External Email - Use Caution
Dear Community!
I have an issue with recon-all in this subject. Below is the terminal output.
Renes-MacBook-Air-2:~ andraderenew$ recon-all -all -s IXI_25_Guys_DTI_recon
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
Actual FREESURFER_HOME /Applications/freesurfer
-rwxrwxrwx@ 1 andraderenew staff 117313 Aug 6 06:11 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/scripts/recon-all.log
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# MotionCor Mon Aug 6 14:40:17 -05 2018
Found 1 runs
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
\n cp /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig/001.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/rawavg.mgz \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon
\n mri_convert /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig.mgz --conform \n
mri_convert.bin /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/rawavg.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig.mgz...
\n mri_add_xform_to_header -c /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach.xfm /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig.mgz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/orig.mgz \n
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mon Aug 6 14:40:26 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
/Applications/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Mon Aug 6 14:40:26 -05 2018
Program nu_correct, built from:
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.3771
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3771/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3771/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, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.3771/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Aug 6 14:40:31 -05 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.3771/nu0.mnc ./tmp.mri_nu_correct.mni.3771/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3771/0/ -iterations 1000 -distance 50
/Applications/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3771/0/ ./tmp.mri_nu_correct.mni.3771/nu0.mnc ./tmp.mri_nu_correct.mni.3771/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 29
CV of field change: 0.000980995
mri_convert ./tmp.mri_nu_correct.mni.3771/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.3771/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.3771/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
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...
Mon Aug 6 14:41:40 -05 2018
mri_nu_correct.mni done
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
talairach_avi log file is transforms/talairach_avi.log...
Started at Mon Aug 6 14:41:41 -05 2018
Ended at Mon Aug 6 14:42:19 -05 2018
talairach_avi done
\nINFO: transforms/talairach.xfm already exists!
The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm
This is done to retain any edits made to transforms/talairach.xfm
Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm\n
#--------------------------------------------
#@# Talairach Failure Detection Mon Aug 6 14:42:19 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6333, pval=0.3663 >= threshold=0.0050)
\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach_avi.log \n
\n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach_avi.log \n
TalAviQA: 0.93090
z-score: -10
WARNING: Talairach QA check failed!
z-score of -10 is <= threshold of -9\n
\nManual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:\n
INFO: Retrying Talairach align using 3T-based atlas...\n
#--------------------------------------------
#@# Talairach Mon Aug 6 14:42:19 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
/Applications/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Mon Aug 6 14:42:20 -05 2018
Program nu_correct, built from:
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.5323
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5323/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5323/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, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.5323/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Aug 6 14:42:25 -05 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.5323/nu0.mnc ./tmp.mri_nu_correct.mni.5323/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5323/0/ -iterations 1000 -distance 50
/Applications/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5323/0/ ./tmp.mri_nu_correct.mni.5323/nu0.mnc ./tmp.mri_nu_correct.mni.5323/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 29
CV of field change: 0.000980995
mri_convert ./tmp.mri_nu_correct.mni.5323/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.5323/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.5323/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
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...
Mon Aug 6 14:43:33 -05 2018
mri_nu_correct.mni done
\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig \n
talairach_avi log file is transforms/talairach_avi.log...
Started at Mon Aug 6 14:43:34 -05 2018
Ended at Mon Aug 6 14:44:11 -05 2018
talairach_avi done
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#--------------------------------------------
#@# Talairach Failure Detection Mon Aug 6 14:44:13 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3389, pval=0.0406 >= threshold=0.0050)
\n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach_avi.log \n
\n tal_QC_AZS /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach_avi.log \n
TalAviQA: 0.90309
z-score: -17
WARNING: Talairach QA check failed!
z-score of -17 is <= threshold of -9\n
\nManual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:\n
INFO: Trying MINC mritotal to perform Talairach align...\n
#--------------------------------------------
#@# Talairach Mon Aug 6 14:44:14 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
/Applications/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Mon Aug 6 14:44:15 -05 2018
Program nu_correct, built from:
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.6795
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6795/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6795/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, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.6795/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Aug 6 14:44:22 -05 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.6795/nu0.mnc ./tmp.mri_nu_correct.mni.6795/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6795/0/ -iterations 1000 -distance 50
/Applications/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6795/0/ ./tmp.mri_nu_correct.mni.6795/nu0.mnc ./tmp.mri_nu_correct.mni.6795/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 29
CV of field change: 0.000980995
mri_convert ./tmp.mri_nu_correct.mni.6795/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.6795/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.6795/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
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...
