reference-preprocessing
/
ABIDE_fs-6.0.0


			
			
				
					
						
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							/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050990/mri
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux tars-539 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 17:15:20 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
tmpdir is ./tmp.mri_nu_correct.mni.8300
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050990/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8300/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8300/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.8300/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 17:15:22 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.8300/nu0.mnc ./tmp.mri_nu_correct.mni.8300/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8300/0/
[ntraut@tars-539:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050990/mri/] [2017-10-07 17:15:22] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8300/0/ ./tmp.mri_nu_correct.mni.8300/nu0.mnc ./tmp.mri_nu_correct.mni.8300/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00111018
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 17:16:14 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.8300/nu1.mnc ./tmp.mri_nu_correct.mni.8300/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.8300/1/
[ntraut@tars-539:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050990/mri/] [2017-10-07 17:16:14] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8300/1/ ./tmp.mri_nu_correct.mni.8300/nu1.mnc ./tmp.mri_nu_correct.mni.8300/nu2.imp

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Number of iterations: 28 
CV of field change: 0.000995582
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.8300/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8300/ones.mgz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050990/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.8300/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8300/ones.mgz 
sysname  Linux
hostname tars-539
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.8300/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.8300/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8300/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8300/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8300/input.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8300/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8300/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8300/input.mean.dat 
sysname  Linux
hostname tars-539
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.8300/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.8300/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8300/ones.mgz --i ./tmp.mri_nu_correct.mni.8300/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8300/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8300/output.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8300/ones.mgz --i ./tmp.mri_nu_correct.mni.8300/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8300/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8300/output.mean.dat 
sysname  Linux
hostname tars-539
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.8300/ones.mgz
Loading ./tmp.mri_nu_correct.mni.8300/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.8300/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.8300/nu2.mnc ./tmp.mri_nu_correct.mni.8300/nu2.mnc mul 1.00344456756994644416
mri_convert ./tmp.mri_nu_correct.mni.8300/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.8300/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.8300/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
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 8 seconds.
mapping ( 7, 144) to ( 3, 110)
 
 
Sat Oct  7 17:17:29 CEST 2017
mri_nu_correct.mni done