mri_nu_correct.mni.log 10 KB

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  1. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051371/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-596 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 17:00:31 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.21649
  11. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051371/mri
  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21649/nu0.mnc -odt float
  13. mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.21649/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.21649/nu0.mnc...
  22. --------------------------------------------------------
  23. Iteration 1 Sat Oct 7 17:00:34 CEST 2017
  24. nu_correct -clobber ./tmp.mri_nu_correct.mni.21649/nu0.mnc ./tmp.mri_nu_correct.mni.21649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.21649/0/
  25. [ntraut@tars-596:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051371/mri/] [2017-10-07 17:00:34] 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.21649/0/ ./tmp.mri_nu_correct.mni.21649/nu0.mnc ./tmp.mri_nu_correct.mni.21649/nu1.imp
  27. Processing:.................................................................Done
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  64. Processing:.................................................................Done
  65. Number of iterations: 38
  66. CV of field change: 0.000989694
  67. --------------------------------------------------------
  68. Iteration 2 Sat Oct 7 17:01:22 CEST 2017
  69. nu_correct -clobber ./tmp.mri_nu_correct.mni.21649/nu1.mnc ./tmp.mri_nu_correct.mni.21649/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.21649/1/
  70. [ntraut@tars-596:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051371/mri/] [2017-10-07 17:01:22] running:
  71. /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.21649/1/ ./tmp.mri_nu_correct.mni.21649/nu1.mnc ./tmp.mri_nu_correct.mni.21649/nu2.imp
  72. Processing:.................................................................Done
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  87. Processing:.................................................................Done
  88. Processing:.................................................................Done
  89. Number of iterations: 17
  90. CV of field change: 0.000979973
  91. mri_binarize --i ./tmp.mri_nu_correct.mni.21649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21649/ones.mgz
  92. $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
  93. cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051371/mri
  94. cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.21649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21649/ones.mgz
  95. sysname Linux
  96. hostname tars-596
  97. machine x86_64
  98. user ntraut
  99. input ./tmp.mri_nu_correct.mni.21649/nu2.mnc
  100. frame 0
  101. nErode3d 0
  102. nErode2d 0
  103. output ./tmp.mri_nu_correct.mni.21649/ones.mgz
  104. Binarizing based on threshold
  105. min -1
  106. max +infinity
  107. binval 1
  108. binvalnot 0
  109. fstart = 0, fend = 0, nframes = 1
  110. Found 16777216 values in range
  111. Counting number of voxels in first frame
  112. Found 16777216 voxels in final mask
  113. Count: 16777216 16777216.000000 16777216 100.000000
  114. mri_binarize done
  115. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21649/input.mean.dat
  116. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  117. cwd
  118. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21649/input.mean.dat
  119. sysname Linux
  120. hostname tars-596
  121. machine x86_64
  122. user ntraut
  123. UseRobust 0
  124. Loading ./tmp.mri_nu_correct.mni.21649/ones.mgz
  125. Loading orig.mgz
  126. Voxel Volume is 1 mm^3
  127. Generating list of segmentation ids
  128. Found 1 segmentations
  129. Computing statistics for each segmentation
  130. Reporting on 1 segmentations
  131. Using PrintSegStat
  132. Computing spatial average of each frame
  133. 0
  134. Writing to ./tmp.mri_nu_correct.mni.21649/input.mean.dat
  135. mri_segstats done
  136. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21649/ones.mgz --i ./tmp.mri_nu_correct.mni.21649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21649/output.mean.dat
  137. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  138. cwd
  139. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21649/ones.mgz --i ./tmp.mri_nu_correct.mni.21649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21649/output.mean.dat
  140. sysname Linux
  141. hostname tars-596
  142. machine x86_64
  143. user ntraut
  144. UseRobust 0
  145. Loading ./tmp.mri_nu_correct.mni.21649/ones.mgz
  146. Loading ./tmp.mri_nu_correct.mni.21649/nu2.mnc
  147. Voxel Volume is 1 mm^3
  148. Generating list of segmentation ids
  149. Found 1 segmentations
  150. Computing statistics for each segmentation
  151. Reporting on 1 segmentations
  152. Using PrintSegStat
  153. Computing spatial average of each frame
  154. 0
  155. Writing to ./tmp.mri_nu_correct.mni.21649/output.mean.dat
  156. mri_segstats done
  157. mris_calc -o ./tmp.mri_nu_correct.mni.21649/nu2.mnc ./tmp.mri_nu_correct.mni.21649/nu2.mnc mul 1.02918776370662887903
  158. mri_convert ./tmp.mri_nu_correct.mni.21649/nu2.mnc nu.mgz --like orig.mgz
  159. mri_convert.bin ./tmp.mri_nu_correct.mni.21649/nu2.mnc nu.mgz --like orig.mgz
  160. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
  161. reading from ./tmp.mri_nu_correct.mni.21649/nu2.mnc...
  162. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  163. i_ras = (-1, 0, 0)
  164. j_ras = (0, 0, -1)
  165. k_ras = (0, 1, 0)
  166. INFO: transform src into the like-volume: orig.mgz
  167. writing to nu.mgz...
  168. mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
  169. type change took 0 minutes and 8 seconds.
  170. mapping (15, 149) to ( 3, 110)
  171. Sat Oct 7 17:02:40 CEST 2017
  172. mri_nu_correct.mni done