/data/out/sub-02/mri
/opt/freesurfer/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 3dcbcfbafa99 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Sat Jan 14 08:36:08 UTC 2017
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.200
/data/out/sub-02/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.200/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.200/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=9.62, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -1.86265e-09)
j_ras = (1.86265e-09, 1.45519e-11, -1)
k_ras = (-3.11857e-10, 1, 6.13909e-12)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.200/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Jan 14 08:36:10 UTC 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.200/nu0.mnc ./tmp.mri_nu_correct.mni.200/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.200/0/ -iterations 1000 -distance 50
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 170.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 211.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1051.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1054.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1449.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1455.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1457.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1481.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1631.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1633.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1635.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1637.
	(Maybe you should just omit the defined()?)
defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1639.
	(Maybe you should just omit the defined()?)
[root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:36:10] running:
  /opt/freesurfer/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.200/0/ ./tmp.mri_nu_correct.mni.200/nu0.mnc ./tmp.mri_nu_correct.mni.200/nu1.imp

Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Number of iterations: 25 
CV of field change: 0.000958471
[root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:36:34] running:
  /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.200/nu0.mnc ./tmp.mri_nu_correct.mni.200/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.200/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.200/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.200/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -1.86265e-09)
j_ras = (1.86264e-09, 1.45519e-11, -1)
k_ras = (-3.11857e-10, 1, 6.13909e-12)
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...
 
 
Sat Jan 14 08:36:43 UTC 2017
mri_nu_correct.mni done