mri_nu_correct.mni.log 12 KB

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  1. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051113/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-117 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 17:49:18 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.23032
  11. /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051113/mri
  12. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23032/nu0.mnc -odt float
  13. mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.23032/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.23032/nu0.mnc...
  22. --------------------------------------------------------
  23. Iteration 1 Sat Oct 7 17:49:20 CEST 2017
  24. nu_correct -clobber ./tmp.mri_nu_correct.mni.23032/nu0.mnc ./tmp.mri_nu_correct.mni.23032/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23032/0/
  25. [ntraut@tars-117:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051113/mri/] [2017-10-07 17:49:20] 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.23032/0/ ./tmp.mri_nu_correct.mni.23032/nu0.mnc ./tmp.mri_nu_correct.mni.23032/nu1.imp
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  77. Number of iterations: 50
  78. CV of field change: 0.00105414
  79. --------------------------------------------------------
  80. Iteration 2 Sat Oct 7 17:50:10 CEST 2017
  81. nu_correct -clobber ./tmp.mri_nu_correct.mni.23032/nu1.mnc ./tmp.mri_nu_correct.mni.23032/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23032/1/
  82. [ntraut@tars-117:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051113/mri/] [2017-10-07 17:50:10] running:
  83. /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.23032/1/ ./tmp.mri_nu_correct.mni.23032/nu1.mnc ./tmp.mri_nu_correct.mni.23032/nu2.imp
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  114. Number of iterations: 30
  115. CV of field change: 0.000984509
  116. mri_binarize --i ./tmp.mri_nu_correct.mni.23032/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23032/ones.mgz
  117. $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
  118. cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051113/mri
  119. cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.23032/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23032/ones.mgz
  120. sysname Linux
  121. hostname tars-117
  122. machine x86_64
  123. user ntraut
  124. input ./tmp.mri_nu_correct.mni.23032/nu2.mnc
  125. frame 0
  126. nErode3d 0
  127. nErode2d 0
  128. output ./tmp.mri_nu_correct.mni.23032/ones.mgz
  129. Binarizing based on threshold
  130. min -1
  131. max +infinity
  132. binval 1
  133. binvalnot 0
  134. fstart = 0, fend = 0, nframes = 1
  135. Found 16777216 values in range
  136. Counting number of voxels in first frame
  137. Found 16777216 voxels in final mask
  138. Count: 16777216 16777216.000000 16777216 100.000000
  139. mri_binarize done
  140. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23032/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23032/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23032/input.mean.dat
  141. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  142. cwd
  143. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23032/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23032/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23032/input.mean.dat
  144. sysname Linux
  145. hostname tars-117
  146. machine x86_64
  147. user ntraut
  148. UseRobust 0
  149. Loading ./tmp.mri_nu_correct.mni.23032/ones.mgz
  150. Loading orig.mgz
  151. Voxel Volume is 1 mm^3
  152. Generating list of segmentation ids
  153. Found 1 segmentations
  154. Computing statistics for each segmentation
  155. Reporting on 1 segmentations
  156. Using PrintSegStat
  157. Computing spatial average of each frame
  158. 0
  159. Writing to ./tmp.mri_nu_correct.mni.23032/input.mean.dat
  160. mri_segstats done
  161. mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23032/ones.mgz --i ./tmp.mri_nu_correct.mni.23032/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23032/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23032/output.mean.dat
  162. $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
  163. cwd
  164. cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23032/ones.mgz --i ./tmp.mri_nu_correct.mni.23032/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23032/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23032/output.mean.dat
  165. sysname Linux
  166. hostname tars-117
  167. machine x86_64
  168. user ntraut
  169. UseRobust 0
  170. Loading ./tmp.mri_nu_correct.mni.23032/ones.mgz
  171. Loading ./tmp.mri_nu_correct.mni.23032/nu2.mnc
  172. Voxel Volume is 1 mm^3
  173. Generating list of segmentation ids
  174. Found 1 segmentations
  175. Computing statistics for each segmentation
  176. Reporting on 1 segmentations
  177. Using PrintSegStat
  178. Computing spatial average of each frame
  179. 0
  180. Writing to ./tmp.mri_nu_correct.mni.23032/output.mean.dat
  181. mri_segstats done
  182. mris_calc -o ./tmp.mri_nu_correct.mni.23032/nu2.mnc ./tmp.mri_nu_correct.mni.23032/nu2.mnc mul .88375136259033469255
  183. mri_convert ./tmp.mri_nu_correct.mni.23032/nu2.mnc nu.mgz --like orig.mgz
  184. mri_convert.bin ./tmp.mri_nu_correct.mni.23032/nu2.mnc nu.mgz --like orig.mgz
  185. $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
  186. reading from ./tmp.mri_nu_correct.mni.23032/nu2.mnc...
  187. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
  188. i_ras = (-1, 0, 0)
  189. j_ras = (0, 0, -1)
  190. k_ras = (0, 1, 0)
  191. INFO: transform src into the like-volume: orig.mgz
  192. writing to nu.mgz...
  193. mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
  194. type change took 0 minutes and 8 seconds.
  195. mapping ( 8, 165) to ( 3, 110)
  196. Sat Oct 7 17:51:23 CEST 2017
  197. mri_nu_correct.mni done