/autofs/cluster/freesurfer/subjects/test/buckner_data/stable6/004/mri /space/freesurfer/build/pub-releases/v6.0.0/freesurfer/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 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux compute-0-39 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Jan 19 03:28:54 EST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.28283 /autofs/cluster/freesurfer/subjects/test/buckner_data/stable6/004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28283/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28283/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28283/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jan 19 03:29:02 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28283/nu0.mnc ./tmp.mri_nu_correct.mni.28283/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28283/0/ [zkaufman@compute-0-39:/autofs/cluster/freesurfer/subjects/test/buckner_data/stable6/004/mri/] [2017-01-19 03:29:02] running: /space/freesurfer/build/pub-releases/v6.0.0/freesurfer/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.28283/0/ ./tmp.mri_nu_correct.mni.28283/nu0.mnc ./tmp.mri_nu_correct.mni.28283/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000972061 -------------------------------------------------------- Iteration 2 Thu Jan 19 03:30:42 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.28283/nu1.mnc ./tmp.mri_nu_correct.mni.28283/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28283/1/ [zkaufman@compute-0-39:/autofs/cluster/freesurfer/subjects/test/buckner_data/stable6/004/mri/] [2017-01-19 03:30:43] running: /space/freesurfer/build/pub-releases/v6.0.0/freesurfer/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.28283/1/ ./tmp.mri_nu_correct.mni.28283/nu1.mnc ./tmp.mri_nu_correct.mni.28283/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 Number of iterations: 16 CV of field change: 0.0009954 mri_binarize --i ./tmp.mri_nu_correct.mni.28283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28283/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/freesurfer/subjects/test/buckner_data/stable6/004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28283/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28283/ones.mgz sysname Linux hostname compute-0-39 machine x86_64 user zkaufman input ./tmp.mri_nu_correct.mni.28283/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.28283/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28283/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28283/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28283/input.mean.dat sysname Linux hostname compute-0-39 machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28283/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.28283/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28283/ones.mgz --i ./tmp.mri_nu_correct.mni.28283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28283/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28283/ones.mgz --i ./tmp.mri_nu_correct.mni.28283/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28283/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28283/output.mean.dat sysname Linux hostname compute-0-39 machine x86_64 user zkaufman UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28283/ones.mgz Loading ./tmp.mri_nu_correct.mni.28283/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.28283/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.28283/nu2.mnc ./tmp.mri_nu_correct.mni.28283/nu2.mnc mul 1.04028551443469413709 mri_convert ./tmp.mri_nu_correct.mni.28283/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.28283/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.28283/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) 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 11 seconds. mapping (13, 124) to ( 3, 110) Thu Jan 19 03:33:38 EST 2017 mri_nu_correct.mni done