orig_nu.log 16 KB

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  1. /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
  2. /opt/freesurfer/5.3/bin/mri_nu_correct.mni
  3. --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
  4. nIters 1
  5. $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
  6. Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
  7. Fri Jun 20 09:59:18 CEST 2014
  8. Program nu_correct, built from:
  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. tmpdir is ./tmp.mri_nu_correct.mni.16147
  11. /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16147/nu0.mnc -odt float
  13. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16147/nu0.mnc -odt float
  14. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
  15. reading from orig.mgz...
  16. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  17. i_ras = (-1, 3.72529e-08, 7.07805e-08)
  18. j_ras = (-1.37836e-07, 5.00586e-09, -1)
  19. k_ras = (-1.11759e-08, 1, 1.86265e-09)
  20. changing data type from uchar to float (noscale = 0)...
  21. writing to ./tmp.mri_nu_correct.mni.16147/nu0.mnc...
  22. --------------------------------------------------------
  23. Iteration 1 Fri Jun 20 09:59:21 CEST 2014
  24. nu_correct -clobber ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16147/0/ -iterations 1000 -distance 50
  25. [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 09:59:22] running:
  26. /opt/freesurfer/5.3/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.16147/0/ ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/nu1.imp
  27. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  28. Processing:.................................................................Done
  29. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  30. Processing:.................................................................Done
  31. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  32. Processing:.................................................................Done
  33. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  34. Processing:.................................................................Done
  35. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  36. Processing:.................................................................Done
  37. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  38. Processing:.................................................................Done
  39. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  40. Processing:.................................................................Done
  41. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  42. Processing:.................................................................Done
  43. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  44. Processing:.................................................................Done
  45. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  46. Processing:.................................................................Done
  47. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  48. Processing:.................................................................Done
  49. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  50. Processing:.................................................................Done
  51. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  52. Processing:.................................................................Done
  53. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  54. Processing:.................................................................Done
  55. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  56. Processing:.................................................................Done
  57. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  58. Processing:.................................................................Done
  59. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  60. Processing:.................................................................Done
  61. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  62. Processing:.................................................................Done
  63. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  64. Processing:.................................................................Done
  65. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  66. Processing:.................................................................Done
  67. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  68. Processing:.................................................................Done
  69. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  70. Processing:.................................................................Done
  71. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  72. Processing:.................................................................Done
  73. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  74. Processing:.................................................................Done
  75. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  76. Processing:.................................................................Done
  77. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  78. Processing:.................................................................Done
  79. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  80. Processing:.................................................................Done
  81. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  82. Processing:.................................................................Done
  83. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  84. Processing:.................................................................Done
  85. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  86. Processing:.................................................................Done
  87. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  88. Processing:.................................................................Done
  89. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  90. Processing:.................................................................Done
  91. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  92. Processing:.................................................................Done
  93. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  94. Processing:.................................................................Done
  95. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  96. Processing:.................................................................Done
  97. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  98. Processing:.................................................................Done
  99. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  100. Processing:.................................................................Done
  101. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  102. Processing:.................................................................Done
  103. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  104. Processing:.................................................................Done
  105. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  106. Processing:.................................................................Done
  107. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  108. Processing:.................................................................Done
  109. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  110. Processing:.................................................................Done
  111. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  112. Processing:.................................................................Done
  113. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  114. Processing:.................................................................Done
  115. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  116. Processing:.................................................................Done
  117. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  118. Processing:.................................................................Done
  119. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  120. Processing:.................................................................Done
  121. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  122. Processing:.................................................................Done
  123. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  124. Processing:.................................................................Done
  125. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  126. Processing:.................................................................Done
  127. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  128. Processing:.................................................................Done
  129. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  130. Processing:.................................................................Done
  131. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  132. Processing:.................................................................Done
  133. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  134. Processing:.................................................................Done
  135. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  136. Processing:.................................................................Done
  137. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  138. Processing:.................................................................Done
  139. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  140. Processing:.................................................................Done
  141. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  142. Processing:.................................................................Done
  143. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  144. Processing:.................................................................Done
  145. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  146. Processing:.................................................................Done
  147. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  148. Processing:.................................................................Done
  149. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  150. Processing:.................................................................Done
  151. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  152. Processing:.................................................................Done
  153. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  154. Processing:.................................................................Done
  155. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  156. Processing:.................................................................Done
  157. Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
  158. Processing:.................................................................Done
  159. Number of iterations: 66
  160. CV of field change: 0.000977411
  161. [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:01:00] running:
  162. /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/0//template.mnc
  163. Transforming slices:......................................................................................Done
  164. Transforming slices:................................................................................................................................................................................................................................................................Done
  165. mri_convert ./tmp.mri_nu_correct.mni.16147/nu1.mnc orig_nu.mgz --like orig.mgz --conform
  166. mri_convert ./tmp.mri_nu_correct.mni.16147/nu1.mnc orig_nu.mgz --like orig.mgz --conform
  167. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
  168. reading from ./tmp.mri_nu_correct.mni.16147/nu1.mnc...
  169. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  170. i_ras = (-1, 3.72529e-08, 7.07805e-08)
  171. j_ras = (-1.37836e-07, 5.00586e-09, -1)
  172. k_ras = (-1.11759e-08, 1, 1.86265e-09)
  173. Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
  174. Data is conformed to 1 mm size and 256 voxels for all directions
  175. INFO: transform src into the like-volume: orig.mgz
  176. changing data type from float to uchar (noscale = 0)...
  177. MRIchangeType: Building histogram
  178. writing to orig_nu.mgz...
  179. Fri Jun 20 10:01:12 CEST 2014
  180. mri_nu_correct.mni done