ds114_test1_freesurfer/sub-02/mri/mri_nu_correct.mni.log

/data/out/sub-02/mri
/opt/freesurfer/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 1.18.2.1 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 08:37:16 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.716
/data/out/sub-02/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.716/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.716/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.716/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Jan 14 08:37:18 UTC 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.716/0/
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 08:37:18] running:
  /opt/freesurfer/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.716/0/ ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/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
Number of iterations: 18 
CV of field change: 0.000964001
[root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:30] running:
  /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Sat Jan 14 08:37:34 UTC 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.716/1/
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 08:37:34] running:
  /opt/freesurfer/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.716/1/ ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/nu2.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
Number of iterations: 16 
CV of field change: 0.0009728
[root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:44] running:
  /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.716/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/out/sub-02/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.716/ones.mgz 
sysname  Linux
hostname 3dcbcfbafa99
machine  x86_64
user     root

input      ./tmp.mri_nu_correct.mni.716/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.716/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.716/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/input.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/input.mean.dat 
sysname  Linux
hostname 3dcbcfbafa99
machine  x86_64
user     root
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.716/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  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.716/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/output.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/output.mean.dat 
sysname  Linux
hostname 3dcbcfbafa99
machine  x86_64
user     root
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.716/ones.mgz
Loading ./tmp.mri_nu_correct.mni.716/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                     16777216  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.716/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.716/nu2.mnc ./tmp.mri_nu_correct.mni.716/nu2.mnc mul 1.10275123692108037959
mri_convert ./tmp.mri_nu_correct.mni.716/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.716/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.716/nu2.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)
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 6 seconds.
mapping ( 7, 90) to ( 3, 110)
 
 
Sat Jan 14 08:38:17 UTC 2017
mri_nu_correct.mni done