mri_nu_correct.mni.log 11 KB

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  1. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051258/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-904 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 21:17:20 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.10464
  11. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051258/mri
  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10464/nu0.mnc -odt float
  13. mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10464/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.10464/nu0.mnc...
  22. --------------------------------------------------------
  23. Iteration 1 Sat Oct 7 21:17:22 CEST 2017
  24. nu_correct -clobber ./tmp.mri_nu_correct.mni.10464/nu0.mnc ./tmp.mri_nu_correct.mni.10464/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10464/0/
  25. [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051258/mri/] [2017-10-07 21:17:23] 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.10464/0/ ./tmp.mri_nu_correct.mni.10464/nu0.mnc ./tmp.mri_nu_correct.mni.10464/nu1.imp
  27. Processing:.................................................................Done
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  64. Number of iterations: 37
  65. CV of field change: 0.000984645
  66. --------------------------------------------------------
  67. Iteration 2 Sat Oct 7 21:18:13 CEST 2017
  68. nu_correct -clobber ./tmp.mri_nu_correct.mni.10464/nu1.mnc ./tmp.mri_nu_correct.mni.10464/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10464/1/
  69. [ntraut@tars-904:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051258/mri/] [2017-10-07 21:18:13] running:
  70. /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.10464/1/ ./tmp.mri_nu_correct.mni.10464/nu1.mnc ./tmp.mri_nu_correct.mni.10464/nu2.imp
  71. Processing:.................................................................Done
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  90. Processing:.................................................................Done
  91. Processing:.................................................................Done
  92. Number of iterations: 21
  93. CV of field change: 0.000981212
  94. mri_binarize --i ./tmp.mri_nu_correct.mni.10464/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10464/ones.mgz
  95. $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
  96. cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051258/mri
  97. cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10464/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10464/ones.mgz
  98. sysname Linux
  99. hostname tars-904
  100. machine x86_64
  101. user ntraut
  102. input ./tmp.mri_nu_correct.mni.10464/nu2.mnc
  103. frame 0
  104. nErode3d 0
  105. nErode2d 0
  106. output ./tmp.mri_nu_correct.mni.10464/ones.mgz
  107. Binarizing based on threshold
  108. min -1
  109. max +infinity
  110. binval 1
  111. binvalnot 0
  112. fstart = 0, fend = 0, nframes = 1
  113. Found 16777216 values in range
  114. Counting number of voxels in first frame
  115. Found 16777216 voxels in final mask
  116. Count: 16777216 16777216.000000 16777216 100.000000
  117. mri_binarize done
  118. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10464/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10464/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10464/input.mean.dat
  119. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  120. cwd
  121. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10464/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10464/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10464/input.mean.dat
  122. sysname Linux
  123. hostname tars-904
  124. machine x86_64
  125. user ntraut
  126. UseRobust 0
  127. Loading ./tmp.mri_nu_correct.mni.10464/ones.mgz
  128. Loading orig.mgz
  129. Voxel Volume is 1 mm^3
  130. Generating list of segmentation ids
  131. Found 1 segmentations
  132. Computing statistics for each segmentation
  133. Reporting on 1 segmentations
  134. Using PrintSegStat
  135. Computing spatial average of each frame
  136. 0
  137. Writing to ./tmp.mri_nu_correct.mni.10464/input.mean.dat
  138. mri_segstats done
  139. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10464/ones.mgz --i ./tmp.mri_nu_correct.mni.10464/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10464/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10464/output.mean.dat
  140. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  141. cwd
  142. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10464/ones.mgz --i ./tmp.mri_nu_correct.mni.10464/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10464/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10464/output.mean.dat
  143. sysname Linux
  144. hostname tars-904
  145. machine x86_64
  146. user ntraut
  147. UseRobust 0
  148. Loading ./tmp.mri_nu_correct.mni.10464/ones.mgz
  149. Loading ./tmp.mri_nu_correct.mni.10464/nu2.mnc
  150. Voxel Volume is 1 mm^3
  151. Generating list of segmentation ids
  152. Found 1 segmentations
  153. Computing statistics for each segmentation
  154. Reporting on 1 segmentations
  155. Using PrintSegStat
  156. Computing spatial average of each frame
  157. 0
  158. Writing to ./tmp.mri_nu_correct.mni.10464/output.mean.dat
  159. mri_segstats done
  160. mris_calc -o ./tmp.mri_nu_correct.mni.10464/nu2.mnc ./tmp.mri_nu_correct.mni.10464/nu2.mnc mul 1.03711543040954392320
  161. mri_convert ./tmp.mri_nu_correct.mni.10464/nu2.mnc nu.mgz --like orig.mgz
  162. mri_convert.bin ./tmp.mri_nu_correct.mni.10464/nu2.mnc nu.mgz --like orig.mgz
  163. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
  164. reading from ./tmp.mri_nu_correct.mni.10464/nu2.mnc...
  165. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  166. i_ras = (-1, 0, 0)
  167. j_ras = (0, 0, -1)
  168. k_ras = (0, 1, 0)
  169. INFO: transform src into the like-volume: orig.mgz
  170. writing to nu.mgz...
  171. mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
  172. type change took 0 minutes and 10 seconds.
  173. mapping (17, 125) to ( 3, 110)
  174. Sat Oct 7 21:19:41 CEST 2017
  175. mri_nu_correct.mni done