/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri /opt/freesurfer/5.3/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux Fri Jun 20 10:02:00 CEST 2014 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.17604 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-08, 7.07805e-08) j_ras = (-1.37836e-07, 5.00586e-09, -1) k_ras = (-1.11759e-08, 1, 1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17604/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Jun 20 10:02:04 CEST 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/0/ [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:04] running: /opt/freesurfer/5.3/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17604/0/ ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 37 CV of field change: 0.000995657 [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:41] running: /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Jun 20 10:02:47 CEST 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/1/ [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:47] running: /opt/freesurfer/5.3/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17604/1/ ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 34 CV of field change: 0.000989176 [spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:03:24] running: /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz sysname Linux hostname medusa machine x86_64 user spark input ./tmp.mri_nu_correct.mni.17604/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.17604/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/input.mean.dat sysname Linux hostname medusa machine x86_64 user spark UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17604/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17604/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/output.mean.dat sysname Linux hostname medusa machine x86_64 user spark UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17604/ones.mgz Loading ./tmp.mri_nu_correct.mni.17604/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.17604/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.17604/nu2.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc mul .90202857338110148963 mri_convert ./tmp.mri_nu_correct.mni.17604/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.17604/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.17604/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-08, 7.07805e-08) j_ras = (-1.37836e-07, 5.00586e-09, -1) k_ras = (-1.11759e-08, 1, 1.86265e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (18, 177) to ( 3, 110) Fri Jun 20 10:04:10 CEST 2014 mri_nu_correct.mni done