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orig_nu.log

orig_nu.log 6.8 KB
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  1. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
    2. 

  2. /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
    3. 

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

  4. nIters 1
    5. 

  5. $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
    6. 

  6. Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
    7. 

  7. Thu Aug  8 10:55:06 CEST 2013
    8. 

  8. Program nu_correct, built from:
    9. 

  9. Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
    10. 

  10. tmpdir is ./tmp.mri_nu_correct.mni.4163
    11. 

  11. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri
    12. 

  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4163/nu0.mnc -odt float
    13. 

  13. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4163/nu0.mnc -odt float 
    14. 

  14. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    15. 

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

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

  17. i_ras = (-1, 4.65661e-09, -1.86265e-09)
    18. 

  18. j_ras = (1.86265e-09, 2.79397e-09, -1)
    19. 

  19. k_ras = (-8.3528e-09, 1, -9.31323e-10)
    20. 

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

  21. writing to ./tmp.mri_nu_correct.mni.4163/nu0.mnc...
    22. 

  22.  
    23. 

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

  24. Iteration 1 Thu Aug  8 10:55:10 CEST 2013
    25. 

  25. nu_correct -clobber ./tmp.mri_nu_correct.mni.4163/nu0.mnc ./tmp.mri_nu_correct.mni.4163/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4163/0/ -iterations 1000 -distance 50
    26. 

  26. [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:55:10] running:
    27. 

  27.   /opt/freesurfer/5.3.0/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 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4163/0/ ./tmp.mri_nu_correct.mni.4163/nu0.mnc ./tmp.mri_nu_correct.mni.4163/nu1.imp
    28. 

  28. 

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

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

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

  32. Processing:.................................................................Done
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  33. Processing:.................................................................Done
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  34. Processing:.................................................................Done
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  35. Processing:.................................................................Done
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  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
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  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
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  57. Processing:.................................................................Done
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  58. Processing:.................................................................Done
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  59. Processing:.................................................................Done
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  60. Processing:.................................................................Done
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  61. Processing:.................................................................Done
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  62. Processing:.................................................................Done
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  63. Processing:.................................................................Done
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  64. Processing:.................................................................Done
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  65. Processing:.................................................................Done
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  66. Processing:.................................................................Done
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  67. Processing:.................................................................Done
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  68. Processing:.................................................................Done
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  69. Processing:.................................................................Done
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  70. Processing:.................................................................Done
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  71. Processing:.................................................................Done
    72. 

  72. Processing:.................................................................Done
    73. 

  73. Number of iterations: 44 
    74. 

  74. CV of field change: 0.000982994
    75. 

  75. [fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub003/mri/] [2013-08-08 10:56:33] running:
    76. 

  76.   /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4163/nu0.mnc ./tmp.mri_nu_correct.mni.4163/0//template.mnc
    77. 

  77. 

  78. Transforming slices:......................................................................................Done
    79. 

  79. Transforming slices:................................................................................................................................................................................................................................................................Done
    80. 

  80.  
    81. 

  81.  
    82. 

  82.  
    83. 

  83. mri_convert ./tmp.mri_nu_correct.mni.4163/nu1.mnc orig_nu.mgz --like orig.mgz --conform
    84. 

  84. mri_convert ./tmp.mri_nu_correct.mni.4163/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
    85. 

  85. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    86. 

  86. reading from ./tmp.mri_nu_correct.mni.4163/nu1.mnc...
    87. 

  87. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    88. 

  88. i_ras = (-1, 4.65661e-09, -1.86265e-09)
    89. 

  89. j_ras = (1.86265e-09, 2.79397e-09, -1)
    90. 

  90. k_ras = (-8.3528e-09, 1, -9.31322e-10)
    91. 

  91. Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
    92. 

  92. Data is conformed to 1 mm size and 256 voxels for all directions
    93. 

  93. INFO: transform src into the like-volume: orig.mgz
    94. 

  94. changing data type from float to uchar (noscale = 0)...
    95. 

  95. MRIchangeType: Building histogram 
    96. 

  96. writing to orig_nu.mgz...
    97. 

  97.  
    98. 

  98.  
    99. 

  99. Thu Aug  8 10:56:51 CEST 2013
    100. 

  100. mri_nu_correct.mni done
    101.