: 0.2500, sse=1908006.9, rms=4.547 (2.202%)
  1518. rms = 4.55, time step reduction 2 of 3 to 0.125...
  1519. 045: dt: 0.1250, sse=1889321.9, rms=4.492 (1.213%)
  1520. 046: dt: 0.1250, sse=1865297.1, rms=4.419 (1.625%)
  1521. rms = 4.41, time step reduction 3 of 3 to 0.062...
  1522. 047: dt: 0.1250, sse=1861733.8, rms=4.408 (0.262%)
  1523. positioning took 3.0 minutes
  1524. mean border=63.6, 2859 (6) missing vertices, mean dist 0.2 [0.2 (%21.3)->0.5 (%78.7))]
  1525. %34 local maxima, %31 large gradients and %29 min vals, 202 gradients ignored
  1526. tol=1.0e-04, sigma=1.0, host= runc, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1527. mom=0.00, dt=0.50
  1528. smoothing T1 volume with sigma = 0.500
  1529. averaging target values for 5 iterations...
  1530. 000: dt: 0.0000, sse=2962615.5, rms=6.319
  1531. 048: dt: 0.5000, sse=2800627.2, rms=5.971 (5.507%)
  1532. 049: dt: 0.5000, sse=2541933.2, rms=5.416 (9.302%)
  1533. 050: dt: 0.5000, sse=2470480.8, rms=5.240 (3.247%)
  1534. 051: dt: 0.5000, sse=2237697.0, rms=4.659 (11.089%)
  1535. 052: dt: 0.5000, sse=2181439.8, rms=4.496 (3.495%)
  1536. 053: dt: 0.5000, sse=1996659.8, rms=3.958 (11.962%)
  1537. rms = 3.99, time step reduction 1 of 3 to 0.250...
  1538. 054: dt: 0.2500, sse=1767146.9, rms=3.047 (23.024%)
  1539. 055: dt: 0.2500, sse=1675221.1, rms=2.591 (14.966%)
  1540. 056: dt: 0.2500, sse=1650481.6, rms=2.458 (5.117%)
  1541. 057: dt: 0.2500, sse=1633871.2, rms=2.371 (3.540%)
  1542. rms = 2.34, time step reduction 2 of 3 to 0.125...
  1543. 058: dt: 0.2500, sse=1628528.6, rms=2.343 (1.203%)
  1544. 059: dt: 0.1250, sse=1566622.1, rms=1.961 (16.281%)
  1545. 060: dt: 0.1250, sse=1558236.2, rms=1.910 (2.620%)
  1546. rms = 1.90, time step reduction 3 of 3 to 0.062...
  1547. 061: dt: 0.1250, sse=1556054.1, rms=1.898 (0.634%)
  1548. positioning took 3.0 minutes
  1549. mean border=62.3, 3520 (3) missing vertices, mean dist 0.1 [0.2 (%24.2)->0.2 (%75.8))]
  1550. %43 local maxima, %22 large gradients and %28 min vals, 158 gradients ignored
  1551. tol=1.0e-04, sigma=0.5, host= runc, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1552. mom=0.00, dt=0.50
  1553. smoothing T1 volume with sigma = 0.250
  1554. averaging target values for 5 iterations...
  1555. 000: dt: 0.0000, sse=1786225.5, rms=2.909
  1556. rms = 3.40, time step reduction 1 of 3 to 0.250...
  1557. 062: dt: 0.2500, sse=1692032.2, rms=2.453 (15.676%)
  1558. 063: dt: 0.2500, sse=1646585.6, rms=2.195 (10.529%)
  1559. rms = 2.15, time step reduction 2 of 3 to 0.125...
  1560. 064: dt: 0.2500, sse=1636863.8, rms=2.154 (1.882%)
  1561. 065: dt: 0.1250, sse=1610111.2, rms=1.979 (8.100%)
  1562. rms = 1.93, time step reduction 3 of 3 to 0.062...
  1563. 066: dt: 0.1250, sse=1602620.6, rms=1.935 (2.247%)
  1564. positioning took 1.2 minutes
  1565. mean border=61.7, 7347 (3) missing vertices, mean dist 0.0 [0.2 (%30.6)->0.1 (%69.4))]
  1566. %47 local maxima, %18 large gradients and %27 min vals, 141 gradients ignored
  1567. tol=1.0e-04, sigma=0.2, host= runc, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.563, l_nspring=0.625, l_intensity=0.200, l_curv=1.000
  1568. mom=0.00, dt=0.50
  1569. writing pial surface to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.pial...
