2018. 07. 09. (���) 12:08:25 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG /home/kt/Downloads/freesurferDev/bin/recon-all -i rf161019_x3DT1_SAG.nii -subjid 161019_x3DT1_SAG -all subjid 161019_x3DT1_SAG setenv SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Actual FREESURFER_HOME /home/kt/Downloads/freesurferDev build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20180703-82d87f8 Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63693 maxlocks unlimited maxsignal 63693 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16330356 16099068 231288 40508 585236 2004312 -/+ buffers/cache: 13509520 2820836 Swap: 244141052 1133868 243007184 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:25-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:25-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:25-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:25-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2wmseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:25-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_binarize.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 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00:05:53 Id: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT 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2018 00:05:53 Id: $Id: mris_diff.c,v 1.20 2014/03/21 23:57:48 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_divide_parcellation ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_divide_parcellation.c,v 1.12 2012/10/24 19:50:06 maritza Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 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mris_left_right_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_surface_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_stats2seg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surfcluster.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_volmask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2vol.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_voldiff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: tkregister2_cmdl ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/09-03:08:26-GMT BuildTimeStamp: Jul 3 2018 00:05:53 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: kt Machine: kt-B85M-DS3H-A Platform: Linux PlatformVersion: 4.4.0-130-generic CompilerName: GCC CompilerVersion: 40800 FLIRT version 6.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /home/kt/Downloads/freesurferDev/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/kt/Downloads/freesurferDev/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_convert /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/kt/Downloads/Thalamus/rf161019_x3DT1_SAG.nii... TR=8.11, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999872, -0.0151213, -0.00525495) j_ras = (-0.0154345, 0.997714, 0.0657858) k_ras = (-0.00424817, -0.0658585, 0.99782) writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor 2018. 07. 09. (���) 12:08:31 KST Found 1 runs /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig/001.mgz /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_convert /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz --conform Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz... TR=8.11, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999872, -0.0151213, -0.00525495) j_ras = (-0.0154345, 0.997714, 0.0657858) k_ras = (-0.00424817, -0.0658585, 0.99782) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz... mri_add_xform_to_header -c /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/talairach.xfm /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz Could not set locale No such file or directory Could not set locale INFO: extension is mgz #-------------------------------------------- #@# Talairach 2018. 07. 09. (���) 12:08:44 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri /home/kt/Downloads/freesurferDev/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 2018. 07. 09. (���) 12:08:44 KST Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.13015 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.13015/nu0.mnc -odt float Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin orig.mgz /dev/shm/tmp.mri_nu_correct.mni.13015/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=8.11, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.85803e-10, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-1.68802e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to /dev/shm/tmp.mri_nu_correct.mni.13015/nu0.mnc... -------------------------------------------------------- Iteration 1 2018. 07. 09. (���) 12:08:49 KST nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.13015/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.13015/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.13015/0/ -iterations 1000 -distance 50 [kt@kt-B85M-DS3H-A:/home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/] [2018-07-09 12:08:49] running: /home/kt/Downloads/freesurferDev/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 /dev/shm/tmp.mri_nu_correct.mni.13015/0/ /dev/shm/tmp.mri_nu_correct.mni.13015/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.13015/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 Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000948739 mri_convert /dev/shm/tmp.mri_nu_correct.mni.13015/nu1.mnc orig_nu.mgz --like orig.mgz --conform Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin /dev/shm/tmp.mri_nu_correct.mni.13015/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /dev/shm/tmp.mri_nu_correct.mni.13015/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.85803e-10, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-1.68802e-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... 2018. 07. 09. (���) 12:09:49 KST mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2018. 07. 09. (���) 12:09:49 KST Ended at 2018. 07. 09. (���) 12:10:25 KST talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection 2018. 07. 09. (���) 12:10:27 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm Could not set locale No such file or directory Could not set locale talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8107, pval=0.8469 >= threshold=0.0050) awk -f /home/kt/Downloads/freesurferDev/bin/extract_talairach_avi_QA.awk /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/talairach_avi.log tal_QC_AZS /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/talairach_avi.log TalAviQA: 0.97500 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 2018. 07. 09. (���) 12:10:27 KST mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri /home/kt/Downloads/freesurferDev/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 2018. 07. 09. (���) 12:10:27 KST Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.13616 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.13616/nu0.mnc -odt float Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin orig.mgz /dev/shm/tmp.mri_nu_correct.mni.13616/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=8.11, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.85803e-10, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-1.68802e-09, 1, 7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to /dev/shm/tmp.mri_nu_correct.mni.13616/nu0.mnc... -------------------------------------------------------- Iteration 1 2018. 07. 09. (���) 12:10:31 KST nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.13616/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.13616/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.13616/0/ [kt@kt-B85M-DS3H-A:/home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/] [2018-07-09 12:10:31] running: /home/kt/Downloads/freesurferDev/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 /dev/shm/tmp.mri_nu_correct.mni.13616/0/ /dev/shm/tmp.mri_nu_correct.mni.13616/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.13616/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 Number of iterations: 27 CV of field change: 0.000995668 -------------------------------------------------------- Iteration 2 2018. 07. 09. (���) 12:11:15 KST nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.13616/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.13616/1/ [kt@kt-B85M-DS3H-A:/home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/] [2018-07-09 12:11:15] running: /home/kt/Downloads/freesurferDev/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 /dev/shm/tmp.mri_nu_correct.mni.13616/1/ /dev/shm/tmp.mri_nu_correct.mni.13616/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.imp 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: 11 CV of field change: 0.000970529 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz Could not set locale No such file or directory Could not set locale $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri cmdline mri_binarize.bin --i /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt input /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.13616/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 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.13616/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.13616/input.mean.dat Could not set locale No such file or directory Could not set locale $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.13616/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.13616/input.mean.dat sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.13616/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 /dev/shm/tmp.mri_nu_correct.mni.13616/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.13616/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.13616/output.mean.dat Could not set locale No such file or directory Could not set locale $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.13616/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.13616/output.mean.dat sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.13616/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.13616/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 /dev/shm/tmp.mri_nu_correct.mni.13616/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc mul 1.01611665763207130437 Could not set locale No such file or directory Could not set locale Saving result to '/dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc' (type = MINC ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc nu.mgz --like orig.mgz Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale mri_convert.bin /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /dev/shm/tmp.mri_nu_correct.mni.13616/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 7.85803e-10, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-1.68802e-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 Could not set locale No such file or directory Could not set locale type change took 0 minutes and 7 seconds. mapping ( 9, 173) to ( 3, 110) 2018. 