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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: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /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 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/] [2018-08-06 14:40:31] running: /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 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 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 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
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: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /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 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/] [2018-08-06 14:42:25] running: /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 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 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 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
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: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /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 [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/] [2018-08-06 14:44:22] running: /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 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 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: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 /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/ [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/] [2018-08-06 14:46:19] running: /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/ [andraderenew@Renes-MacBook-Air-2.local:/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_25_Guys_DTI_recon/mri/] [2018-08-06 14:47:27] running: /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 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting