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mri_nu_correct.mni.log.bak

mri_nu_correct.mni.log.bak 8.3 KB
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  1. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
    7. 

  7. Thu Aug  8 10:55:05 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.15214
    11. 

  11. /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
    12. 

  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15214/nu0.mnc -odt float
    13. 

  13. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15214/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, 4.19095e-09, 3.72529e-09)
    18. 

  18. j_ras = (7.45058e-09, 1.49012e-08, -1)
    19. 

  19. k_ras = (-6.0536e-09, 1, -1.49012e-08)
    20. 

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

  21. writing to ./tmp.mri_nu_correct.mni.15214/nu0.mnc...
    22. 

  22.  
    23. 

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

  24. Iteration 1 Thu Aug  8 10:55:09 CEST 2013
    25. 

  25. nu_correct -clobber ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15214/0/ -iterations 1000 -distance 50
    26. 

  26. [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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.15214/0/ ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/nu1.imp
    28. 

  28. 

  29. Processing:.................................................................Done
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  30. Processing:.................................................................Done
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  31. Processing:.................................................................Done
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  32. Processing:.................................................................Done
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  89. Processing:.................................................................Done
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  90. Processing:.................................................................Done
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  91. Processing:.................................................................Done
    92. 

  92. Number of iterations: 63 
    93. 

  93. CV of field change: 0.000991682
    94. 

  94. [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:56:56] running:
    95. 

  95.   /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/0//template.mnc
    96. 

  96. 

  97. Transforming slices:......................................................................................Done
    98. 

  98. Transforming slices:................................................................................................................................................................................................................................................................Done
    99. 

  99.  
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  100.  
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  101.  
    102. 

  102. mri_convert ./tmp.mri_nu_correct.mni.15214/nu1.mnc orig_nu.mgz --like orig.mgz --conform
    103. 

  103. mri_convert ./tmp.mri_nu_correct.mni.15214/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
    104. 

  104. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    105. 

  105. reading from ./tmp.mri_nu_correct.mni.15214/nu1.mnc...
    106. 

  106. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    107. 

  107. i_ras = (-1, 4.19095e-09, 3.72529e-09)
    108. 

  108. j_ras = (7.45058e-09, 1.49012e-08, -1)
    109. 

  109. k_ras = (-6.0536e-09, 1, -1.49012e-08)
    110. 

  110. Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
    111. 

  111. Data is conformed to 1 mm size and 256 voxels for all directions
    112. 

  112. INFO: transform src into the like-volume: orig.mgz
    113. 

  113. changing data type from float to uchar (noscale = 0)...
    114. 

  114. MRIchangeType: Building histogram 
    115. 

  115. writing to orig_nu.mgz...
    116. 

  116.  
    117. 

  117.  
    118. 

  118. Thu Aug  8 10:57:12 CEST 2013
    119. 

  119. mri_nu_correct.mni done
    120.