cortical-surfaces-freesurfer/sub-21/mri/orig_nu.log

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
/opt/freesurfer/5.3/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 medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
Fri Jun 20 09:59:18 CEST 2014
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.16147
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16147/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16147/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, 3.72529e-08, 7.07805e-08)
j_ras = (-1.37836e-07, 5.00586e-09, -1)
k_ras = (-1.11759e-08, 1, 1.86265e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.16147/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Fri Jun 20 09:59:21 CEST 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16147/0/ -iterations 1000 -distance 50
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 09:59:22] running:
  /opt/freesurfer/5.3/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.16147/0/ ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/nu1.imp

Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Number of iterations: 66 
CV of field change: 0.000977411
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:01:00] running:
  /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16147/nu0.mnc ./tmp.mri_nu_correct.mni.16147/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.16147/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.16147/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.16147/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 3.72529e-08, 7.07805e-08)
j_ras = (-1.37836e-07, 5.00586e-09, -1)
k_ras = (-1.11759e-08, 1, 1.86265e-09)
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...
 
 
Fri Jun 20 10:01:12 CEST 2014
mri_nu_correct.mni done