/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri /usr/local/freesurfer/stable5/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 2011/03/02 20:16:39 nicks Exp $ Linux compute-0-1.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Mon Mar 21 18:00:21 EDT 2011 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.23859 /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23859/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23859/nu0.mnc -odt float input_transform: error reading transform. error loading transform from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks 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.23859/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Mar 21 18:00:30 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23859/0/ [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:00:33] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/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.23859/0/ ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 28 CV of field change: 0.000996719 [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:02:09] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23859/nu0.mnc ./tmp.mri_nu_correct.mni.23859/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Mar 21 18:02:27 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23859/1/ [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:02:31] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/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.23859/1/ ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000983558 [khoa@compute-0-1.local:/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/] [2011-03-21 18:04:04] running: /autofs/space/tinia_001/users/astevens/freesurfer5.1_030711/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23859/nu1.mnc ./tmp.mri_nu_correct.mni.23859/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23859/ones.mgz $Id: mri_binarize.c,v 1.26 2011/03/02 00:04:13 nicks Exp $ cwd /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23859/ones.mgz sysname Linux hostname compute-0-1.local machine x86_64 user khoa input ./tmp.mri_nu_correct.mni.23859/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23859/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.23859/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/input.mean.dat $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/input.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.23859/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23859/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/output.mean.dat $Id: mri_segstats.c,v 1.75 2011/03/02 00:04:24 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23859/ones.mgz --i ./tmp.mri_nu_correct.mni.23859/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23859/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23859/output.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user khoa Loading ./tmp.mri_nu_correct.mni.23859/ones.mgz Loading ./tmp.mri_nu_correct.mni.23859/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23859/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.23859/nu2.mnc ./tmp.mri_nu_correct.mni.23859/nu2.mnc mul 1.05068900363734836688 mri_convert ./tmp.mri_nu_correct.mni.23859/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23859/nu2.mnc nu.mgz --like orig.mgz input_transform: error reading transform. error loading transform from /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/good_output_5.1/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179 2011/03/16 21:23:48 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.23859/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 10 seconds. mapping (13, 126) to ( 3, 110) Mon Mar 21 18:05:47 EDT 2011 mri_nu_correct.mni done