Mon Aug 6 14:45:52 -05 2018
mri_nu_correct.mni done
\n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
/Applications/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Mon Aug 6 14:45:52 -05 2018
tmpdir is transforms/tmp.talairach.7685
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.7685/src.mnc
mri_convert.bin orig_nu.mgz transforms/tmp.talairach.7685/src.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig_nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
writing to transforms/tmp.talairach.7685/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7685/src.mnc transforms/talairach.auto.xfm
Transforming slices:................................................................................................................................Done
Copying chunks:......................................................................................................................................................Done.
Copying chunks:..........................................................................................................Done.
Transforming slices:......................................................................................................................................................Done
Copying chunks:....................................................................................................................Done.
Copying chunks:....................................................................................................................Done.
Source volume size: 74 by 106 by 106
Source voxel size = 2.000 2.000 2.000
Source min/max real range = -0.000 164.298
Source min/max voxel= -0.000 164.298
Target volume size: 58 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.970 123.710
Target min/max voxel = -0.000 123.710
AFTER init_params()
Transform matrix = 1.0000 0.0000 0.0000 1.5580
0.0000 1.0000 0.0000 -25.6781
0.0000 0.0000 1.0000 -8.6102
Transform center = -1.230 8.087 18.065
Transform rotations = 0.000 0.000 0.000
Transform trans = 1.558 -25.678 -8.610
Transform scale = 1.000 1.000 1.000
Transform shear = 0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -85.095 -125.510 -47.250
Lattice count = 43 55 29
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = -0.000 232.183
Source min/max voxel= -0.000 232.183
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= -0.000 144.070
Target min/max voxel = -0.000 144.070
AFTER init_params()
Transform matrix = 1.2153 0.2526 0.1517 -3.7258
-0.2847 1.1724 0.3288 -34.3194
-0.0758 -0.3541 1.1969 -9.1699
Transform center = -1.230 8.087 18.065
Transform rotations = -0.288 0.061 -0.230
Transform trans = 0.793 -26.635 -8.383
Transform scale = 1.250 1.250 1.250
Transform shear = -0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -85.095 -125.510 -57.250
Lattice count = 43 55 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.109 25.191
Source min/max voxel= 0.109 25.191
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 1.2114 0.2544 0.2002 -2.5502
-0.3108 1.1309 0.4435 -32.6411
-0.0906 -0.4781 1.1556 -9.7526
Transform center = -1.230 8.087 18.065
Transform rotations = -0.392 0.072 -0.251
Transform trans = 2.865 -23.188 -10.697
Transform scale = 1.254 1.254 1.254
Transform shear = 0.000 -0.000 -0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.109 25.191
Source min/max voxel= 0.109 25.191
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 1.0541 0.1305 -0.1479 4.6259
-0.1164 1.0608 0.1062 -21.5916
0.1592 -0.0883 1.0568 -15.2192
Transform center = -1.230 8.087 18.065
Transform rotations = -0.083 -0.149 -0.110
Transform trans = 2.943 -19.039 -15.103
Transform scale = 1.072 1.072 1.072
Transform shear = -0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.109 25.191
Source min/max voxel= 0.109 25.191
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 1.0963 0.0565 0.0051 1.5417
-0.0478 0.9255 0.0117 -17.0956
-0.0043 -0.0140 1.0883 -16.0951
Transform center = -1.230 8.087 18.065
Transform rotations = -0.013 0.004 -0.052
Transform trans = 1.972 -17.427 -14.609
Transform scale = 1.098 0.927 1.088
Transform shear = 0.000 0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Source volume size: 84 by 116 by 116
Source voxel size = 2.000 2.000 2.000
Source min/max real range = 0.109 25.191
Source min/max voxel= 0.109 25.191
Target volume size: 68 by 110 by 86
Target voxel = 2.000 2.000 2.000
Target min/max real range= 0.037 11.652
Target min/max voxel = 0.037 11.652
AFTER init_params()
Transform matrix = 1.0963 0.0565 0.0051 1.5417
-0.0478 0.9255 0.0117 -17.0956
-0.0043 -0.0140 1.0883 -16.0951
Transform center = -1.230 8.087 18.065
Transform rotations = -0.013 0.004 -0.052
Transform trans = 1.972 -17.427 -14.609
Transform scale = 1.098 0.927 1.088
Transform shear = 0.000 -0.000 0.000
Target volume is smallest
Lattice step size = 4.000 4.000 4.000
Lattice start = -65.095 -105.510 -57.250
Lattice count = 35 46 34
Mon Aug 6 14:46:09 -05 2018
talairach done
\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n
#--------------------------------------------
#@# Talairach Failure Detection Mon Aug 6 14:46:11 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6333, pval=0.3663 >= threshold=0.0050)
#--------------------------------------------
