/autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri /usr/local/freesurfer/stable4/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.1 2008/07/09 21:05:39 nicks Exp $ Linux node0331 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 21 21:29:58 EST 2008 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 tmpdir is ./tmp.mri_nu_correct.mni.23139 /autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23139/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23139/nu0.mnc $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 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) writing to ./tmp.mri_nu_correct.mni.23139/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 21 21:30:05 EST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.23139/nu0.mnc ./tmp.mri_nu_correct.mni.23139/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23139/0/ [sita@node0331:/autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/] [2008-11-21 21:30:06] running: /usr/local/freesurfer/stable4/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.23139/0/ ./tmp.mri_nu_correct.mni.23139/nu0.mnc ./tmp.mri_nu_correct.mni.23139/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 9 CV of field change: 0.000927856 [sita@node0331:/autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/] [2008-11-21 21:30:20] running: /usr/local/freesurfer/stable4/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23139/nu0.mnc ./tmp.mri_nu_correct.mni.23139/0//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Nov 21 21:30:24 EST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.23139/nu1.mnc ./tmp.mri_nu_correct.mni.23139/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23139/1/ [sita@node0331:/autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/] [2008-11-21 21:30:25] running: /usr/local/freesurfer/stable4/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.23139/1/ ./tmp.mri_nu_correct.mni.23139/nu1.mnc ./tmp.mri_nu_correct.mni.23139/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 9 CV of field change: 0.000999431 [sita@node0331:/autofs/space/birn_045/users/BWH/buckner_data/B40_lat_FSversion/099/mri/] [2008-11-21 21:30:37] running: /usr/local/freesurfer/stable4/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23139/nu1.mnc ./tmp.mri_nu_correct.mni.23139/1//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.23139/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23139/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.23139/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... Fri Nov 21 21:30:50 EST 2008 mri_nu_correct.mni done