cortical-surfaces-freesurfer/sub-21/mri/mri_nu_correct.mni.log

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
/opt/freesurfer/5.3/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 medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
Fri Jun 20 10:02:00 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.17604
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/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.17604/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Fri Jun 20 10:02:04 CEST 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/0/
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:04] running:
  /opt/freesurfer/5.3/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.17604/0/ ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.imp

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.
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.
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.
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.
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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.
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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.
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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.
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.
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.
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.
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.
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.
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.
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: 37 
CV of field change: 0.000995657
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:41] running:
  /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Fri Jun 20 10:02:47 CEST 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/1/
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:47] running:
  /opt/freesurfer/5.3/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.17604/1/ ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.imp

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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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: 34 
CV of field change: 0.000989176
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:03:24] running:
  /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

input      ./tmp.mri_nu_correct.mni.17604/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.17604/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.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/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.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/input.mean.dat 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17604/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.17604/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/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.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/output.mean.dat 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17604/ones.mgz
Loading ./tmp.mri_nu_correct.mni.17604/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.17604/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.17604/nu2.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc mul .90202857338110148963
mri_convert ./tmp.mri_nu_correct.mni.17604/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.17604/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.17604/nu2.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)
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 7 seconds.
mapping (18, 177) to ( 3, 110)
 
 
Fri Jun 20 10:04:10 CEST 2014
mri_nu_correct.mni done