#@# Nu Intensity Correction Mon Aug 6 14:46:11 -05 2018
\n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 \n
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
/Applications/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Mon Aug 6 14:46:12 -05 2018
Program nu_correct, built from:
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.8095
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8095/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8095/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, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.8095/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Aug 6 14:46:19 -05 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.8095/nu0.mnc ./tmp.mri_nu_correct.mni.8095/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8095/0/
/Applications/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8095/0/ ./tmp.mri_nu_correct.mni.8095/nu0.mnc ./tmp.mri_nu_correct.mni.8095/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 19
CV of field change: 0.000946982
--------------------------------------------------------
Iteration 2 Mon Aug 6 14:47:27 -05 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.8095/nu1.mnc ./tmp.mri_nu_correct.mni.8095/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.8095/1/
/Applications/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8095/1/ ./tmp.mri_nu_correct.mni.8095/nu1.mnc ./tmp.mri_nu_correct.mni.8095/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 10
CV of field change: 0.00095123
mri_binarize --i ./tmp.mri_nu_correct.mni.8095/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8095/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.8095/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8095/ones.mgz
sysname Darwin
hostname Renes-MacBook-Air-2.local
machine x86_64
user andraderenew
input ./tmp.mri_nu_correct.mni.8095/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.8095/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.8095/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8095/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8095/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.8095/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8095/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8095/input.mean.dat
sysname Darwin
hostname Renes-MacBook-Air-2.local
machine x86_64
user andraderenew
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.8095/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.8095/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8095/ones.mgz --i ./tmp.mri_nu_correct.mni.8095/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8095/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8095/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.8095/ones.mgz --i ./tmp.mri_nu_correct.mni.8095/nu2.mnc --sum ./tmp.mri_nu_correct.mni.8095/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8095/output.mean.dat
sysname Darwin
hostname Renes-MacBook-Air-2.local
machine x86_64
user andraderenew
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.8095/ones.mgz
Loading ./tmp.mri_nu_correct.mni.8095/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.8095/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.8095/nu2.mnc ./tmp.mri_nu_correct.mni.8095/nu2.mnc mul 1.00543850331096404690
Saving result to './tmp.mri_nu_correct.mni.8095/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.8095/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.8095/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.8095/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.28057e-09, 2.32831e-10)
j_ras = (-1.16415e-10, 0, -1)
k_ras = (-2.38651e-09, 1, -7.45058e-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 9 seconds.
mapping ( 5, 147) to ( 3, 110)
Mon Aug 6 14:48:57 -05 2018
mri_nu_correct.mni done
\n mri_add_xform_to_header -c /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/talairach.xfm nu.mgz nu.mgz \n
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Mon Aug 6 14:48:59 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_normalize -g 1 -mprage nu.mgz T1.mgz \n
using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
1.09627 0.05654 0.00505 1.54172;
-0.04779 0.92548 0.01174 -17.09556;
-0.00429 -0.01403 1.08825 -16.09510;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 14
Starting OpenSpline(): npoints = 14
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 77 (77), valley at 0 (-1)
csf peak at 38, setting threshold to 64
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 41 seconds.
#--------------------------------------------
#@# Skull Stripping Mon Aug 6 14:51:42 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_watershed -rusage /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n
Keeping brain edits brainmask.auto.mgz brainmask.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=118 y=133 z=111 r=64
first estimation of the main basin volume: 1111304 voxels
Looking for seedpoints
2 found in the cerebellum
5 found in the rest of the brain
global maximum in x=114, y=127, z=109, Imax=255
CSF=23, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=983172784576193 voxels, voxel volume =1.000
= 983172784576193 mmm3 = 983172774887.424 cm3
done.