  1570. writing smoothed curvature to lh.curv.pial
  1571. 000: dt: 0.0000, sse=1639057.1, rms=2.136
  1572. rms = 2.71, time step reduction 1 of 3 to 0.250...
  1573. 067: dt: 0.2500, sse=1616624.9, rms=1.990 (6.810%)
  1574. rms = 1.97, time step reduction 2 of 3 to 0.125...
  1575. 068: dt: 0.2500, sse=1611932.5, rms=1.972 (0.899%)
  1576. 069: dt: 0.1250, sse=1600118.9, rms=1.888 (4.281%)
  1577. rms = 1.86, time step reduction 3 of 3 to 0.062...
  1578. 070: dt: 0.1250, sse=1594663.9, rms=1.859 (1.529%)
  1579. positioning took 1.0 minutes
  1580. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.curv.pial
  1581. writing smoothed area to lh.area.pial
  1582. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.area.pial
  1583. vertex spacing 0.81 +- 0.36 (0.03-->7.01) (max @ vno 148104 --> 146796)
  1584. face area 0.26 +- 0.21 (0.00-->8.35)
  1585. measuring cortical thickness...
  1586. writing cortical thickness estimate to 'thickness' file.
  1587. 0 of 212031 vertices processed
  1588. 25000 of 212031 vertices processed
  1589. 50000 of 212031 vertices processed
  1590. 75000 of 212031 vertices processed
  1591. 100000 of 212031 vertices processed
  1592. 125000 of 212031 vertices processed
  1593. 150000 of 212031 vertices processed
  1594. 175000 of 212031 vertices processed
  1595. 200000 of 212031 vertices processed
  1596. 0 of 212031 vertices processed
  1597. 25000 of 212031 vertices processed
  1598. 50000 of 212031 vertices processed
  1599. 75000 of 212031 vertices processed
  1600. 100000 of 212031 vertices processed
  1601. 125000 of 212031 vertices processed
  1602. 150000 of 212031 vertices processed
  1603. 175000 of 212031 vertices processed
  1604. 200000 of 212031 vertices processed
  1605. thickness calculation complete, 301:1245 truncations.
  1606. 36934 vertices at 0 distance
  1607. 119921 vertices at 1 distance
  1608. 128044 vertices at 2 distance
  1609. 74077 vertices at 3 distance
  1610. 30492 vertices at 4 distance
  1611. 10024 vertices at 5 distance
  1612. 3071 vertices at 6 distance
  1613. 949 vertices at 7 distance
  1614. 332 vertices at 8 distance
  1615. 153 vertices at 9 distance
  1616. 91 vertices at 10 distance
  1617. 72 vertices at 11 distance
  1618. 59 vertices at 12 distance
  1619. 68 vertices at 13 distance
  1620. 31 vertices at 14 distance
  1621. 31 vertices at 15 distance
  1622. 9 vertices at 16 distance
  1623. 27 vertices at 17 distance
  1624. 17 vertices at 18 distance
  1625. 6 vertices at 19 distance
  1626. 4 vertices at 20 distance
  1627. writing curvature file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/lh.thickness
  1628. positioning took 20.7 minutes
  1629. #--------------------------------------------
  1630. #@# Refine Pial Surfs w/ T2/FLAIR Fri Dec 6 06:12:41 UTC 2019
  1631.  
  1632. bbregister --s sub-TOME3024 --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz --lta /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/T2raw.auto.lta --init-coreg --T2
  1633.  
  1634. tmp /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073
  1635. Log file is /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/T2raw.auto.dat.log
  1636. Fri Dec 6 06:12:41 UTC 2019
  1637.  
  1638. setenv SUBJECTS_DIR /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer
  1639. cd /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1640. /opt/freesurfer/bin/bbregister --s sub-TOME3024 --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz --lta /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/T2raw.auto.lta --init-coreg --T2
  1641.  
