/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri /opt/freesurfer/5.3.0/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 snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:58:19 CEST 2013 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.24677 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24677/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24677/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, 6.98492e-09, -3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-1.00117e-08, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.24677/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:58:23 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24677/0/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:58:23] running: /opt/freesurfer/5.3.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24677/0/ ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 25 CV of field change: 0.00098862 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:58:54] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24677/nu0.mnc ./tmp.mri_nu_correct.mni.24677/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Aug 8 10:59:00 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24677/1/ [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:59:00] running: /opt/freesurfer/5.3.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24677/1/ ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.00099029 [fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri/] [2013-08-08 10:59:27] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24677/nu1.mnc ./tmp.mri_nu_correct.mni.24677/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24677/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub020/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24677/ones.mgz sysname Linux hostname snake6 machine x86_64 user fkaule input ./tmp.mri_nu_correct.mni.24677/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/input.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24677/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.24677/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24677/ones.mgz --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/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.24677/ones.mgz --i ./tmp.mri_nu_correct.mni.24677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24677/output.mean.dat sysname Linux hostname snake6 machine x86_64 user fkaule UseRobust 0 Loading ./tmp.mri_nu_correct.mni.24677/ones.mgz Loading ./tmp.mri_nu_correct.mni.24677/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.24677/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.24677/nu2.mnc ./tmp.mri_nu_correct.mni.24677/nu2.mnc mul .96658600609259052332 mri_convert ./tmp.mri_nu_correct.mni.24677/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24677/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.24677/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 6.98492e-09, -3.72529e-09) j_ras = (3.72529e-09, 0, -1) k_ras = (-1.00117e-08, 1, 7.45058e-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 (10, 150) to ( 3, 110) Thu Aug 8 11:00:14 CEST 2013 mri_nu_correct.mni done