PostAnalyze...Basin Prior
37 basins merged thanks to atlas
ambiguous basin, merged: at least 49 ambiguous voxels; size: 116744 voxels
***** 1 basin(s) merged in 2 iteration(s)
***** 116744 voxel(s) added to the main basin
ambiguous basin, non merged: 12 ambiguous voxels; size: 20473 voxels
ambiguous basin, non merged: 4 ambiguous voxels; size: 2912 voxels
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=119,y=142, z=113, r=10387 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=42 , nb = 18582
RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=31 , nb = 1086310830
LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = -1069450356
RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1037928638
LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=20 , nb = 547
OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=50 , nb = 1086332314
Problem with the least square interpolation in GM_MIN calculation.
Problem with the least square interpolation in GM_MIN calculation.
Problem with the least square interpolation in GM_MIN calculation.
Problem with the least square interpolation in GM_MIN calculation.
Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 42, 77, 84, 91
after analyzing : 42, 81, 84, 83
RIGHT_CER
before analyzing : 31, 70, 83, 92
after analyzing : 31, 78, 83, 81
LEFT_CER
before analyzing : 16, 56, 83, 92
after analyzing : 16, 74, 83, 78
RIGHT_BRAIN
before analyzing : 34, 62, 76, 92
after analyzing : 34, 71, 76, 76
LEFT_BRAIN
before analyzing : 20, 62, 84, 91
after analyzing : 20, 76, 84, 79
OTHER
before analyzing : 50, 76, 82, 91
after analyzing : 50, 80, 82, 82
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...63 iterations
*********************VALIDATION*********************
curvature mean = -0.017, std = 0.017
curvature mean = 53.554, std = 8.717
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 10.61, sigma = 20.74
after rotation: sse = 10.61, sigma = 20.74
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 15.56, its var is 26.10
before Erosion-Dilatation 17.22% of inacurate vertices
after Erosion-Dilatation 27.66% of inacurate vertices
46.17% of 'positive' inacurate vertices
53.83% of 'negative' inacurate vertices
The surface validation has detected a possible Error
If the final segmentation is not valid,
try using the option '-atlas'
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...43 iterations
mri_strip_skull: done peeling brain
Brain Size = 622091 voxels, voxel volume = 1.000 mm3
= 622091 mmm3 = 622.091 cm3
******************************
Saving brainmask.auto.mgz
Keeping edits ...
Saving kept edits to brainmask.mgz .....
done
mri_watershed utimesec 36.072640
mri_watershed stimesec 0.673701
mri_watershed ru_maxrss 729980928
mri_watershed ru_ixrss 0
mri_watershed ru_idrss 0
mri_watershed ru_isrss 0
mri_watershed ru_minflt 199651
mri_watershed ru_majflt 249
mri_watershed ru_nswap 0
mri_watershed ru_inblock 0
mri_watershed ru_oublock 12
mri_watershed ru_msgsnd 0
mri_watershed ru_msgrcv 0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw 34
mri_watershed ru_nivcsw 40895
mri_watershed done
\nINFO: brainmask.mgz already exists!
The new brainmask.auto.mgz will not be copied to brainmask.mgz.
This is done to retain any edits made to brainmask.mgz.
Add the -clean-bm flag to recon-all to overwrite brainmask.mgz.\n
#-------------------------------------
#@# EM Registration Mon Aug 6 14:52:20 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_em_register -rusage /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta \n
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=35.0
skull bounding box = (80, 105, 46) --> (162, 168, 161)
using (107, 126, 104) as brain centroid...
mean wm in atlas = 107, using box (97,118,90) --> (116, 133,118) to find MRI wm
before smoothing, mri peak at 51
robust fit to distribution - 54 +- 5.8
distribution too broad for accurate scaling - disabling
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.624
************************************************
First Search limited to translation only.