  1642. $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
  1643. Linux runc 4.15.0-1029-gcp #31-Ubuntu SMP Thu Mar 21 09:40:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
  1644. FREESURFER_HOME /opt/freesurfer
  1645. mri_convert /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii
  1646. mri_convert.bin /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii
  1647. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
  1648. reading from /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz...
  1649. TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
  1650. i_ras = (0.996215, -0.0738526, -0.0458488)
  1651. j_ras = (0.0776606, 0.993111, 0.0877416)
  1652. k_ras = (0.039053, -0.0909701, 0.995088)
  1653. writing to /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii...
  1654. mri_coreg --s sub-TOME3024 --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii --regdat /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/reg.init.dat --reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/mri_coreg.lta --nthreads 3 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask
  1655.  
  1656. $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
  1657. cwd /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1658. cmdline mri_coreg --s sub-TOME3024 --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii --regdat /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/reg.init.dat --reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/mri_coreg.lta --nthreads 3 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask
  1659. sysname Linux
  1660. hostname runc
  1661. machine x86_64
  1662. user root
  1663. dof 6
  1664. nsep 1
  1665. cras0 1
  1666. ftol 0.000100
  1667. linmintol 0.010000
  1668. bf 1
  1669. bflim 30.000000
  1670. bfnsamp 30
  1671. SmoothRef 0
  1672. SatPct 99.990000
  1673. MovOOB 0
  1674. optschema 1
  1675. Reading in mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii
  1676. Reading in ref /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/brainmask.mgz
  1677. Setting cras translation parameters to align centers
  1678. Creating random numbers for coordinate dithering
  1679. Performing intensity dithering
  1680. Initial parameters 4.5349 3.3765 1.2388 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
  1681. Separation list (1): 4 min = 4
  1682. DoSmoothing 1
  1683. DoCoordDither 1
  1684. DoIntensityDither 1
  1685. nitersmax 4
  1686. ftol 1.000e-04
  1687. linmintol 1.000e-02
  1688. SatPct 99.990000
  1689. Hist FWHM 7.000000 7.000000
  1690. nthreads 3
  1691. movsat = 2820.0000
  1692. mov gstd 1.9140 1.9140 1.9140
  1693. Smoothing mov
  1694. refsat = 114.0000
  1695. ref gstd 1.9140 1.9140 1.9140
  1696. Smoothing ref
  1697. COREGpreproc() done
  1698. Testing if mov and target overlap
  1699. Init cost -1.0401521383
  1700. nhits = 302112 out of 32768000, Percent Overlap: 59.0
  1701. Initial RefRAS-to-MovRAS
  1702. 1.00000 0.00000 0.00000 4.53490;
  1703. 0.00000 1.00000 0.00000 3.37648;
  1704. 0.00000 0.00000 1.00000 1.23878;
  1705. 0.00000 0.00000 0.00000 1.00000;
  1706. Initial RefVox-to-MovVox
  1707. -0.99613 0.04585 -0.07385 266.84949;
  1708. -0.07765 -0.08773 0.99303 17.49121;
  1709. -0.03905 -0.99501 -0.09096 338.94052;
  1710. 0.00000 0.00000 0.00000 1.00000;
  1711. sep = 4 -----------------------------------
  1712. COREGoptBruteForce() 30 1 30
  1713. Turning on MovOOB for BruteForce Search
  1714. #BF# sep= 4 iter=0 lim=30.0 delta=2.00 0.53490 -0.62352 1.23878 0.00000 0.00000 2.00000 -1.0393932
  1715. Turning MovOOB back off after brute force search
  1716.  
  1717.  