07. 09. (���) 12:12:27 KST mri_nu_correct.mni done mri_add_xform_to_header -c /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/talairach.xfm nu.mgz nu.mgz Could not set locale No such file or directory Could not set locale INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization 2018. 07. 09. (���) 12:12:29 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz Could not set locale No such file or directory Could not set locale using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.12866 -0.00265 -0.04011 -4.05556; 0.05999 1.14364 0.18888 -25.59003; 0.04016 -0.10220 1.11734 -5.77843; 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 = 19 Starting OpenSpline(): npoints = 19 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 109 gm peak at 68 (68), valley at 44 (44) csf peak at 17, setting threshold to 51 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 66 (66), valley at 35 (35) csf peak at 17, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 27 seconds. #-------------------------------------------- #@# Skull Stripping 2018. 07. 09. (���) 12:14:57 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_em_register -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /home/kt/Downloads/freesurferDev/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale No such file or directory aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/kt/Downloads/freesurferDev/average/RB_all_withskull_2016-05-10.vc700.gca'... GCAread took 0 minutes and 2 seconds. average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=12.0 skull bounding box = (50, 47, 33) --> (205, 244, 215) finding center of left hemi white matter using (102, 113, 124) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 108, using box (83,89,102) --> (121, 137,146) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 105 +- 7.6 after smoothing, mri peak at 105, scaling input intensities by 1.029 scaling channel 0 by 1.02857 initial log_p = -4.501 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.511695 @ (0.000, 0.000, 0.000) max log p = -4.382319 @ (5.263, -5.263, -15.789) max log p = -4.374716 @ (-2.632, 2.632, 2.632) max log p = -4.342784 @ (-3.947, -1.316, 3.947) max log p = -4.327992 @ (-0.658, 0.658, 0.658) max log p = -4.316478 @ (0.987, 0.329, 0.329) max log p = -4.316478 @ (0.000, 0.000, 0.000) max log p = -4.316478 @ (0.000, 0.000, 0.000) Found translation: (-1.0, -3.0, -8.2): log p = -4.316 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.882, old_max_log_p =-4.316 (thresh=-4.3) 1.15000 0.00000 0.00000 -19.86616; 0.00000 1.22567 0.16136 -47.43951; 0.00000 -0.15011 1.14016 -3.13804; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 57 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.882, old_max_log_p =-3.882 (thresh=-3.9) 1.15000 0.00000 0.00000 -19.86616; 0.00000 1.22567 0.16136 -47.43951; 0.00000 -0.15011 1.14016 -3.13804; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 51 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.837, old_max_log_p =-3.882 (thresh=-3.9) 1.12783 -0.03949 -0.00394 -11.11611; 0.03692 1.20640 0.12021 -44.53477; 0.00000 -0.11338 1.16530 -11.22197; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 19 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.837, old_max_log_p =-3.837 (thresh=-3.8) 1.12783 -0.03949 -0.00394 -11.11611; 0.03692 1.20640 0.12021 -44.53477; 0.00000 -0.11338 1.16530 -11.22197; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 21 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.811, old_max_log_p =-3.837 (thresh=-3.8) 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 44 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.811, old_max_log_p =-3.811 (thresh=-3.8) 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.811 (old=-4.501) transform before final EM align: 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.12429 -0.06093 0.01313 -10.64439; 0.05558 1.20785 0.11108 -45.99665; -0.01798 -0.10269 1.16479 -11.32548; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 737.732000 mri_em_register stimesec 1.716000 mri_em_register ru_maxrss 613364 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 164506 mri_em_register ru_majflt 8 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150816 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 21 mri_em_register ru_nivcsw 67827 registration took 16 minutes and 1 seconds. mri_watershed -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mri_watershed.dat -T1 -brain_atlas /home/kt/Downloads/freesurferDev/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.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=127 y=117 z=118 r=88 first estimation of the main basin volume: 2871684 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=107, y=102, z=87, Imax=255 CSF=12, 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=7786187567 voxels, voxel volume =1.000 = 7786187567 mmm3 = 7786187.776 cm3 done. PostAnalyze...Basin Prior 4 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=125,y=121, z=111, r=9357 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=14, CSF_MAX=42 , nb = 41292 RIGHT_CER CSF_MIN=0, CSF_intensity=14, CSF_MAX=31 , nb = 3150 LEFT_CER CSF_MIN=0, CSF_intensity=12, CSF_MAX=37 , nb = 2556 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=41 , nb = 17208 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=45 , nb = 17442 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 936 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 42, 38, 33, 71 after analyzing : 32, 38, 38, 46 RIGHT_CER before analyzing : 31, 38, 49, 74 after analyzing : 31, 45, 49, 52 LEFT_CER before analyzing : 37, 42, 48, 77 after analyzing : 37, 46, 48, 53 RIGHT_BRAIN before analyzing : 41, 36, 31, 71 after analyzing : 30, 36, 36, 44 LEFT_BRAIN before analyzing : 45, 39, 32, 69 after analyzing : 32, 39, 39, 46 OTHER before analyzing : 23, 25, 31, 91 after analyzing : 23, 29, 31, 44 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.012 curvature mean = 64.100, std = 4.946 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.75, sigma = 9.49 after rotation: sse = 5.75, sigma = 9.49 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.76, its var is 9.43 before Erosion-Dilatation 5.00% of inacurate vertices after Erosion-Dilatation 7.14% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...36 iterations mri_strip_skull: done peeling brain Brain Size = 1290642 voxels, voxel volume = 1.000 mm3 = 1290642 mmm3 = 1290.642 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 18.716000 mri_watershed stimesec 0.184000 mri_watershed ru_maxrss 835060 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212522 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 10040 mri_watershed ru_oublock 2144 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 52 mri_watershed ru_nivcsw 2122 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration 2018. 07. 09. (���) 12:31:30 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_em_register -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale No such file or directory 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 '/home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca'... GCAread took 0 minutes and 1 seconds. 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=13.0 skull bounding box = (64, 64, 43) --> (188, 180, 194) finding center of left hemi white matter using (105, 103, 119) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,89,100) --> (120, 117,137) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 6.1 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.187 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.195286 @ (0.000, 0.000, 0.000) max log p = -4.089171 @ (5.263, -5.263, -15.789) max log p = -4.037311 @ (-7.895, -2.632, 13.158) max log p = -4.014410 @ (3.947, 1.316, -9.211) max log p = -4.004234 @ (-0.658, -0.658, 0.658) max log p = -4.004234 @ (0.000, 0.000, 0.000) max log p = -4.004234 @ (0.000, 0.000, 0.000) max log p = -4.004234 @ (0.000, 0.000, 0.000) Found translation: (0.7, -7.2, -11.2): log p = -4.004 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.723, old_max_log_p =-4.004 (thresh=-4.0) 1.15000 0.00000 0.00000 -18.25398; 0.00000 1.07500 0.00000 -9.22636; 0.00000 0.00000 1.15000 -28.67849; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 17 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.687, old_max_log_p =-3.723 (thresh=-3.7) 1.15000 0.00000 0.00000 -18.25398; 0.00000 1.15563 0.00000 -18.86509; 0.00000 0.00000 1.15000 -28.67849; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 25 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.687, old_max_log_p =-3.687 (thresh=-3.7) 1.15000 0.00000 0.00000 -18.25398; 0.00000 1.15563 0.00000 -18.86509; 0.00000 0.00000 1.15000 -28.67849; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 2 minutes and 17 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.516, old_max_log_p =-3.687 (thresh=-3.7) 1.12521 -0.07395 -0.00482 -7.60045; 0.07803 1.19383 0.07787 -44.22779; 0.00000 -0.07558 1.14754 -15.60555; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 58 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.512, old_max_log_p =-3.516 (thresh=-3.5) 1.10536 -0.03794 0.03570 -14.02522; 0.04039 1.17026 0.11210 -40.44221; -0.03937 -0.11212 1.14392 -5.73327; 0.00000 0.00000 0.00000 1.00000; iteration took 2 minutes and 8 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.512, old_max_log_p =-3.512 (thresh=-3.5) 1.10536 -0.03794 0.03570 -14.02522; 0.04039 1.17026 0.11210 -40.44221; -0.03937 -0.11212 1.14392 -5.73327; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 2 minutes and 0 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.488, old_max_log_p =-3.512 (thresh=-3.5) 1.10563 -0.03733 0.02631 -13.06869; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 49 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.487, old_max_log_p =-3.488 (thresh=-3.5) 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 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 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.487 (old=-4.187) transform before final EM align: 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 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 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.10822 -0.03742 0.02637 -13.39637; 0.04155 1.17055 0.07444 -37.29090; -0.02895 -0.07399 1.14589 -11.91005; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 4.0 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) pass 2 through quasi-newton minimization... dfp_em_step_func: 012: -log(p) = 4.0 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 013: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 014: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 015: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) pass 3 through quasi-newton minimization... dfp_em_step_func: 016: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.07, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 017: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 018: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 019: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) pass 4 through quasi-newton minimization... dfp_em_step_func: 020: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 021: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) pass 5 through quasi-newton minimization... dfp_em_step_func: 022: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 023: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 024: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) dfp_em_step_func: 025: -log(p) = 3.9 after pass:transform: ( 1.11, -0.04, 0.03, -13.40) ( 0.04, 1.17, 0.08, -37.29) ( -0.03, -0.07, 1.15, -11.91) pass 6 through quasi-newton minimization... outof QuasiNewtonEMA: 027: -log(p) = 3.9 tol 0.000000 final transform: 1.10983 -0.03579 0.02776 -13.39637; 0.04296 1.17169 0.07571 -37.29090; -0.02909 -0.07417 1.14582 -11.91005; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 996.484000 mri_em_register stimesec 2.496000 mri_em_register ru_maxrss 602696 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 165148 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 48 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 3 mri_em_register ru_nivcsw 90086 registration took 20 minutes and 37 seconds. #-------------------------------------- #@# CA Normalize 2018. 07. 09. (���) 12:52:07 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz Could not set locale No such file or directory Could not set locale Could not set locale writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/home/kt/Downloads/freesurferDev/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=13.0 skull bounding box = (64, 64, 43) --> (188, 180, 194) finding center of left hemi white matter using (105, 103, 119) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,89,100) --> (120, 117,137) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 6.1 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.10983 -0.03579 0.02776 -13.39637; 0.04296 1.17169 0.07571 -37.29090; -0.02909 -0.07417 1.14582 -11.91005; 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 (127, 64, 45) --> (187, 164, 191) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 822 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (69, 65, 44) --> (128, 167, 191) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 432 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 139, 66) --> (174, 174, 113) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 20 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 139, 64) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 97) --> (144, 191, 124) Brain_Stem: limiting intensities to 112.0 --> 132.0 16 of 37 (43.2%) samples deleted using 1323 total control points for intensity normalization... bias field = 0.961 +- 0.058 3 of 1307 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 64, 45) --> (187, 164, 191) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 988 (0.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (69, 65, 44) --> (128, 167, 191) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 673 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 139, 66) --> (174, 174, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 20 of 89 (22.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 139, 64) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 78 (1.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 97) --> (144, 191, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 13 of 156 (8.3%) samples deleted using 1984 total control points for intensity normalization... bias field = 1.001 +- 0.065 0 of 1920 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 64, 45) --> (187, 164, 191) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 999 (0.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (69, 65, 44) --> (128, 167, 191) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 770 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 139, 66) --> (174, 174, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 31 of 109 (28.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 139, 64) --> (129, 176, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 78 (17.9%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 131, 97) --> (144, 191, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 82 of 191 (42.9%) samples deleted using 2147 total control points for intensity normalization... bias field = 1.010 +- 0.049 2 of 1953 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 13 seconds. #-------------------------------------- #@# CA Reg 2018. 07. 09. (���) 12:53:20 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_ca_register -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z Could not set locale No such file or directory Could not set locale No such file or directory Could not set locale No such file or directory 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 '/home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.50 (predicted orig area = 5.3) 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 0.156 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.902, neg=0, invalid=762 0001: dt=243.482873, rms=0.814 (9.734%), neg=0, invalid=762 0002: dt=200.267943, rms=0.783 (3.834%), neg=0, invalid=762 0003: dt=187.600000, rms=0.771 (1.471%), neg=0, invalid=762 0004: dt=235.136104, rms=0.763 (1.016%), neg=0, invalid=762 0005: dt=148.459016, rms=0.758 (0.713%), neg=0, invalid=762 0006: dt=369.920000, rms=0.753 (0.698%), neg=0, invalid=762 0007: dt=129.472000, rms=0.748 (0.553%), neg=0, invalid=762 0008: dt=443.904000, rms=0.745 (0.456%), neg=0, invalid=762 0009: dt=129.472000, rms=0.742 (0.460%), neg=0, invalid=762 0010: dt=295.936000, rms=0.740 (0.273%), neg=0, invalid=762 0011: dt=129.472000, rms=0.738 (0.238%), neg=0, invalid=762 0012: dt=129.472000, rms=0.737 (0.142%), neg=0, invalid=762 0013: dt=129.472000, rms=0.735 (0.235%), neg=0, invalid=762 0014: dt=129.472000, rms=0.733 (0.329%), neg=0, invalid=762 0015: dt=129.472000, rms=0.730 (0.374%), neg=0, invalid=762 0016: dt=129.472000, rms=0.727 (0.418%), neg=0, invalid=762 0017: dt=129.472000, rms=0.724 (0.423%), neg=0, invalid=762 0018: dt=129.472000, rms=0.721 (0.395%), neg=0, invalid=762 0019: dt=129.472000, rms=0.718 (0.388%), neg=0, invalid=762 0020: dt=129.472000, rms=0.715 (0.360%), neg=0, invalid=762 0021: dt=129.472000, rms=0.713 (0.359%), neg=0, invalid=762 0022: dt=129.472000, rms=0.711 (0.325%), neg=0, invalid=762 0023: dt=129.472000, rms=0.709 (0.283%), neg=0, invalid=762 0024: dt=129.472000, rms=0.707 (0.260%), neg=0, invalid=762 0025: dt=129.472000, rms=0.705 (0.235%), neg=0, invalid=762 0026: dt=129.472000, rms=0.704 (0.225%), neg=0, invalid=762 0027: dt=129.472000, rms=0.702 (0.204%), neg=0, invalid=762 0028: dt=129.472000, rms=0.701 (0.189%), neg=0, invalid=762 0029: dt=129.472000, rms=0.700 (0.170%), neg=0, invalid=762 0030: dt=129.472000, rms=0.698 (0.151%), neg=0, invalid=762 0031: dt=129.472000, rms=0.697 (0.153%), neg=0, invalid=762 0032: dt=129.472000, rms=0.696 (0.137%), neg=0, invalid=762 0033: dt=129.472000, rms=0.696 (0.126%), neg=0, invalid=762 0034: dt=129.472000, rms=0.695 (0.118%), neg=0, invalid=762 0035: dt=129.472000, rms=0.694 (0.096%), neg=0, invalid=762 0036: dt=295.936000, rms=0.694 (0.011%), neg=0, invalid=762 0037: dt=295.936000, rms=0.694 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.694, neg=0, invalid=762 0038: dt=129.472000, rms=0.694 (0.141%), neg=0, invalid=762 0039: dt=295.936000, rms=0.693 (0.046%), neg=0, invalid=762 0040: dt=295.936000, rms=0.693 (0.011%), neg=0, invalid=762 0041: dt=295.936000, rms=0.693 (0.009%), neg=0, invalid=762 0042: dt=295.936000, rms=0.693 (0.033%), neg=0, invalid=762 0043: dt=295.936000, rms=0.693 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.615 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0044: dt=25.920000, rms=0.704 (0.139%), neg=0, invalid=762 0045: dt=20.736000, rms=0.704 (0.019%), neg=0, invalid=762 0046: dt=20.736000, rms=0.704 (0.012%), neg=0, invalid=762 0047: dt=20.736000, rms=0.704 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0048: dt=0.000000, rms=0.704 (0.060%), neg=0, invalid=762 0049: dt=0.000000, rms=0.704 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.353 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.740, neg=0, invalid=762 0050: dt=15.135135, rms=0.731 (1.307%), neg=0, invalid=762 0051: dt=11.200000, rms=0.729 (0.163%), neg=0, invalid=762 0052: dt=11.200000, rms=0.729 (0.013%), neg=0, invalid=762 0053: dt=11.200000, rms=0.729 (-0.157%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=762 0054: dt=0.000000, rms=0.729 (0.060%), neg=0, invalid=762 0055: dt=0.000000, rms=0.729 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 8.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.781, neg=0, invalid=762 0056: dt=0.000000, rms=0.780 (0.053%), neg=0, invalid=762 0057: dt=0.000000, rms=0.780 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.781, neg=0, invalid=762 0058: dt=0.000000, rms=0.780 (0.053%), neg=0, invalid=762 0059: dt=0.000000, rms=0.780 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 20.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.880, neg=0, invalid=762 0060: dt=0.547059, rms=0.872 (0.889%), neg=0, invalid=762 0061: dt=0.448000, rms=0.868 (0.399%), neg=0, invalid=762 0062: dt=0.384000, rms=0.864 (0.450%), neg=0, invalid=762 0063: dt=0.256000, rms=0.863 (0.193%), neg=0, invalid=762 0064: dt=0.256000, rms=0.861 (0.233%), neg=0, invalid=762 0065: dt=0.256000, rms=0.858 (0.285%), neg=0, invalid=762 0066: dt=0.256000, rms=0.856 (0.261%), neg=0, invalid=762 0067: dt=0.256000, rms=0.855 (0.156%), neg=0, invalid=762 0068: dt=0.256000, rms=0.854 (0.132%), neg=0, invalid=762 0069: dt=0.256000, rms=0.853 (0.048%), neg=0, invalid=762 0070: dt=0.256000, rms=0.853 (-0.033%), neg=0, invalid=762 0071: dt=0.821192, rms=0.850 (0.322%), neg=0, invalid=762 0072: dt=0.256000, rms=0.848 (0.276%), neg=0, invalid=762 0073: dt=0.112000, rms=0.848 (0.034%), neg=0, invalid=762 0074: dt=0.112000, rms=0.848 (0.020%), neg=0, invalid=762 0075: dt=0.112000, rms=0.847 (0.034%), neg=0, invalid=762 0076: dt=0.112000, rms=0.847 (0.051%), neg=0, invalid=762 0077: dt=0.112000, rms=0.846 (0.069%), neg=0, invalid=762 0078: dt=0.112000, rms=0.846 (0.078%), neg=0, invalid=762 0079: dt=0.112000, rms=0.845 (0.074%), neg=0, invalid=762 0080: dt=0.112000, rms=0.844 (0.065%), neg=0, invalid=762 0081: dt=0.384000, rms=0.844 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.845, neg=0, invalid=762 0082: dt=0.448000, rms=0.844 (0.117%), neg=0, invalid=762 0083: dt=0.000000, rms=0.844 (0.001%), neg=0, invalid=762 0084: dt=0.100000, rms=0.844 (-0.012%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 40.