************************************************
max log p = -4.536795 @ (9.091, 9.091, -9.091)
max log p = -4.494132 @ (-4.545, 4.545, 4.545)
max log p = -4.491376 @ (-2.273, -2.273, -2.273)
max log p = -4.478565 @ (1.136, 3.409, 1.136)
max log p = -4.463528 @ (0.568, -1.705, -1.705)
max log p = -4.463528 @ (0.000, 0.000, 0.000)
Found translation: (4.0, 13.1, -7.4): log p = -4.464
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.458, old_max_log_p =-4.464 (thresh=-4.5)
1.06580 0.01831 0.13912 -21.74265;
0.00000 0.91709 -0.12074 35.49821;
-0.12074 0.11970 0.90924 -2.53948;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.458, old_max_log_p =-4.458 (thresh=-4.5)
1.15288 0.00272 0.02069 -16.36129;
0.00000 0.84831 -0.11168 49.28259;
0.01796 0.11199 0.85065 -11.51312;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.430, old_max_log_p =-4.458 (thresh=-4.5)
1.20401 0.13142 0.09435 -47.94740;
-0.14950 0.83879 -0.12790 66.64242;
-0.09582 0.11711 0.85998 -1.37744;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.430, old_max_log_p =-4.430 (thresh=-4.4)
1.20401 0.13142 0.09435 -47.94740;
-0.14950 0.83879 -0.12790 66.64242;
-0.09582 0.11711 0.85998 -1.37744;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.425, old_max_log_p =-4.430 (thresh=-4.4)
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.425, old_max_log_p =-4.425 (thresh=-4.4)
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
nsamples 2830
Quasinewton: input matrix
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -4.425 (old=-4.624)
transform before final EM align:
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 315557 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
nsamples 315557
Quasinewton: input matrix
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.7 tol 0.000000
final transform:
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta...
mri_em_register utimesec 917.554305
mri_em_register stimesec 3.622811
mri_em_register ru_maxrss 482205696
mri_em_register ru_ixrss 0
mri_em_register ru_idrss 0
mri_em_register ru_isrss 0
mri_em_register ru_minflt 124695
mri_em_register ru_majflt 208
mri_em_register ru_nswap 0
mri_em_register ru_inblock 2
mri_em_register ru_oublock 6
mri_em_register ru_msgsnd 0
mri_em_register ru_msgrcv 0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw 15
mri_em_register ru_nivcsw 442694
registration took 15 minutes and 36 seconds.
#--------------------------------------
#@# CA Normalize Mon Aug 6 15:07:56 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz \n
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=35.0
skull bounding box = (79, 105, 46) --> (162, 168, 161)
using (107, 126, 104) as brain centroid...
mean wm in atlas = 107, using box (97,118,90) --> (117, 133,118) to find MRI wm
before smoothing, mri peak at 51
robust fit to distribution - 54 +- 5.4
distribution too broad for accurate scaling - disabling
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
1.20802 0.12486 0.09562 -47.45150;
-0.13978 0.84082 -0.12727 65.14833;
-0.09571 0.11698 0.85897 -1.25226;
0.00000 0.00000 0.00000 1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (117, 26, 31) --> (179, 172, 225)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
12 of 12 (100.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (69, 22, 32) --> (130, 164, 224)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
20 of 20 (100.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (124, 120, 51) --> (162, 174, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
16 of 16 (100.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 120, 48) --> (125, 167, 114)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
22 of 22 (100.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 114, 86) --> (135, 194, 128)
Brain_Stem: limiting intensities to 88.0 --> 132.0
7 of 7 (100.0%) samples deleted
using 77 total control points for intensity normalization...
0 of 0 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (117, 26, 31) --> (179, 172, 225)
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (69, 22, 32) --> (130, 164, 224)
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (124, 120, 51) --> (162, 174, 115)
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 120, 48) --> (125, 167, 114)
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 114, 86) --> (135, 194, 128)
skipping region 2 with no control points detected
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (117, 26, 31) --> (179, 172, 225)
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (69, 22, 32) --> (130, 164, 224)
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (124, 120, 51) --> (162, 174, 115)
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 120, 48) --> (125, 167, 114)
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (105, 114, 86) --> (135, 194, 128)
skipping region 3 with no control points detected
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 0 minutes and 42 seconds.