  1718. ---------------------------------
  1719. Init Powel Params dof = 6
  1720. Starting OpenPowel2(), sep = 4
  1721. InitialCost -1.0477005243
  1722. #@# 4 188 0.53490 -0.62352 1.23878 0.00000 0.00000 2.00000 -1.0477005
  1723. fs_powell::minimize
  1724. nparams 6
  1725. maxfev 4
  1726. ftol 0.000100
  1727. linmin_xtol_ 0.010000
  1728. powell nthiter 0: fret = -1.047701
  1729. #@# 4 193 -0.08314 -0.62352 1.23878 0.00000 0.00000 2.00000 -1.0481125
  1730. #@# 4 195 -0.21599 -0.62352 1.23878 0.00000 0.00000 2.00000 -1.0481294
  1731. #@# 4 196 -0.22599 -0.62352 1.23878 0.00000 0.00000 2.00000 -1.0481298
  1732. #@# 4 204 -0.23599 -0.24155 1.23878 0.00000 0.00000 2.00000 -1.0482473
  1733. #@# 4 205 -0.23599 -0.13272 1.23878 0.00000 0.00000 2.00000 -1.0482484
  1734. #@# 4 206 -0.23599 -0.17902 1.23878 0.00000 0.00000 2.00000 -1.0482495
  1735. #@# 4 214 -0.23599 -0.19324 0.62074 0.00000 0.00000 2.00000 -1.0483452
  1736. #@# 4 216 -0.23599 -0.19324 0.80433 0.00000 0.00000 2.00000 -1.0483649
  1737. #@# 4 217 -0.23599 -0.19324 0.79433 0.00000 0.00000 2.00000 -1.0483650
  1738. #@# 4 225 -0.23599 -0.19324 0.79433 -0.27633 0.00000 2.00000 -1.0483861
  1739. #@# 4 233 -0.23599 -0.19324 0.79433 -0.27633 -0.61803 2.00000 -1.0484196
  1740. #@# 4 235 -0.23599 -0.19324 0.79433 -0.27633 -0.42547 2.00000 -1.0484290
  1741. #@# 4 238 -0.23599 -0.19324 0.79433 -0.27633 -0.43624 2.00000 -1.0484294
  1742. #@# 4 243 -0.23599 -0.19324 0.79433 -0.27633 -0.43624 1.38197 -1.0486079
  1743. #@# 4 245 -0.23599 -0.19324 0.79433 -0.27633 -0.43624 1.21416 -1.0486159
  1744. #@# 4 249 -0.23599 -0.19324 0.79433 -0.27633 -0.43624 1.17558 -1.0486165
  1745. powell nthiter 1: fret = -1.048617
  1746. #@# 4 258 -0.40213 -0.19324 0.79433 -0.27633 -0.43624 1.17558 -1.0486474
  1747. #@# 4 267 -0.40213 -0.15783 0.79433 -0.27633 -0.43624 1.17558 -1.0486492
  1748. #@# 4 268 -0.40213 -0.14451 0.79433 -0.27633 -0.43624 1.17558 -1.0486497
  1749. #@# 4 278 -0.40213 -0.14451 0.83873 -0.27633 -0.43624 1.17558 -1.0486511
  1750. #@# 4 288 -0.40213 -0.14451 0.82873 -0.35629 -0.43624 1.17558 -1.0486537
  1751. #@# 4 289 -0.40213 -0.14451 0.82873 -0.36966 -0.43624 1.17558 -1.0486541
  1752. #@# 4 298 -0.40213 -0.14451 0.82873 -0.36966 -0.28002 1.17558 -1.0486631
  1753. #@# 4 307 -0.40213 -0.14451 0.82873 -0.36966 -0.28002 1.04074 -1.0486660
  1754. #@# 4 308 -0.40213 -0.14451 0.82873 -0.36966 -0.28002 1.07215 -1.0486670
  1755. #@# 4 309 -0.40213 -0.14451 0.82873 -0.36966 -0.28002 1.08689 -1.0486674
  1756. #@# 4 311 -0.40213 -0.14451 0.82873 -0.36966 -0.28002 1.09689 -1.0486676
  1757. Powell done niters total = 1
  1758. OptTimeSec 18.9 sec
  1759. OptTimeMin 0.32 min
  1760. nEvals 312
  1761. Final parameters -0.40212858 -0.14451160 0.82873374 -0.36966497 -0.28002363 1.09688735
  1762. Final cost -1.048667501028306
  1763.  
  1764.  
