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ds000114
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freesurfer-6.0.1
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sub-09
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mri
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mri_nu_correct.mni.log.bak

mri_nu_correct.mni.log.bak 5.1 KB
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  1. /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/mri
    2. 

  2. /opt/freesurfer/bin/mri_nu_correct.mni
    3. 

  3. --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
    4. 

  4. nIters 1
    5. 

  5. $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
    6. 

  6. Linux nid00784 4.4.103-6.38_4.0.95-cray_ari_c #1 SMP Fri Feb 9 17:52:44 UTC 2018 (172b90b) x86_64 x86_64 x86_64 GNU/Linux
    7. 

  7. Wed Oct 16 15:51:39 UTC 2019
    8. 

  8. Program nu_correct, built from:
    9. 

  9. Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
    10. 

  10. tmpdir is ./tmp.mri_nu_correct.mni.28594
    11. 

  11. /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/mri
    12. 

  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28594/nu0.mnc -odt float
    13. 

  13. mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28594/nu0.mnc -odt float 
    14. 

  14. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
    15. 

  15. reading from orig.mgz...
    16. 

  16. TR=9.68, TE=0.00, TI=0.00, flip angle=0.00
    17. 

  17. i_ras = (-1, 6.98492e-10, 3.72529e-09)
    18. 

  18. j_ras = (3.72529e-09, 1.49012e-08, -1)
    19. 

  19. k_ras = (6.98492e-10, 1, 0)
    20. 

  20. changing data type from uchar to float (noscale = 0)...
    21. 

  21. writing to ./tmp.mri_nu_correct.mni.28594/nu0.mnc...
    22. 

  22.  
    23. 

  23. --------------------------------------------------------
    24. 

  24. Iteration 1 Wed Oct 16 15:51:41 UTC 2019
    25. 

  25. nu_correct -clobber ./tmp.mri_nu_correct.mni.28594/nu0.mnc ./tmp.mri_nu_correct.mni.28594/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28594/0/ -iterations 1000 -distance 50
    26. 

  26. [oesteban@nid00784:/corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/mri/] [2019-10-16 15:51:41] running:
    27. 

  27.   /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28594/0/ ./tmp.mri_nu_correct.mni.28594/nu0.mnc ./tmp.mri_nu_correct.mni.28594/nu1.imp
    28. 

  28. 

  29. Processing:.................................................................Done
    30. 

  30. Processing:.................................................................Done
    31. 

  31. Processing:.................................................................Done
    32. 

  32. Processing:.................................................................Done
    33. 

  33. Processing:.................................................................Done
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  34. Processing:.................................................................Done
    35. 

  35. Processing:.................................................................Done
    36. 

  36. Processing:.................................................................Done
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  37. Processing:.................................................................Done
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  38. Processing:.................................................................Done
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  39. Processing:.................................................................Done
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  40. Processing:.................................................................Done
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  41. Processing:.................................................................Done
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  42. Processing:.................................................................Done
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  43. Processing:.................................................................Done
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  44. Processing:.................................................................Done
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  45. Processing:.................................................................Done
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  46. Processing:.................................................................Done
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  47. Processing:.................................................................Done
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  48. Processing:.................................................................Done
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  49. Processing:.................................................................Done
    50. 

  50. Processing:.................................................................Done
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  51. Processing:.................................................................Done
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  52. Processing:.................................................................Done
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  53. Processing:.................................................................Done
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  54. Processing:.................................................................Done
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  55. Processing:.................................................................Done
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  56. Processing:.................................................................Done
    57. 

  57. Processing:.................................................................Done
    58. 

  58. Processing:.................................................................Done
    59. 

  59. Processing:.................................................................Done
    60. 

  60. Number of iterations: 31 
    61. 

  61. CV of field change: 0.00098941
    62. 

  62.  
    63. 

  63.  
    64. 

  64.  
    65. 

  65. mri_convert ./tmp.mri_nu_correct.mni.28594/nu1.mnc orig_nu.mgz --like orig.mgz --conform
    66. 

  66. mri_convert.bin ./tmp.mri_nu_correct.mni.28594/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
    67. 

  67. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
    68. 

  68. reading from ./tmp.mri_nu_correct.mni.28594/nu1.mnc...
    69. 

  69. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    70. 

  70. i_ras = (-1, 6.98492e-10, 3.72529e-09)
    71. 

  71. j_ras = (3.72529e-09, 1.49012e-08, -1)
    72. 

  72. k_ras = (6.98492e-10, 1, 0)
    73. 

  73. INFO: transform src into the like-volume: orig.mgz
    74. 

  74. changing data type from float to uchar (noscale = 0)...
    75. 

  75. MRIchangeType: Building histogram 
    76. 

  76. writing to orig_nu.mgz...
    77. 

  77.  
    78. 

  78.  
    79. 

  79. Wed Oct 16 15:52:33 UTC 2019
    80. 

  80. mri_nu_correct.mni done
    81.