#--------------------------------------
#@# CA Reg Mon Aug 6 15:08:38 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
\n mri_ca_register -rusage /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z \n
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 0.91 (predicted orig area = 8.8)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0001: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0002: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0003: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0004: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0005: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0006: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0007: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0008: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0009: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0010: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0011: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0012: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0013: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0014: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0015: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0016: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0017: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0018: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0019: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0020: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0021: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0022: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0023: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0024: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
gca peak = 0.15565 (16)
gca peak = 0.26829 (96)
gca peak = 0.20183 (93)
gca peak = 0.21683 (55)
gca peak = 0.30730 (58)
gca peak = 0.11430 (101)
gca peak = 0.12076 (102)
gca peak = 0.14995 (59)
gca peak = 0.15082 (58)
gca peak = 0.14161 (67)
gca peak = 0.15243 (71)
gca peak = 0.13336 (57)
gca peak = 0.13252 (56)
gca peak = 0.18181 (84)
gca peak = 0.20573 (83)
gca peak = 0.21969 (57)
gca peak = 0.39313 (56)
gca peak = 0.14181 (85)
gca peak = 0.11978 (83)
gca peak = 0.13399 (79)
gca peak = 0.14159 (79)
gca peak = 0.10025 (80)
gca peak = 0.13281 (86)
gca peak = 0.12801 (89)
gca peak = 0.20494 (23)
gca peak = 0.15061 (21)
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Cerebral_White_Matter = 0.12076 (102)
gca peak Left_Cerebral_Cortex = 0.14995 (59)
gca peak Left_Lateral_Ventricle = 0.10027 (20)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Cerebellum_White_Matter = 0.18181 (84)
gca peak Left_Cerebellum_Cortex = 0.13336 (57)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Left_Thalamus_Proper = 0.14181 (85)
gca peak Left_Caudate = 0.15243 (71)
gca peak Left_Putamen = 0.13399 (79)
gca peak Left_Pallidum = 0.20183 (93)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak Brain_Stem = 0.10025 (80)
gca peak Left_Hippocampus = 0.30730 (58)
gca peak Left_Amygdala = 0.21969 (57)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_VentralDC = 0.12801 (89)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Cerebral_White_Matter = 0.11430 (101)
gca peak Right_Cerebral_Cortex = 0.15082 (58)
gca peak Right_Lateral_Ventricle = 0.15565 (16)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Cerebellum_White_Matter = 0.20573 (83)
gca peak Right_Cerebellum_Cortex = 0.13252 (56)
gca peak Right_Thalamus_Proper = 0.11978 (83)
gca peak Right_Caudate = 0.14161 (67)
gca peak Right_Putamen = 0.14159 (79)
gca peak Right_Pallidum = 0.26829 (96)
gca peak Right_Hippocampus = 0.21683 (55)
gca peak Right_Amygdala = 0.39313 (56)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_VentralDC = 0.13281 (86)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.00 x + 0.0
setting left cbm cortex = 1.00 x + 0.00
setting right cbm cortex = 1.00 x + 0.00
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0025: dt=0.005645, rms=2.177 (0.184%), neg=0, invalid=762
0026: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0027: dt=0.850000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0028: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0029: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0030: dt=0.850000, rms=2.177 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0031: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0032: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0033: dt=0.450000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0034: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0035: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0036: dt=0.450000, rms=2.177 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0037: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0038: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0039: dt=0.250000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0040: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0041: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0042: dt=0.250000, rms=2.177 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0043: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0044: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0045: dt=0.150000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0046: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0047: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0048: dt=0.150000, rms=2.177 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0049: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0050: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0051: dt=0.100000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0052: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0053: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0054: dt=0.100000, rms=2.177 (-0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0055: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0056: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0057: dt=0.050000, rms=2.177 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0058: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0059: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
0060: dt=0.050000, rms=2.177 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0061: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0062: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0063: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0064: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0065: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0066: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0067: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0068: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0069: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0070: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0071: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0072: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0073: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0074: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0075: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0076: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0077: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0078: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0079: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0080: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0081: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0082: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0083: dt=0.000000, rms=2.177 (0.184%), neg=0, invalid=762
0084: dt=0.000000, rms=2.177 (0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0085: dt=4734.976000, rms=2.181 (0.000%), neg=0, invalid=762
0086: dt=4734.976000, rms=2.181 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0087: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0088: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0089: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0090: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762
0091: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762
0092: dt=716.800000, rms=2.181 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0093: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0094: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
0095: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
0096: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0097: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
0098: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
0099: dt=46.080000, rms=2.181 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0100: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
0101: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
0102: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0103: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
0104: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
0105: dt=6.144000, rms=2.181 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0106: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=2.181, neg=0, invalid=762
0107: dt=0.000000, rms=2.181 (0.000%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 1 hours, 15 minutes and 45 seconds.
