/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri /opt/freesurfer/5.3.0/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux Thu Aug 8 10:55:05 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.15214 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15214/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15214/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, 4.19095e-09, 3.72529e-09) j_ras = (7.45058e-09, 1.49012e-08, -1) k_ras = (-6.0536e-09, 1, -1.49012e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.15214/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 8 10:55:09 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15214/0/ -iterations 1000 -distance 50 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:55:10] running: /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.15214/0/ ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/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 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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 63 CV of field change: 0.000991682 [fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:56:56] running: /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15214/nu0.mnc ./tmp.mri_nu_correct.mni.15214/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.15214/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.15214/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.15214/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.19095e-09, 3.72529e-09) j_ras = (7.45058e-09, 1.49012e-08, -1) k_ras = (-6.0536e-09, 1, -1.49012e-08) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Aug 8 10:57:12 CEST 2013 mri_nu_correct.mni done