  1765. ---------------------------------
  1766. mri_coreg utimesec 284.519623
  1767. mri_coreg stimesec 2.076202
  1768. mri_coreg ru_maxrss 821324
  1769. mri_coreg ru_ixrss 0
  1770. mri_coreg ru_idrss 0
  1771. mri_coreg ru_isrss 0
  1772. mri_coreg ru_minflt 303481
  1773. mri_coreg ru_majflt 31
  1774. mri_coreg ru_nswap 0
  1775. mri_coreg ru_inblock 7472
  1776. mri_coreg ru_oublock 16
  1777. mri_coreg ru_msgsnd 0
  1778. mri_coreg ru_msgrcv 0
  1779. mri_coreg ru_nsignals 0
  1780. mri_coreg ru_nvcsw 631
  1781. mri_coreg ru_nivcsw 20989
  1782. Final RefRAS-to-MovRAS
  1783. 0.99980 0.01914 -0.00489 -0.40213;
  1784. -0.01917 0.99980 -0.00645 -0.14451;
  1785. 0.00476 0.00654 0.99997 0.82873;
  1786. 0.00000 0.00000 0.00000 1.00000;
  1787. Final RefVox-to-MovVox
  1788. -0.99714 0.05024 -0.05506 257.42838;
  1789. -0.05902 -0.08095 0.99489 8.23091;
  1790. -0.04553 -0.99537 -0.08369 338.48834;
  1791. 0.00000 0.00000 0.00000 1.00000;
  1792. Final parameters -0.4021 -0.1445 0.8287 -0.3697 -0.2800 1.0969
  1793. nhits = 302409 out of 32768000, Percent Overlap: 59.1
  1794. mri_coreg RunTimeSec 134.0 sec
  1795. To check run:
  1796. tkregisterfv --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii --targ /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/brainmask.mgz --reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/mri_coreg.lta --s sub-TOME3024 --surfs
  1797.  
  1798. mri_coreg done
  1799.  
  1800. mri_segreg --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii --init-reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/reg.init.dat --out-reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
  1801. $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
  1802. setenv SUBJECTS_DIR /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer
  1803. cd /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts
  1804. mri_segreg --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii --init-reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/reg.init.dat --out-reg /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
  1805. sysname Linux
  1806. hostname runc
  1807. machine x86_64
  1808. user root
  1809. movvol /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/template.nii
  1810. regfile /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/reg.init.dat
  1811. subject sub-TOME3024
  1812. dof 6
  1813. outregfile /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/tmp.bbregister.10073/bbr.pass1.dat
  1814. UseMask 0
  1815. UseLH 1
  1816. UseRH 1
  1817. nsubsamp 100
  1818. PenaltySign -1
  1819. PenaltySlope 0.500000
  1820. PenaltyCenter 0.000000
  1821. surfname white
  1822. GMProjFrac 0.500000
  1823. WMProjAbs 2.000000
  1824. lhcostfile (null)
  1825. rhcostfile (null)
  1826. interp trilinear (1)
  1827. frame 0
  1828. TolPowell 0.000100
  1829. nMaxItersPowell 36
  1830. n1dmin 3
  1831. Profile 0
  1832. Gdiag_no -1
  1833. AddNoise 0 (0)
  1834. SynthSeed 1576008909
  1835. TransRandMax 0.000000
  1836. RotRandMax 0.000000
  1837. Translations 0.000000 0.000000 0.000000
  1838. Rotations 0.000000 0.000000 0.000000
  1839. Input reg
  1840. -0.99722 0.05507 0.05024 5.50861;
  1841. 0.04553 -0.08369 0.99545 -1.15556;
  1842. -0.05902 -0.99497 -0.08095 3.98474;
  1843. 0.00000 0.00000 0.00000 1.00000;
  1844.  
  1845. Loading mov
  1846. Projecting LH Surfs
  1847. Loading lh.white surf
  1848. Loading lh.thickness for GM
  1849. MRISread(/flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/surf/rh.white): could not open file
  1850. GM Proj: 1 0.500000 2.000000
  1851. WM Proj: 0 0.500000 2.000000
  1852. Projecting RH Surfs
  1853. Loading rh.white surf
  1854. No such file or directory
  1855. Linux runc 4.15.0-1029-gcp #31-Ubuntu SMP Thu Mar 21 09:40:28 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
  1856.  
  1857. recon-all -s sub-TOME3024 exited with ERRORS at Fri Dec 6 06:15:04 UTC 2019
  1858.  
  1859. For more details, see the log file /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/scripts/recon-all-lh.log
  1860. To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  1861.  
  1862. Standard error:
  1863.  
  1864. Return code: 1
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