mri_ca_register utimesec 4292.110272
mri_ca_register stimesec 30.339200
mri_ca_register ru_maxrss 1274769408
mri_ca_register ru_ixrss 0
mri_ca_register ru_idrss 0
mri_ca_register ru_isrss 0
mri_ca_register ru_minflt 761256
mri_ca_register ru_majflt 251
mri_ca_register ru_nswap 0
mri_ca_register ru_inblock 2
mri_ca_register ru_oublock 7
mri_ca_register ru_msgsnd 0
mri_ca_register ru_msgrcv 0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw 16
mri_ca_register ru_nivcsw 4259738
FSRUNTIME@ mri_ca_register 1.2625 hours 1 threads
#--------------------------------------
#@# SubCort Seg Mon Aug 6 16:24:24 -05 2018
\n mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz \n
sysname Darwin
hostname Renes-MacBook-Air-2.local
machine x86_64
setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
cd /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
== Number of threads available to mri_ca_label for OpenMP = 1 ==
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
reading 1 input volumes
reading classifier array from /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 8.76
Atlas used for the 3D morph was /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16259 (20)
gca peak = 0.17677 (13)
gca peak = 0.28129 (95)
gca peak = 0.16930 (96)
gca peak = 0.24553 (55)
gca peak = 0.30264 (59)
gca peak = 0.07580 (103)
gca peak = 0.07714 (104)
gca peak = 0.09712 (58)
gca peak = 0.11620 (58)
gca peak = 0.30970 (66)
gca peak = 0.15280 (69)
gca peak = 0.13902 (56)
gca peak = 0.14777 (55)
gca peak = 0.16765 (84)
gca peak = 0.18739 (84)
gca peak = 0.29869 (57)
gca peak = 0.33601 (57)
gca peak = 0.11131 (90)
gca peak = 0.11793 (83)
gca peak = 0.08324 (81)
gca peak = 0.10360 (77)
gca peak = 0.08424 (78)
gca peak = 0.12631 (89)
gca peak = 0.14500 (87)
gca peak = 0.14975 (24)
gca peak = 0.19357 (14)
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Cerebral_White_Matter = 0.07714 (104)
gca peak Left_Cerebral_Cortex = 0.09712 (58)
gca peak Left_Lateral_Ventricle = 0.16259 (20)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Cerebellum_White_Matter = 0.16765 (84)
gca peak Left_Cerebellum_Cortex = 0.13902 (56)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Left_Thalamus_Proper = 0.11131 (90)
gca peak Left_Caudate = 0.15280 (69)
gca peak Left_Putamen = 0.08324 (81)
gca peak Left_Pallidum = 0.16930 (96)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak Brain_Stem = 0.08424 (78)
gca peak Left_Hippocampus = 0.30264 (59)
gca peak Left_Amygdala = 0.29869 (57)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_VentralDC = 0.14500 (87)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Cerebral_White_Matter = 0.07580 (103)
gca peak Right_Cerebral_Cortex = 0.11620 (58)
gca peak Right_Lateral_Ventricle = 0.17677 (13)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Cerebellum_White_Matter = 0.18739 (84)
gca peak Right_Cerebellum_Cortex = 0.14777 (55)
gca peak Right_Thalamus_Proper = 0.11793 (83)
gca peak Right_Caudate = 0.30970 (66)
gca peak Right_Putamen = 0.10360 (77)
gca peak Right_Pallidum = 0.28129 (95)
gca peak Right_Hippocampus = 0.24553 (55)
gca peak Right_Amygdala = 0.33601 (57)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_VentralDC = 0.12631 (89)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.00 x + 0.0
setting left cbm cortex = 1.00 x + 0.00
setting right cbm cortex = 1.00 x + 0.00
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16259 (20)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.17677 (13)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.28129 (95)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.16930 (96)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.24553 (55)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.30264 (59)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.07580 (103)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.07714 (104)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.09712 (58)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.11620 (58)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.30970 (66)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15280 (69)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.13902 (56)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.14777 (55)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.16765 (84)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.18739 (84)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.29869 (57)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.33601 (57)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.11131 (90)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.11793 (83)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.08324 (81)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.10360 (77)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.08424 (78)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.12631 (89)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.14500 (87)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.14975 (24)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.19357 (14)