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.799, neg=0, invalid=762 0085: dt=0.269943, rms=0.792 (0.890%), neg=0, invalid=762 0086: dt=0.028000, rms=0.792 (0.047%), neg=0, invalid=762 0087: dt=0.028000, rms=0.792 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0088: dt=0.012000, rms=0.792 (0.057%), neg=0, invalid=762 0089: dt=0.001750, rms=0.792 (0.000%), neg=0, invalid=762 0090: dt=0.001750, rms=0.792 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12929 (17) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (2041 voxels, overlap=0.572) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (2041 voxels, peak = 16), gca=16.3 gca peak = 0.15565 (16) mri peak = 0.11674 (17) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (1416 voxels, overlap=0.769) Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (1416 voxels, peak = 15), gca=14.6 gca peak = 0.26829 (96) mri peak = 0.07800 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (711 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (711 voxels, peak = 100), gca=100.3 gca peak = 0.20183 (93) mri peak = 0.08067 (98) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (597 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (597 voxels, peak = 96), gca=96.3 gca peak = 0.21683 (55) mri peak = 0.09759 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (626 voxels, overlap=0.223) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (626 voxels, peak = 62), gca=62.4 gca peak = 0.30730 (58) mri peak = 0.10260 (63) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (665 voxels, overlap=0.866) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (665 voxels, peak = 64), gca=63.5 gca peak = 0.11430 (101) mri peak = 0.07708 (106) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (41649 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (41649 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.08003 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44256 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (44256 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.03208 (72) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (16238 voxels, overlap=0.139) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (16238 voxels, peak = 71), gca=70.5 gca peak = 0.15082 (58) mri peak = 0.03823 (67) Right_Cerebral_Cortex (42): linear fit = 1.17 x + 0.0 (17498 voxels, overlap=0.125) Right_Cerebral_Cortex (42): linear fit = 1.17 x + 0.0 (17498 voxels, peak = 68), gca=68.1 gca peak = 0.14161 (67) mri peak = 0.09037 (78) Right_Caudate (50): linear fit = 1.14 x + 0.0 (425 voxels, overlap=0.423) Right_Caudate (50): linear fit = 1.14 x + 0.0 (425 voxels, peak = 77), gca=76.7 gca peak = 0.15243 (71) mri peak = 0.11151 (80) Left_Caudate (11): linear fit = 1.07 x + 0.0 (396 voxels, overlap=0.460) Left_Caudate (11): linear fit = 1.07 x + 0.0 (396 voxels, peak = 76), gca=75.6 gca peak = 0.13336 (57) mri peak = 0.04474 (58) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (16979 voxels, overlap=0.902) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (16979 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.04727 (57) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (21960 voxels, overlap=0.944) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (21960 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.05967 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7891 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7891 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.08348 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6606 voxels, overlap=0.680) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6606 voxels, peak = 89), gca=89.2 gca peak = 0.21969 (57) mri peak = 0.11296 (62) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (309 voxels, overlap=0.880) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (309 voxels, peak = 61), gca=61.3 gca peak = 0.39313 (56) mri peak = 0.11765 (64) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (295 voxels, overlap=0.399) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (295 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06888 (88) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (3379 voxels, overlap=0.909) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (3379 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.06723 (90) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (2577 voxels, overlap=0.805) Right_Thalamus (49): linear fit = 1.07 x + 0.0 (2577 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.06755 (83) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1947 voxels, overlap=0.956) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1947 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.07994 (84) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1952 voxels, overlap=0.845) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1952 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.08593 (86) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9377 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9377 voxels, peak = 88), gca=88.4 gca peak = 0.13281 (86) mri peak = 0.08811 (98) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (782 voxels, overlap=0.079) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (782 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.08131 (98) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1045 voxels, overlap=0.430) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1045 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.21053 (18) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (95 voxels, overlap=0.189) Third_Ventricle (14): linear fit = 0.75 x + 0.0 (95 voxels, peak = 17), gca=17.4 gca peak = 0.15061 (21) mri peak = 0.14850 (16) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (292 voxels, overlap=0.496) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (292 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak = 0.64095 (94) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) 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_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) 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 1.14 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.83 x + 0.0 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=0.842, neg=0, invalid=762 0091: dt=132.045596, rms=0.810 (3.841%), neg=0, invalid=762 0092: dt=391.296618, rms=0.790 (2.516%), neg=0, invalid=762 0093: dt=369.920000, rms=0.776 (1.685%), neg=0, invalid=762 0094: dt=129.472000, rms=0.772 (0.596%), neg=0, invalid=762 0095: dt=369.920000, rms=0.768 (0.466%), neg=0, invalid=762 0096: dt=129.472000, rms=0.765 (0.480%), neg=0, invalid=762 0097: dt=369.920000, rms=0.761 (0.464%), neg=0, invalid=762 0098: dt=129.472000, rms=0.758 (0.411%), neg=0, invalid=762 0099: dt=295.936000, rms=0.756 (0.270%), neg=0, invalid=762 0100: dt=129.472000, rms=0.753 (0.342%), neg=0, invalid=762 0101: dt=369.920000, rms=0.751 (0.263%), neg=0, invalid=762 0102: dt=129.472000, rms=0.749 (0.358%), neg=0, invalid=762 0103: dt=221.952000, rms=0.747 (0.196%), neg=0, invalid=762 0104: dt=129.472000, rms=0.746 (0.209%), neg=0, invalid=762 0105: dt=517.888000, rms=0.743 (0.341%), neg=0, invalid=762 0106: dt=129.472000, rms=0.741 (0.292%), neg=0, invalid=762 0107: dt=129.472000, rms=0.740 (0.117%), neg=0, invalid=762 0108: dt=517.888000, rms=0.737 (0.385%), neg=0, invalid=762 0109: dt=129.472000, rms=0.736 (0.150%), neg=0, invalid=762 0110: dt=295.936000, rms=0.735 (0.181%), neg=0, invalid=762 0111: dt=129.472000, rms=0.734 (0.145%), neg=0, invalid=762 0112: dt=295.936000, rms=0.732 (0.153%), neg=0, invalid=762 0113: dt=129.472000, rms=0.731 (0.145%), neg=0, invalid=762 0114: dt=221.952000, rms=0.730 (0.133%), neg=0, invalid=762 0115: dt=129.472000, rms=0.730 (0.107%), neg=0, invalid=762 0116: dt=443.904000, rms=0.728 (0.186%), neg=0, invalid=762 0117: dt=110.976000, rms=0.727 (0.162%), neg=0, invalid=762 0118: dt=443.904000, rms=0.726 (0.170%), neg=0, invalid=762 0119: dt=110.976000, rms=0.725 (0.145%), neg=0, invalid=762 0120: dt=443.904000, rms=0.724 (0.148%), neg=0, invalid=762 0121: dt=110.976000, rms=0.723 (0.148%), neg=0, invalid=762 0122: dt=443.904000, rms=0.722 (0.135%), neg=0, invalid=762 0123: dt=110.976000, rms=0.721 (0.146%), neg=0, invalid=762 0124: dt=443.904000, rms=0.720 (0.114%), neg=0, invalid=762 0125: dt=110.976000, rms=0.719 (0.143%), neg=0, invalid=762 0126: dt=369.920000, rms=0.718 (0.108%), neg=0, invalid=762 0127: dt=110.976000, rms=0.717 (0.105%), neg=0, invalid=762 0128: dt=517.888000, rms=0.716 (0.135%), neg=0, invalid=762 0129: dt=110.976000, rms=0.715 (0.127%), neg=0, invalid=762 0130: dt=369.920000, rms=0.715 (0.096%), neg=0, invalid=762 0131: dt=110.976000, rms=0.714 (0.097%), neg=0, invalid=762 0132: dt=517.888000, rms=0.713 (0.121%), neg=0, invalid=762 0133: dt=110.976000, rms=0.712 (0.120%), neg=0, invalid=762 0134: dt=369.920000, rms=0.712 (0.081%), neg=0, invalid=762 0135: dt=110.976000, rms=0.711 (0.095%), neg=0, invalid=762 0136: dt=443.904000, rms=0.710 (0.104%), neg=0, invalid=762 0137: dt=110.976000, rms=0.710 (0.091%), neg=0, invalid=762 0138: dt=443.904000, rms=0.709 (0.090%), neg=0, invalid=762 0139: dt=110.976000, rms=0.708 (0.094%), neg=0, invalid=762 0140: dt=369.920000, rms=0.708 (0.081%), neg=0, invalid=762 0141: dt=110.976000, rms=0.707 (0.077%), neg=0, invalid=762 0142: dt=443.904000, rms=0.707 (0.090%), neg=0, invalid=762 0143: dt=110.976000, rms=0.706 (0.085%), neg=0, invalid=762 0144: dt=369.920000, rms=0.705 (0.073%), neg=0, invalid=762 0145: dt=110.976000, rms=0.705 (0.072%), neg=0, invalid=762 0146: dt=369.920000, rms=0.704 (0.074%), neg=0, invalid=762 0147: dt=110.976000, rms=0.704 (0.062%), neg=0, invalid=762 0148: dt=443.904000, rms=0.703 (0.075%), neg=0, invalid=762 0149: dt=110.976000, rms=0.703 (0.068%), neg=0, invalid=762 0150: dt=369.920000, rms=0.703 (0.065%), neg=0, invalid=762 