mri_nu_correct.mni.log 9.6 KB

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  1. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri
  2. /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/mri_nu_correct.mni
  3. --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
  4. nIters 2
  5. $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
  6. Linux tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
  7. Sat Oct 7 16:12:00 CEST 2017
  8. Program nu_correct, built from:
  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. tmpdir is ./tmp.mri_nu_correct.mni.2541
  11. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri
  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2541/nu0.mnc -odt float
  13. mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2541/nu0.mnc -odt float
  14. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 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, 0, 0)
  18. j_ras = (0, 0, -1)
  19. k_ras = (0, 1, 0)
  20. changing data type from uchar to float (noscale = 0)...
  21. writing to ./tmp.mri_nu_correct.mni.2541/nu0.mnc...
  22. --------------------------------------------------------
  23. Iteration 1 Sat Oct 7 16:12:02 CEST 2017
  24. nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/0/
  25. [ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:02] running:
  26. /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2541/0/ ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/nu1.imp
  27. Processing:.................................................................Done
  28. Processing:.................................................................Done
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  65. Processing:.................................................................Done
  66. Number of iterations: 39
  67. CV of field change: 0.000952228
  68. --------------------------------------------------------
  69. Iteration 2 Sat Oct 7 16:12:49 CEST 2017
  70. nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/1/
  71. [ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:49] running:
  72. /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.2541/1/ ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.imp
  73. Processing:.................................................................Done
  74. Processing:.................................................................Done
  75. Processing:.................................................................Done
  76. Processing:.................................................................Done
  77. Processing:.................................................................Done
  78. Processing:.................................................................Done
  79. Processing:.................................................................Done
  80. Processing:.................................................................Done
  81. Number of iterations: 8
  82. CV of field change: 0.00093359
  83. mri_binarize --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/ones.mgz
  84. $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
  85. cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri
  86. cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/ones.mgz
  87. sysname Linux
  88. hostname tars-542
  89. machine x86_64
  90. user ntraut
  91. input ./tmp.mri_nu_correct.mni.2541/nu2.mnc
  92. frame 0
  93. nErode3d 0
  94. nErode2d 0
  95. output ./tmp.mri_nu_correct.mni.2541/ones.mgz
  96. Binarizing based on threshold
  97. min -1
  98. max +infinity
  99. binval 1
  100. binvalnot 0
  101. fstart = 0, fend = 0, nframes = 1
  102. Found 16777216 values in range
  103. Counting number of voxels in first frame
  104. Found 16777216 voxels in final mask
  105. Count: 16777216 16777216.000000 16777216 100.000000
  106. mri_binarize done
  107. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/input.mean.dat
  108. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  109. cwd
  110. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/input.mean.dat
  111. sysname Linux
  112. hostname tars-542
  113. machine x86_64
  114. user ntraut
  115. UseRobust 0
  116. Loading ./tmp.mri_nu_correct.mni.2541/ones.mgz
  117. Loading orig.mgz
  118. Voxel Volume is 1 mm^3
  119. Generating list of segmentation ids
  120. Found 1 segmentations
  121. Computing statistics for each segmentation
  122. Reporting on 1 segmentations
  123. Using PrintSegStat
  124. Computing spatial average of each frame
  125. 0
  126. Writing to ./tmp.mri_nu_correct.mni.2541/input.mean.dat
  127. mri_segstats done
  128. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/output.mean.dat
  129. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  130. cwd
  131. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/output.mean.dat
  132. sysname Linux
  133. hostname tars-542
  134. machine x86_64
  135. user ntraut
  136. UseRobust 0
  137. Loading ./tmp.mri_nu_correct.mni.2541/ones.mgz
  138. Loading ./tmp.mri_nu_correct.mni.2541/nu2.mnc
  139. Voxel Volume is 1 mm^3
  140. Generating list of segmentation ids
  141. Found 1 segmentations
  142. Computing statistics for each segmentation
  143. Reporting on 1 segmentations
  144. Using PrintSegStat
  145. Computing spatial average of each frame
  146. 0
  147. Writing to ./tmp.mri_nu_correct.mni.2541/output.mean.dat
  148. mri_segstats done
  149. mris_calc -o ./tmp.mri_nu_correct.mni.2541/nu2.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc mul .97354204708638120492
  150. mri_convert ./tmp.mri_nu_correct.mni.2541/nu2.mnc nu.mgz --like orig.mgz
  151. mri_convert.bin ./tmp.mri_nu_correct.mni.2541/nu2.mnc nu.mgz --like orig.mgz
  152. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
  153. reading from ./tmp.mri_nu_correct.mni.2541/nu2.mnc...
  154. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  155. i_ras = (-1, 0, 0)
  156. j_ras = (0, 0, -1)
  157. k_ras = (0, 1, 0)
  158. INFO: transform src into the like-volume: orig.mgz
  159. writing to nu.mgz...
  160. mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
  161. type change took 0 minutes and 7 seconds.
  162. mapping ( 9, 129) to ( 3, 110)
  163. Sat Oct 7 16:13:50 CEST 2017
  164. mri_nu_correct.mni done