uniform distribution in MR - rejecting arbitrary fit
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Cerebral_White_Matter = 0.07714 (104)
gca peak Left_Cerebral_Cortex = 0.09712 (58)
gca peak Left_Lateral_Ventricle = 0.16259 (20)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Cerebellum_White_Matter = 0.16765 (84)
gca peak Left_Cerebellum_Cortex = 0.13902 (56)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Left_Thalamus_Proper = 0.11131 (90)
gca peak Left_Caudate = 0.15280 (69)
gca peak Left_Putamen = 0.08324 (81)
gca peak Left_Pallidum = 0.16930 (96)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak Brain_Stem = 0.08424 (78)
gca peak Left_Hippocampus = 0.30264 (59)
gca peak Left_Amygdala = 0.29869 (57)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_VentralDC = 0.14500 (87)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Cerebral_White_Matter = 0.07580 (103)
gca peak Right_Cerebral_Cortex = 0.11620 (58)
gca peak Right_Lateral_Ventricle = 0.17677 (13)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Cerebellum_White_Matter = 0.18739 (84)
gca peak Right_Cerebellum_Cortex = 0.14777 (55)
gca peak Right_Thalamus_Proper = 0.11793 (83)
gca peak Right_Caudate = 0.30970 (66)
gca peak Right_Putamen = 0.10360 (77)
gca peak Right_Pallidum = 0.28129 (95)
gca peak Right_Hippocampus = 0.24553 (55)
gca peak Right_Amygdala = 0.33601 (57)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_VentralDC = 0.12631 (89)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.00 x + 0.0
setting left cbm cortex = 1.00 x + 0.00
setting right cbm cortex = 1.00 x + 0.00
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
23554 voxels changed in iteration 0 of unlikely voxel relabeling
39 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
344 gm and wm labels changed (%100 to gray, % 0 to white out of all changed labels)
392 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 32267 changed. image ll: -5.372, PF=0.500
pass 2: 6290 changed.
pass 3: 3011 changed.
17835 voxels changed in iteration 0 of unlikely voxel relabeling
16 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
6634 voxels changed in iteration 0 of unlikely voxel relabeling
10 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
7921 voxels changed in iteration 0 of unlikely voxel relabeling
22 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
10136 voxels changed in iteration 0 of unlikely voxel relabeling
71 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec 10636.834927
mri_ca_label stimesec 64.912876
mri_ca_label ru_maxrss 1280380928
mri_ca_label ru_ixrss 0
mri_ca_label ru_idrss 0
mri_ca_label ru_isrss 0
mri_ca_label ru_minflt 2434013
mri_ca_label ru_majflt 510
mri_ca_label ru_nswap 0
mri_ca_label ru_inblock 3
mri_ca_label ru_oublock 7
mri_ca_label ru_msgsnd 0
mri_ca_label ru_msgrcv 0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw 813
mri_ca_label ru_nivcsw 7137900
auto-labeling took 187 minutes and 36 seconds.
\n mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/cc_up.lta IXI_25_Guys_DTI_recon \n
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/transforms/cc_up.lta
reading aseg from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/aseg.auto_noCCseg.mgz
reading norm from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/norm.mgz
28267 voxels in left wm, 32301 in right wm, xrange [114, 131]
searching rotation angles z=[-13 1], y=[-2 12]
searching scale 1 Z rot 0.6 global minimum found at slice 124.0, rotations (4.11, -6.18)
final transformation (x=124.0, yr=4.114, zr=-6.175):
0.99164 0.10757 0.07132 -15.45528;
-0.10729 0.99420 -0.00772 41.93151;
-0.07174 0.00000 0.99742 2.24310;
0.00000 0.00000 0.00000 1.00000;
mri_cc: no WM voxels found with norm > 40 -- check skull stripping
No such file or directory
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
recon-all -s IXI_25_Guys_DTI_recon exited with ERRORS at Mon Aug 6 19:33:20 -05 2018
For more details, see the log file /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/scripts/recon-all.log