0151: dt=110.976000, rms=0.702 (0.054%), neg=0, invalid=762 0152: dt=443.904000, rms=0.702 (0.068%), neg=0, invalid=762 0153: dt=92.480000, rms=0.701 (0.060%), neg=0, invalid=762 0154: dt=2071.552000, rms=0.699 (0.331%), neg=0, invalid=762 0155: dt=92.480000, rms=0.698 (0.126%), neg=0, invalid=762 0156: dt=517.888000, rms=0.698 (0.070%), neg=0, invalid=762 0157: dt=129.472000, rms=0.697 (0.041%), neg=0, invalid=762 0158: dt=129.472000, rms=0.697 (0.027%), neg=0, invalid=762 0159: dt=129.472000, rms=0.697 (0.037%), neg=0, invalid=762 0160: dt=129.472000, rms=0.696 (0.063%), neg=0, invalid=762 0161: dt=129.472000, rms=0.696 (0.066%), neg=0, invalid=762 0162: dt=129.472000, rms=0.695 (0.090%), neg=0, invalid=762 0163: dt=129.472000, rms=0.695 (0.091%), neg=0, invalid=762 0164: dt=129.472000, rms=0.694 (0.099%), neg=0, invalid=762 0165: dt=129.472000, rms=0.693 (0.114%), neg=0, invalid=762 0166: dt=129.472000, rms=0.692 (0.106%), neg=0, invalid=762 0167: dt=129.472000, rms=0.692 (0.115%), neg=0, invalid=762 0168: dt=129.472000, rms=0.691 (0.113%), neg=0, invalid=762 0169: dt=129.472000, rms=0.690 (0.120%), neg=0, invalid=762 0170: dt=129.472000, rms=0.689 (0.118%), neg=0, invalid=762 0171: dt=129.472000, rms=0.688 (0.115%), neg=0, invalid=762 0172: dt=129.472000, rms=0.688 (0.107%), neg=0, invalid=762 0173: dt=129.472000, rms=0.687 (0.105%), neg=0, invalid=762 0174: dt=129.472000, rms=0.686 (0.108%), neg=0, invalid=762 0175: dt=129.472000, rms=0.686 (0.101%), neg=0, invalid=762 0176: dt=129.472000, rms=0.685 (0.100%), neg=0, invalid=762 0177: dt=129.472000, rms=0.684 (0.093%), neg=0, invalid=762 0178: dt=129.472000, rms=0.684 (0.093%), neg=0, invalid=762 0179: dt=129.472000, rms=0.683 (0.090%), neg=0, invalid=762 0180: dt=129.472000, rms=0.682 (0.086%), neg=0, invalid=762 0181: dt=129.472000, rms=0.682 (0.080%), neg=0, invalid=762 0182: dt=129.472000, rms=0.681 (0.078%), neg=0, invalid=762 0183: dt=129.472000, rms=0.681 (0.077%), neg=0, invalid=762 0184: dt=129.472000, rms=0.680 (0.072%), neg=0, invalid=762 0185: dt=129.472000, rms=0.680 (0.069%), neg=0, invalid=762 0186: dt=129.472000, rms=0.679 (0.068%), neg=0, invalid=762 0187: dt=129.472000, rms=0.679 (0.069%), neg=0, invalid=762 0188: dt=129.472000, rms=0.678 (0.065%), neg=0, invalid=762 0189: dt=129.472000, rms=0.678 (0.063%), neg=0, invalid=762 0190: dt=129.472000, rms=0.678 (0.061%), neg=0, invalid=762 0191: dt=129.472000, rms=0.677 (0.059%), neg=0, invalid=762 0192: dt=129.472000, rms=0.677 (0.061%), neg=0, invalid=762 0193: dt=129.472000, rms=0.676 (0.054%), neg=0, invalid=762 0194: dt=129.472000, rms=0.676 (0.050%), neg=0, invalid=762 0195: dt=129.472000, rms=0.676 (0.052%), neg=0, invalid=762 0196: dt=129.472000, rms=0.675 (0.050%), neg=0, invalid=762 0197: dt=129.472000, rms=0.675 (0.047%), neg=0, invalid=762 0198: dt=129.472000, rms=0.675 (0.048%), neg=0, invalid=762 0199: dt=129.472000, rms=0.674 (0.045%), neg=0, invalid=762 0200: dt=129.472000, rms=0.674 (0.045%), neg=0, invalid=762 0201: dt=129.472000, rms=0.674 (0.046%), neg=0, invalid=762 0202: dt=129.472000, rms=0.674 (0.046%), neg=0, invalid=762 0203: dt=129.472000, rms=0.673 (0.043%), neg=0, invalid=762 0204: dt=129.472000, rms=0.673 (0.040%), neg=0, invalid=762 0205: dt=129.472000, rms=0.673 (0.047%), neg=0, invalid=762 0206: dt=129.472000, rms=0.672 (0.041%), neg=0, invalid=762 0207: dt=129.472000, rms=0.672 (0.038%), neg=0, invalid=762 0208: dt=129.472000, rms=0.672 (0.038%), neg=0, invalid=762 0209: dt=129.472000, rms=0.672 (0.037%), neg=0, invalid=762 0210: dt=129.472000, rms=0.671 (0.039%), neg=0, invalid=762 0211: dt=129.472000, rms=0.671 (0.039%), neg=0, invalid=762 0212: dt=129.472000, rms=0.671 (0.039%), neg=0, invalid=762 0213: dt=129.472000, rms=0.671 (0.036%), neg=0, invalid=762 0214: dt=129.472000, rms=0.670 (0.035%), neg=0, invalid=762 0215: dt=129.472000, rms=0.670 (0.035%), neg=0, invalid=762 0216: dt=129.472000, rms=0.670 (0.034%), neg=0, invalid=762 0217: dt=129.472000, rms=0.670 (0.034%), neg=0, invalid=762 0218: dt=129.472000, rms=0.669 (0.034%), neg=0, invalid=762 0219: dt=129.472000, rms=0.669 (0.034%), neg=0, invalid=762 0220: dt=129.472000, rms=0.669 (0.034%), neg=0, invalid=762 0221: dt=129.472000, rms=0.669 (0.033%), neg=0, invalid=762 0222: dt=129.472000, rms=0.669 (0.032%), neg=0, invalid=762 0223: dt=129.472000, rms=0.668 (0.031%), neg=0, invalid=762 0224: dt=129.472000, rms=0.668 (0.032%), neg=0, invalid=762 0225: dt=129.472000, rms=0.668 (0.033%), neg=0, invalid=762 0226: dt=129.472000, rms=0.668 (0.031%), neg=0, invalid=762 0227: dt=129.472000, rms=0.667 (0.032%), neg=0, invalid=762 0228: dt=129.472000, rms=0.667 (0.027%), neg=0, invalid=762 0229: dt=129.472000, rms=0.667 (0.029%), neg=0, invalid=762 0230: dt=129.472000, rms=0.667 (0.028%), neg=0, invalid=762 0231: dt=129.472000, rms=0.667 (0.027%), neg=0, invalid=762 0232: dt=129.472000, rms=0.667 (0.027%), neg=0, invalid=762 0233: dt=129.472000, rms=0.666 (0.029%), neg=0, invalid=762 0234: dt=129.472000, rms=0.666 (0.029%), neg=0, invalid=762 0235: dt=129.472000, rms=0.666 (0.028%), neg=0, invalid=762 0236: dt=129.472000, rms=0.666 (0.026%), neg=0, invalid=762 0237: dt=129.472000, rms=0.666 (0.028%), neg=0, invalid=762 0238: dt=129.472000, rms=0.665 (0.026%), neg=0, invalid=762 0239: dt=129.472000, rms=0.665 (0.025%), neg=0, invalid=762 0240: dt=129.472000, rms=0.665 (0.028%), neg=0, invalid=762 0241: dt=129.472000, rms=0.665 (0.023%), neg=0, invalid=762 0242: dt=129.472000, rms=0.665 (0.026%), neg=0, invalid=762 0243: dt=129.472000, rms=0.665 (0.028%), neg=0, invalid=762 0244: dt=129.472000, rms=0.664 (0.024%), neg=0, invalid=762 0245: dt=129.472000, rms=0.664 (0.019%), neg=0, invalid=762 0246: dt=4734.976000, rms=0.664 (0.056%), neg=0, invalid=762 0247: dt=92.480000, rms=0.664 (0.038%), neg=0, invalid=762 0248: dt=92.480000, rms=0.664 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0249: dt=129.472000, rms=0.663 (0.246%), neg=0, invalid=762 0250: dt=443.904000, rms=0.662 (0.121%), neg=0, invalid=762 0251: dt=32.368000, rms=0.662 (-0.002%), neg=0, invalid=762 0252: dt=32.368000, rms=0.662 (0.001%), neg=0, invalid=762 0253: dt=32.368000, rms=0.662 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.666, neg=0, invalid=762 0254: dt=169.004329, rms=0.659 (1.041%), neg=0, invalid=762 0255: dt=168.341232, rms=0.648 (1.632%), neg=0, invalid=762 0256: dt=64.257028, rms=0.643 (0.697%), neg=0, invalid=762 0257: dt=580.608000, rms=0.632 (1.764%), neg=0, invalid=762 0258: dt=62.211180, rms=0.623 (1.429%), neg=0, invalid=762 0259: dt=145.152000, rms=0.620 (0.476%), neg=0, invalid=762 0260: dt=65.090909, rms=0.619 (0.252%), neg=0, invalid=762 0261: dt=145.152000, rms=0.616 (0.344%), neg=0, invalid=762 0262: dt=91.773585, rms=0.615 (0.218%), neg=0, invalid=762 0263: dt=103.680000, rms=0.614 (0.245%), neg=0, invalid=762 0264: dt=76.663102, rms=0.612 (0.199%), neg=0, invalid=762 0265: dt=145.152000, rms=0.611 (0.243%), neg=0, invalid=762 0266: dt=36.288000, rms=0.610 (0.168%), neg=0, invalid=762 0267: dt=331.776000, rms=0.608 (0.352%), neg=0, invalid=762 0268: dt=36.288000, rms=0.606 (0.314%), neg=0, invalid=762 0269: dt=145.152000, rms=0.605 (0.212%), neg=0, invalid=762 0270: dt=64.338624, rms=0.604 (0.142%), neg=0, invalid=762 0271: dt=145.152000, rms=0.602 (0.210%), neg=0, invalid=762 0272: dt=82.944000, rms=0.602 (0.109%), neg=0, invalid=762 0273: dt=124.416000, rms=0.601 (0.152%), neg=0, invalid=762 0274: dt=36.288000, rms=0.600 (0.099%), neg=0, invalid=762 0275: dt=414.720000, rms=0.599 (0.279%), neg=0, invalid=762 0276: dt=69.925926, rms=0.597 (0.269%), neg=0, invalid=762 0277: dt=36.288000, rms=0.596 (0.090%), neg=0, invalid=762 0278: dt=414.720000, rms=0.595 (0.239%), neg=0, invalid=762 0279: dt=36.288000, rms=0.594 (0.197%), neg=0, invalid=762 0280: dt=145.152000, rms=0.593 (0.137%), neg=0, invalid=762 0281: dt=62.208000, rms=0.593 (0.079%), neg=0, invalid=762 0282: dt=248.832000, rms=0.592 (0.144%), neg=0, invalid=762 0283: dt=36.288000, rms=0.591 (0.106%), neg=0, invalid=762 0284: dt=145.152000, rms=0.591 (0.093%), neg=0, invalid=762 0285: dt=82.944000, rms=0.590 (0.072%), neg=0, invalid=762 0286: dt=82.944000, rms=0.590 (0.063%), neg=0, invalid=762 0287: dt=103.680000, rms=0.589 (0.079%), neg=0, invalid=762 0288: dt=62.208000, rms=0.589 (0.054%), neg=0, invalid=762 0289: dt=248.832000, rms=0.588 (0.137%), neg=0, invalid=762 0290: dt=36.288000, rms=0.588 (0.077%), neg=0, invalid=762 0291: dt=145.152000, rms=0.587 (0.072%), neg=0, invalid=762 0292: dt=82.944000, rms=0.587 (0.071%), neg=0, invalid=762 0293: dt=82.944000, rms=0.587 (0.045%), neg=0, invalid=762 0294: dt=82.944000, rms=0.586 (0.066%), neg=0, invalid=762 0295: dt=82.944000, rms=0.586 (0.103%), neg=0, invalid=762 0296: dt=82.944000, rms=0.585 (0.132%), neg=0, invalid=762 0297: dt=82.944000, rms=0.584 (0.169%), neg=0, invalid=762 0298: dt=82.944000, rms=0.583 (0.207%), neg=0, invalid=762 0299: dt=82.944000, rms=0.581 (0.225%), neg=0, invalid=762 0300: dt=82.944000, rms=0.580 (0.220%), neg=0, invalid=762 0301: dt=82.944000, rms=0.579 (0.228%), neg=0, invalid=762 0302: dt=82.944000, rms=0.577 (0.241%), neg=0, invalid=762 0303: dt=82.944000, rms=0.576 (0.238%), neg=0, invalid=762 0304: dt=82.944000, rms=0.575 (0.222%), neg=0, invalid=762 0305: dt=82.944000, rms=0.573 (0.218%), neg=0, invalid=762 0306: dt=82.944000, rms=0.572 (0.223%), neg=0, invalid=762 0307: dt=82.944000, rms=0.571 (0.197%), neg=0, invalid=762 0308: dt=82.944000, rms=0.570 (0.185%), neg=0, invalid=762 0309: dt=82.944000, rms=0.569 (0.179%), neg=0, invalid=762 0310: dt=82.944000, rms=0.568 (0.179%), neg=0, invalid=762 0311: dt=82.944000, rms=0.567 (0.175%), neg=0, invalid=762 0312: dt=82.944000, rms=0.566 (0.156%), neg=0, invalid=762 0313: dt=82.944000, rms=0.565 (0.148%), neg=0, invalid=762 0314: dt=82.944000, rms=0.564 (0.143%), neg=0, invalid=762 0315: dt=82.944000, rms=0.564 (0.135%), neg=0, invalid=762 0316: dt=82.944000, rms=0.563 (0.120%), neg=0, invalid=762 0317: dt=82.944000, rms=0.562 (0.125%), neg=0, invalid=762 0318: dt=82.944000, rms=0.562 (0.121%), neg=0, invalid=762 0319: dt=82.944000, rms=0.561 (0.113%), neg=0, invalid=762 0320: dt=82.944000, rms=0.560 (0.097%), neg=0, invalid=762 0321: dt=82.944000, rms=0.560 (0.093%), neg=0, invalid=762 0322: dt=82.944000, rms=0.559 (0.104%), neg=0, invalid=762 0323: dt=82.944000, rms=0.559 (0.094%), neg=0, invalid=762 0324: dt=82.944000, rms=0.558 (0.084%), neg=0, invalid=762 0325: dt=82.944000, rms=0.558 (0.069%), neg=0, invalid=762 0326: dt=82.944000, rms=0.557 (0.072%), neg=0, invalid=762 0327: dt=82.944000, rms=0.557 (0.075%), neg=0, invalid=762 0328: dt=82.944000, rms=0.557 (0.069%), neg=0, invalid=762 0329: dt=82.944000, rms=0.556 (0.063%), neg=0, invalid=762 0330: dt=82.944000, rms=0.556 (0.063%), neg=0, invalid=762 0331: dt=82.944000, rms=0.556 (0.057%), neg=0, invalid=762 0332: dt=82.944000, rms=0.555 (0.058%), neg=0, invalid=762 0333: dt=82.944000, rms=0.555 (0.056%), neg=0, invalid=762 0334: dt=82.944000, rms=0.555 (0.064%), neg=0, invalid=762 0335: dt=82.944000, rms=0.554 (0.052%), neg=0, invalid=762 0336: dt=82.944000, rms=0.554 (0.039%), neg=0, invalid=762 0337: dt=82.944000, rms=0.554 (0.037%), neg=0, invalid=762 0338: dt=82.944000, rms=0.554 (0.046%), neg=0, invalid=762 0339: dt=82.944000, rms=0.553 (0.045%), neg=0, invalid=762 0340: dt=82.944000, rms=0.553 (0.036%), neg=0, invalid=762 0341: dt=82.944000, rms=0.553 (0.034%), neg=0, invalid=762 0342: dt=82.944000, rms=0.553 (0.038%), neg=0, invalid=762 0343: dt=82.944000, rms=0.553 (0.039%), neg=0, invalid=762 0344: dt=82.944000, rms=0.552 (0.035%), neg=0, invalid=762 0345: dt=82.944000, rms=0.552 (0.027%), neg=0, invalid=762 0346: dt=82.944000, rms=0.552 (0.028%), neg=0, invalid=762 0347: dt=82.944000, rms=0.552 (0.036%), neg=0, invalid=762 0348: dt=82.944000, rms=0.552 (0.035%), neg=0, invalid=762 0349: dt=82.944000, rms=0.552 (0.027%), neg=0, invalid=762 0350: dt=82.944000, rms=0.551 (0.027%), neg=0, invalid=762 0351: dt=82.944000, rms=0.551 (0.033%), neg=0, invalid=762 0352: dt=82.944000, rms=0.551 (0.034%), neg=0, invalid=762 0353: dt=82.944000, rms=0.551 (0.022%), neg=0, invalid=762 0354: dt=82.944000, rms=0.551 (0.017%), neg=0, invalid=762 0355: dt=82.944000, rms=0.551 (0.016%), neg=0, invalid=762 0356: dt=82.944000, rms=0.551 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0357: dt=96.214765, rms=0.549 (0.463%), neg=0, invalid=762 0358: dt=103.680000, rms=0.549 (0.106%), neg=0, invalid=762 0359: dt=36.288000, rms=0.549 (0.019%), neg=0, invalid=762 0360: dt=36.288000, rms=0.549 (0.021%), neg=0, invalid=762 0361: dt=36.288000, rms=0.549 (0.027%), neg=0, invalid=762 0362: dt=36.288000, rms=0.548 (0.033%), neg=0, invalid=762 0363: dt=36.288000, rms=0.548 (0.031%), neg=0, invalid=762 0364: dt=36.288000, rms=0.548 (0.028%), neg=0, invalid=762 0365: dt=36.288000, rms=0.548 (0.026%), neg=0, invalid=762 0366: dt=36.288000, rms=0.548 (0.026%), neg=0, invalid=762 0367: dt=36.288000, rms=0.548 (0.022%), neg=0, invalid=762 0368: dt=36.288000, rms=0.547 (0.026%), neg=0, invalid=762 0369: dt=36.288000, rms=0.547 (0.023%), neg=0, invalid=762 0370: dt=36.288000, rms=0.547 (0.030%), neg=0, invalid=762 0371: dt=36.288000, rms=0.547 (0.037%), neg=0, invalid=762 0372: dt=36.288000, rms=0.547 (0.043%), neg=0, invalid=762 0373: dt=36.288000, rms=0.547 (0.041%), neg=0, invalid=762 0374: dt=36.288000, rms=0.546 (0.044%), neg=0, invalid=762 0375: dt=36.288000, rms=0.546 (0.040%), neg=0, invalid=762 0376: dt=36.288000, rms=0.546 (0.038%), neg=0, invalid=762 0377: dt=36.288000, rms=0.546 (0.039%), neg=0, invalid=762 0378: dt=36.288000, rms=0.545 (0.039%), neg=0, invalid=762 0379: dt=36.288000, rms=0.545 (0.038%), neg=0, invalid=762 0380: dt=36.288000, rms=0.545 (0.033%), neg=0, invalid=762 0381: dt=36.288000, rms=0.545 (0.031%), neg=0, invalid=762 0382: dt=36.288000, rms=0.545 (0.030%), neg=0, invalid=762 0383: dt=36.288000, rms=0.545 (0.029%), neg=0, invalid=762 0384: dt=36.288000, rms=0.544 (0.031%), neg=0, invalid=762 0385: dt=36.288000, rms=0.544 (0.026%), neg=0, invalid=762 0386: dt=36.288000, rms=0.544 (0.027%), neg=0, invalid=762 0387: dt=36.288000, rms=0.544 (0.025%), neg=0, invalid=762 0388: dt=36.288000, rms=0.544 (0.024%), neg=0, invalid=762 0389: dt=36.288000, rms=0.544 (0.023%), neg=0, invalid=762 0390: dt=248.832000, rms=0.544 (0.012%), neg=0, invalid=762 0391: dt=248.832000, rms=0.544 (-0.043%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 0392: dt=32.000000, rms=0.555 (0.491%), neg=0, invalid=762 0393: dt=115.508434, rms=0.551 (0.893%), neg=0, invalid=762 0394: dt=101.734104, rms=0.543 (1.318%), neg=0, invalid=762 0395: dt=32.000000, rms=0.539 (0.804%), neg=0, invalid=762 0396: dt=44.800000, rms=0.537 (0.300%), neg=0, invalid=762 0397: dt=44.800000, rms=0.535 (0.379%), neg=0, invalid=762 0398: dt=44.800000, rms=0.534 (0.264%), neg=0, invalid=762 0399: dt=38.400000, rms=0.532 (0.262%), neg=0, invalid=762 0400: dt=38.400000, rms=0.531 (0.262%), neg=0, invalid=762 0401: dt=32.000000, rms=0.530 (0.190%), neg=0, invalid=762 0402: dt=44.800000, rms=0.529 (0.237%), neg=0, invalid=762 0403: dt=25.600000, rms=0.528 (0.152%), neg=0, invalid=762 0404: dt=102.400000, rms=0.526 (0.286%), neg=0, invalid=762 0405: dt=28.217252, rms=0.525 (0.261%), neg=0, invalid=762 0406: dt=102.400000, rms=0.523 (0.324%), neg=0, invalid=762 0407: dt=25.600000, rms=0.522 (0.215%), neg=0, invalid=762 0408: dt=44.800000, rms=0.521 (0.145%), neg=0, invalid=762 0409: dt=44.800000, rms=0.521 (0.122%), neg=0, invalid=762 0410: dt=32.000000, rms=0.520 (0.111%), neg=0, invalid=762 0411: dt=32.000000, rms=0.520 (0.084%), neg=0, invalid=762 0412: dt=32.000000, rms=0.519 (0.102%), neg=0, invalid=762 0413: dt=32.000000, rms=0.519 (0.066%), neg=0, invalid=762 0414: dt=32.000000, rms=0.518 (0.098%), neg=0, invalid=762 0415: dt=25.600000, rms=0.518 (0.056%), neg=0, invalid=762 0416: dt=44.800000, rms=0.518 (0.115%), neg=0, invalid=762 0417: dt=25.600000, rms=0.517 (0.040%), neg=0, invalid=762 0418: dt=25.600000, rms=0.517 (0.087%), neg=0, invalid=762 0419: dt=25.600000, rms=0.516 (0.106%), neg=0, invalid=762 0420: dt=25.600000, rms=0.516 (0.145%), neg=0, invalid=762 0421: dt=25.600000, rms=0.515 (0.190%), neg=0, invalid=762 0422: dt=25.600000, rms=0.514 (0.212%), neg=0, invalid=762 0423: dt=25.600000, rms=0.512 (0.221%), neg=0, invalid=762 0424: dt=25.600000, rms=0.511 (0.230%), neg=0, invalid=762 0425: dt=25.600000, rms=0.510 (0.244%), neg=0, invalid=762 0426: dt=25.600000, rms=0.509 (0.229%), neg=0, invalid=762 0427: dt=25.600000, rms=0.509 (0.012%), neg=0, invalid=762 0428: dt=25.600000, rms=0.508 (0.056%), neg=0, invalid=762 0429: dt=25.600000, rms=0.508 (0.016%), neg=0, invalid=762 0430: dt=12.800000, rms=0.508 (0.007%), neg=0, invalid=762 0431: dt=11.200000, rms=0.508 (0.011%), neg=0, invalid=762 0432: dt=0.500000, rms=0.508 (0.000%), neg=0, invalid=762 0433: dt=0.062500, rms=0.508 (0.000%), neg=0, invalid=762 0434: dt=0.015625, rms=0.508 (0.000%), neg=0, invalid=762 0435: dt=0.003906, rms=0.508 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 0436: dt=38.400000, rms=0.507 (0.434%), neg=0, invalid=762 0437: dt=44.800000, rms=0.506 (0.113%), neg=0, invalid=762 0438: dt=44.800000, rms=0.506 (0.068%), neg=0, invalid=762 0439: dt=44.800000, rms=0.506 (0.080%), neg=0, invalid=762 0440: dt=11.200000, rms=0.506 (0.019%), neg=0, invalid=762 0441: dt=11.200000, rms=0.506 (0.011%), neg=0, invalid=762 0442: dt=11.200000, rms=0.505 (0.022%), neg=0, invalid=762 0443: dt=11.200000, rms=0.505 (0.039%), neg=0, invalid=762 0444: dt=11.200000, rms=0.505 (0.053%), neg=0, invalid=762 0445: dt=11.200000, rms=0.505 (0.061%), neg=0, invalid=762 0446: dt=11.200000, rms=0.504 (0.065%), neg=0, invalid=762 0447: dt=11.200000, rms=0.504 (0.061%), neg=0, invalid=762 0448: dt=11.200000, rms=0.504 (0.062%), neg=0, invalid=762 0449: dt=11.200000, rms=0.503 (0.066%), neg=0, invalid=762 0450: dt=11.200000, rms=0.503 (0.071%), neg=0, invalid=762 0451: dt=11.200000, rms=0.503 (0.071%), neg=0, invalid=762 0452: dt=11.200000, rms=0.502 (0.075%), neg=0, invalid=762 0453: dt=11.200000, rms=0.502 (0.074%), neg=0, invalid=762 0454: dt=11.200000, rms=0.502 (0.075%), neg=0, invalid=762 0455: dt=11.200000, rms=0.501 (0.071%), neg=0, invalid=762 0456: dt=11.200000, rms=0.501 (0.071%), neg=0, invalid=762 0457: dt=11.200000, rms=0.500 (0.072%), neg=0, invalid=762 0458: dt=11.200000, rms=0.500 (0.070%), neg=0, invalid=762 0459: dt=11.200000, rms=0.500 (0.067%), neg=0, invalid=762 0460: dt=11.200000, rms=0.499 (0.058%), neg=0, invalid=762 0461: dt=11.200000, rms=0.499 (0.062%), neg=0, invalid=762 0462: dt=11.200000, rms=0.499 (0.069%), neg=0, invalid=762 0463: dt=11.200000, rms=0.498 (0.077%), neg=0, invalid=762 0464: dt=11.200000, rms=0.498 (0.076%), neg=0, invalid=762 0465: dt=11.200000, rms=0.498 (0.067%), neg=0, invalid=762 0466: dt=11.200000, rms=0.497 (0.064%), neg=0, invalid=762 0467: dt=11.200000, rms=0.497 (0.060%), neg=0, invalid=762 0468: dt=11.200000, rms=0.497 (0.063%), neg=0, invalid=762 0469: dt=11.200000, rms=0.496 (0.058%), neg=0, invalid=762 0470: dt=11.200000, rms=0.496 (0.060%), neg=0, invalid=762 0471: dt=11.200000, rms=0.496 (0.053%), neg=0, invalid=762 0472: dt=11.200000, rms=0.496 (0.054%), neg=0, invalid=762 0473: dt=11.200000, rms=0.495 (0.053%), neg=0, invalid=762 0474: dt=11.200000, rms=0.495 (0.051%), neg=0, invalid=762 0475: dt=11.200000, rms=0.495 (0.051%), neg=0, invalid=762 0476: dt=11.200000, rms=0.495 (0.039%), neg=0, invalid=762 0477: dt=11.200000, rms=0.495 (0.034%), neg=0, invalid=762 0478: dt=11.200000, rms=0.494 (0.031%), neg=0, invalid=762 0479: dt=11.200000, rms=0.494 (0.027%), neg=0, invalid=762 0480: dt=11.200000, rms=0.494 (0.029%), neg=0, invalid=762 0481: dt=11.200000, rms=0.494 (0.029%), neg=0, invalid=762 0482: dt=11.200000, rms=0.494 (0.031%), neg=0, invalid=762 0483: dt=11.200000, rms=0.494 (0.031%), neg=0, invalid=762 0484: dt=11.200000, rms=0.494 (0.029%), neg=0, invalid=762 0485: dt=11.200000, rms=0.493 (0.038%), neg=0, invalid=762 0486: dt=11.200000, rms=0.493 (0.035%), neg=0, invalid=762 0487: dt=11.200000, rms=0.493 (0.036%), neg=0, invalid=762 0488: dt=11.200000, rms=0.493 (0.035%), neg=0, invalid=762 0489: dt=11.200000, rms=0.493 (0.037%), neg=0, invalid=762 0490: dt=11.200000, rms=0.492 (0.037%), neg=0, invalid=762 0491: dt=11.200000, rms=0.492 (0.035%), neg=0, invalid=762 0492: dt=11.200000, rms=0.492 (0.031%), neg=0, invalid=762 0493: dt=11.200000, rms=0.492 (0.025%), neg=0, invalid=762 0494: dt=11.200000, rms=0.492 (0.024%), neg=0, invalid=762 0495: dt=11.200000, rms=0.492 (0.026%), neg=0, invalid=762 0496: dt=11.200000, rms=0.492 (0.025%), neg=0, invalid=762 0497: dt=11.200000, rms=0.492 (0.020%), neg=0, invalid=762 0498: dt=11.200000, rms=0.491 (0.023%), neg=0, invalid=762 0499: dt=11.200000, rms=0.491 (0.021%), neg=0, invalid=762 0500: dt=11.200000, rms=0.491 (0.001%), neg=0, invalid=762 0501: dt=11.200000, rms=0.491 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0502: dt=0.000000, rms=0.518 (0.160%), neg=0, invalid=762 0503: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 0504: dt=0.150000, rms=0.518 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0505: dt=0.000000, rms=0.518 (0.160%), neg=0, invalid=762 0506: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762 0507: dt=0.150000, rms=0.518 (-0.043%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.573, neg=0, invalid=762 0508: dt=0.448000, rms=0.571 (0.274%), neg=0, invalid=762 0509: dt=0.112000, rms=0.571 (0.009%), neg=0, invalid=762 0510: dt=0.112000, rms=0.571 (0.001%), neg=0, invalid=762 0511: dt=0.112000, rms=0.571 (-0.021%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=762 0512: dt=0.112000, rms=0.571 (0.139%), neg=0, invalid=762 0513: dt=0.096000, rms=0.571 (0.003%), neg=0, invalid=762 0514: dt=0.096000, rms=0.571 (-0.002%), 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=0.491, neg=0, invalid=762 0515: dt=0.448000, rms=0.476 (3.116%), neg=0, invalid=762 0516: dt=0.448000, rms=0.473 (0.702%), neg=0, invalid=762 0517: dt=0.448000, rms=0.471 (0.392%), neg=0, invalid=762 0518: dt=0.448000, rms=0.470 (0.233%), neg=0, invalid=762 0519: dt=0.448000, rms=0.469 (0.175%), neg=0, invalid=762 0520: dt=0.448000, rms=0.468 (0.117%), neg=0, invalid=762 0521: dt=0.448000, rms=0.468 (0.104%), neg=0, invalid=762 0522: dt=0.448000, rms=0.468 (0.069%), neg=0, invalid=762 0523: dt=0.448000, rms=0.467 (0.071%), neg=0, invalid=762 0524: dt=0.448000, rms=0.467 (0.047%), neg=0, invalid=762 0525: dt=0.448000, rms=0.467 (0.049%), neg=0, invalid=762 0526: dt=0.448000, rms=0.467 (0.034%), neg=0, invalid=762 0527: dt=0.448000, rms=0.467 (0.037%), neg=0, invalid=762 0528: dt=0.448000, rms=0.466 (0.061%), neg=0, invalid=762 0529: dt=0.448000, rms=0.466 (0.021%), neg=0, invalid=762 0530: dt=0.448000, rms=0.466 (0.045%), neg=0, invalid=762 0531: dt=0.448000, rms=0.466 (0.020%), neg=0, invalid=762 0532: dt=0.448000, rms=0.466 (0.009%), neg=0, invalid=762 0533: dt=0.384000, rms=0.466 (0.015%), neg=0, invalid=762 0534: dt=0.320000, rms=0.466 (0.010%), neg=0, invalid=762 0535: dt=0.320000, rms=0.466 (0.018%), neg=0, invalid=762 0536: dt=0.320000, rms=0.466 (0.017%), neg=0, invalid=762 0537: dt=0.320000, rms=0.465 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0538: dt=0.384000, rms=0.462 (0.904%), neg=0, invalid=762 0539: dt=0.384000, rms=0.462 (0.143%), neg=0, invalid=762 0540: dt=0.384000, rms=0.461 (0.037%), neg=0, invalid=762 0541: dt=0.384000, rms=0.461 (0.009%), neg=0, invalid=762 0542: dt=0.384000, rms=0.461 (0.004%), neg=0, invalid=762 0543: dt=0.384000, rms=0.461 (0.003%), neg=0, invalid=762 0544: dt=0.256000, rms=0.461 (0.004%), neg=0, invalid=762 0545: dt=0.384000, rms=0.461 (0.010%), neg=0, invalid=762 0546: dt=0.256000, rms=0.461 (0.001%), 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=0.460, neg=0, invalid=762 0547: dt=0.027094, rms=0.459 (0.202%), neg=0, invalid=762 0548: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 0549: dt=221.952000, rms=0.459 (0.267%), neg=0, invalid=762 0550: dt=92.480000, rms=0.459 (0.021%), neg=0, invalid=762 0551: dt=92.480000, rms=0.459 (0.004%), neg=0, invalid=762 0552: dt=92.480000, rms=0.459 (0.024%), neg=0, invalid=762 0553: dt=92.480000, rms=0.459 (0.032%), neg=0, invalid=762 0554: dt=92.480000, rms=0.459 (0.025%), neg=0, invalid=762 0555: dt=92.480000, rms=0.458 (0.013%), neg=0, invalid=762 0556: dt=92.480000, rms=0.458 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0557: dt=24.888889, rms=0.458 (0.243%), neg=0, invalid=762 0558: dt=20.736000, rms=0.458 (0.012%), neg=0, invalid=762 0559: dt=20.736000, rms=0.458 (0.007%), neg=0, invalid=762 0560: dt=20.736000, rms=0.458 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0561: dt=88.994083, rms=0.457 (0.496%), neg=0, invalid=762 0562: dt=36.288000, rms=0.456 (0.115%), neg=0, invalid=762 0563: dt=36.288000, rms=0.456 (0.044%), neg=0, invalid=762 0564: dt=36.288000, rms=0.456 (0.074%), neg=0, invalid=762 0565: dt=36.288000, rms=0.455 (0.117%), neg=0, invalid=762 0566: dt=36.288000, rms=0.455 (0.124%), neg=0, invalid=762 0567: dt=36.288000, rms=0.454 (0.112%), neg=0, invalid=762 0568: dt=36.288000, rms=0.454 (0.099%), neg=0, invalid=762 0569: dt=62.208000, rms=0.454 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0570: dt=38.400000, rms=0.451 (0.751%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0571: dt=38.400000, rms=0.450 (0.362%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0572: dt=23.591241, rms=0.449 (0.215%), neg=0, invalid=762 0573: dt=23.591241, rms=0.448 (0.229%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0574: dt=23.591241, rms=0.447 (0.218%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0575: dt=23.591241, rms=0.446 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0576: dt=23.591241, rms=0.445 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=0, neg = 0 0577: dt=23.591241, rms=0.444 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0578: dt=23.591241, rms=0.444 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 8 iterations, nbhd size=0, neg = 0 0579: dt=23.591241, rms=0.443 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 15 iterations, nbhd size=1, neg = 0 0580: dt=23.591241, rms=0.443 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0581: dt=44.800000, rms=0.442 (0.116%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0582: dt=25.600000, rms=0.442 (0.045%), neg=0, invalid=762 0583: dt=25.600000, rms=0.442 (0.040%), neg=0, invalid=762 0584: dt=25.600000, rms=0.442 (0.066%), neg=0, invalid=762 0585: dt=25.600000, rms=0.441 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0586: dt=25.600000, rms=0.441 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0587: dt=25.600000, rms=0.441 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0588: dt=25.600000, rms=0.440 (0.084%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0589: dt=25.600000, rms=0.440 (0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0590: dt=44.800000, rms=0.438 (0.785%), neg=0, invalid=762 0591: dt=21.497436, rms=0.437 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0592: dt=21.497436, rms=0.436 (0.095%), neg=0, invalid=762 0593: dt=21.497436, rms=0.436 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0594: dt=21.497436, rms=0.435 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0595: dt=21.497436, rms=0.435 (0.100%), neg=0, invalid=762 0596: dt=21.497436, rms=0.434 (0.085%), neg=0, invalid=762 0597: dt=19.200000, rms=0.434 (0.054%), neg=0, invalid=762 0598: dt=19.200000, rms=0.434 (0.031%), neg=0, invalid=762 0599: dt=19.200000, rms=0.434 (0.041%), neg=0, invalid=762 0600: dt=19.200000, rms=0.434 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0601: dt=19.200000, rms=0.433 (0.046%), neg=0, invalid=762 0602: dt=19.200000, rms=0.433 (0.031%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0603: dt=1.008000, rms=0.437 (0.225%), neg=0, invalid=762 0604: dt=0.864000, rms=0.437 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0605: dt=4.307692, rms=0.437 (0.262%), neg=0, invalid=762 0606: dt=5.714286, rms=0.437 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0607: dt=5.714286, rms=0.436 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0608: dt=5.714286, rms=0.436 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0609: dt=5.714286, rms=0.436 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 193 after 15 iterations, nbhd size=1, neg = 0 0610: dt=116.682105, rms=0.427 (2.088%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0611: dt=3.642857, rms=0.427 (0.051%), neg=0, invalid=762 0612: dt=3.642857, rms=0.427 (0.009%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0613: dt=3.642857, rms=0.427 (-0.168%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0614: dt=0.000000, rms=0.432 (0.257%), neg=0, invalid=762 0615: dt=0.000000, rms=0.432 (0.000%), neg=0, invalid=762 0616: dt=0.100000, rms=0.432 (-0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.433, neg=0, invalid=762 0617: dt=0.000000, rms=0.432 (0.257%), neg=0, invalid=762 0618: dt=0.000000, rms=0.432 (0.000%), neg=0, invalid=762 0619: dt=0.100000, rms=0.432 (-0.050%), 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=0.424, neg=0, invalid=762 iter 0, gcam->neg = 1087 after 18 iterations, nbhd size=1, neg = 0 0620: dt=1.716891, rms=0.400 (5.630%), neg=0, invalid=762 0621: dt=0.000013, rms=0.400 (0.023%), neg=0, invalid=762 0622: dt=0.000013, rms=0.400 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0623: dt=0.000000, rms=0.400 (0.287%), neg=0, invalid=762 0624: dt=0.000000, rms=0.400 (0.000%), neg=0, invalid=762 0625: dt=0.050000, rms=0.400 (-0.022%), 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=0.389, neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0626: dt=23.120000, rms=0.389 (0.012%), neg=0, invalid=762 0627: dt=1.734000, rms=0.389 (0.000%), neg=0, invalid=762 0628: dt=1.734000, rms=0.389 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=762 0629: dt=92.480000, rms=0.389 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0630: dt=129.472000, rms=0.389 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0631: dt=129.472000, rms=0.389 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0632: dt=6.480000, rms=0.389 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0633: dt=82.944000, rms=0.389 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0634: dt=124.416000, rms=0.389 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0635: dt=124.416000, rms=0.389 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=762 iter 0, gcam->neg = 15 after 11 iterations, nbhd size=1, neg = 0 0636: dt=11.200000, rms=0.390 (0.028%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0637: dt=8.000000, rms=0.390 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0638: dt=8.000000, rms=0.390 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=762 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 0639: dt=44.800000, rms=0.388 (0.337%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 2 iterations, nbhd size=0, neg = 0 0640: dt=44.800000, rms=0.388 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0641: dt=44.800000, rms=0.387 (0.094%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 8 iterations, nbhd size=1, neg = 0 0642: dt=44.800000, rms=0.387 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 3 iterations, nbhd size=0, neg = 0 0643: dt=44.800000, rms=0.386 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 41 after 15 iterations, nbhd size=1, neg = 0 0644: dt=44.800000, rms=0.386 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 38 after 17 iterations, nbhd size=1, neg = 0 0645: dt=44.800000, rms=0.386 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0646: dt=44.800000, rms=0.386 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0647: dt=44.800000, rms=0.385 (0.076%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0648: dt=44.800000, rms=0.385 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 2 iterations, nbhd size=0, neg = 0 0649: dt=44.800000, rms=0.385 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0650: dt=44.800000, rms=0.385 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 10 iterations, nbhd size=0, neg = 0 0651: dt=44.800000, rms=0.385 (0.042%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.387, neg=0, invalid=762 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0652: dt=4.666667, rms=0.387 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=0, neg = 0 0653: dt=1.728000, rms=0.387 (0.002%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=0, neg = 0 0654: dt=1.728000, rms=0.387 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=762 iter 0, gcam->neg = 38 after 15 iterations, nbhd size=1, neg = 0 0655: dt=21.523810, rms=0.386 (0.261%), neg=0, invalid=762 iter 0, gcam->neg = 64 after 17 iterations, nbhd size=1, neg = 0 0656: dt=22.193548, rms=0.386 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 91 after 19 iterations, nbhd size=1, neg = 0 0657: dt=22.193548, rms=0.386 (-0.086%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=762 0658: dt=0.000078, rms=0.390 (0.000%), neg=0, invalid=762 0659: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=762 0660: dt=0.000000, rms=0.390 (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=0.382, neg=0, invalid=762 iter 0, gcam->neg = 662 after 17 iterations, nbhd size=1, neg = 0 0661: dt=0.893864, rms=0.375 (1.904%), neg=0, invalid=762 0662: dt=0.000040, rms=0.375 (0.000%), neg=0, invalid=762 0663: dt=0.000040, rms=0.375 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=762 0664: dt=0.112000, rms=0.375 (0.091%), neg=0, invalid=762 0665: dt=0.112000, rms=0.374 (0.054%), neg=0, invalid=762 0666: dt=0.112000, rms=0.374 (0.049%), neg=0, invalid=762 0667: dt=0.112000, rms=0.374 (0.050%), neg=0, invalid=762 0668: dt=0.112000, rms=0.374 (0.002%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 9 iterations, nbhd size=1, neg = 0 0669: dt=0.112000, rms=0.374 (-0.116%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 2 minutes and 57 seconds. mri_ca_register utimesec 10116.100000 mri_ca_register stimesec 2.732000 mri_ca_register ru_maxrss 1339356 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 1151045 mri_ca_register ru_majflt 66 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 12760 mri_ca_register ru_oublock 63032 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 72 mri_ca_register ru_nivcsw 600733 FSRUNTIME@ mri_ca_register 3.0491 hours 1 threads #-------------------------------------- #@# SubCort Seg 2018. 07. 09. (���) 15:56:17 KST mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz Could not set locale No such file or directory sysname Linux hostname kt-B85M-DS3H-A machine x86_64 setenv SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs cd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz Could not set locale == Number of threads available to mri_ca_label for OpenMP = 1 == Could not set locale 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 /home/kt/Downloads/freesurferDev/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 5.34 Atlas used for the 3D morph was /home/kt/Downloads/freesurferDev/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) mri peak = 0.12705 (16) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (9101 voxels, overlap=0.741) Left_Lateral_Ventricle (4): linear fit = 0.76 x + 0.0 (9101 voxels, peak = 15), gca=15.3 gca peak = 0.17677 (13) mri peak = 0.12823 (16) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (7686 voxels, overlap=0.744) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (7686 voxels, peak = 14), gca=14.5 gca peak = 0.28129 (95) mri peak = 0.09196 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (345 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (345 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.11248 (100) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (362 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (362 voxels, peak = 99), gca=99.4 gca peak = 0.24553 (55) mri peak = 0.09117 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (701 voxels, overlap=0.396) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (701 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.09311 (63) Left_Hippocampus (17): linear fit = 1.11 x + 0.0 (807 voxels, overlap=0.714) Left_Hippocampus (17): linear fit = 1.11 x + 0.0 (807 voxels, peak = 65), gca=65.2 gca peak = 0.07580 (103) mri peak = 0.07888 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (22079 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (22079 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.08602 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (22805 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (22805 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.04055 (70) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (19256 voxels, overlap=0.275) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (19256 voxels, peak = 70), gca=70.5 gca peak = 0.11620 (58) mri peak = 0.04153 (70) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (18457 voxels, overlap=0.321) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (18457 voxels, peak = 69), gca=69.3 gca peak = 0.30970 (66) mri peak = 0.10848 (78) Right_Caudate (50): linear fit = 1.17 x + 0.0 (684 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.17 x + 0.0 (684 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.12511 (80) Left_Caudate (11): linear fit = 1.10 x + 0.0 (547 voxels, overlap=0.506) Left_Caudate (11): linear fit = 1.10 x + 0.0 (547 voxels, peak = 76), gca=75.6 gca peak = 0.13902 (56) mri peak = 0.07049 (60) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (16691 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (16691 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.06432 (60) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17418 voxels, overlap=0.971) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17418 voxels, peak = 57), gca=57.5 gca peak = 0.16765 (84) mri peak = 0.10438 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4035 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4035 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.11771 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (3827 voxels, overlap=0.466) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (3827 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.11818 (66) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (437 voxels, overlap=0.786) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (437 voxels, peak = 64), gca=63.6 gca peak = 0.33601 (57) mri peak = 0.10897 (63) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (312 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (312 voxels, peak = 64), gca=63.6 gca peak = 0.11131 (90) mri peak = 0.07506 (88) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (2690 voxels, overlap=0.973) Left_Thalamus (10): linear fit = 1.02 x + 0.0 (2690 voxels, peak = 92), gca=92.2 gca peak = 0.11793 (83) mri peak = 0.07758 (90) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (2618 voxels, overlap=0.864) Right_Thalamus (49): linear fit = 1.09 x + 0.0 (2618 voxels, peak = 90), gca=90.1 gca peak = 0.08324 (81) mri peak = 0.08925 (80) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1042 voxels, overlap=0.851) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1042 voxels, peak = 83), gca=83.0 gca peak = 0.10360 (77) mri peak = 0.08582 (82) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1104 voxels, overlap=0.809) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1104 voxels, peak = 80), gca=79.7 gca peak = 0.08424 (78) mri peak = 0.07995 (86) Brain_Stem (16): linear fit = 1.11 x + 0.0 (8618 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (8618 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.08284 (98) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (875 voxels, overlap=0.085) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (875 voxels, peak = 102), gca=101.9 gca peak = 0.14500 (87) mri peak = 0.08686 (100) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (994 voxels, overlap=0.382) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (994 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.20219 (18) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (364 voxels, overlap=0.245) Third_Ventricle (14): linear fit = 0.69 x + 0.0 (364 voxels, peak = 17), gca=16.7 gca peak = 0.19357 (14) mri peak = 0.16993 (16) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (190 voxels, overlap=0.762) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (190 voxels, peak = 13), gca=12.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak = 1.00000 (94) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) 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_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) 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 1.15 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.88 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.18464 (14) mri peak = 0.12705 (16) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (9101 voxels, overlap=0.958) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (9101 voxels, peak = 14), gca=14.5 gca peak = 0.17084 (14) mri peak = 0.12823 (16) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (7686 voxels, overlap=0.656) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (7686 voxels, peak = 14), gca=14.5 gca peak = 0.29310 (100) mri peak = 0.09196 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (345 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (345 voxels, peak = 100), gca=100.5 gca peak = 0.16005 (100) mri peak = 0.11248 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (362 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (362 voxels, peak = 100), gca=100.5 gca peak = 0.26878 (63) mri peak = 0.09117 (64) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (701 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (701 voxels, peak = 62), gca=62.1 gca peak = 0.29271 (62) mri peak = 0.09311 (63) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (807 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (807 voxels, peak = 62), gca=62.0 gca peak = 0.07496 (106) mri peak = 0.07888 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22079 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (22079 voxels, peak = 105), gca=105.5 gca peak = 0.07686 (107) mri peak = 0.08602 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (22805 voxels, overlap=0.722) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (22805 voxels, peak = 107), gca=107.0 gca peak = 0.08093 (70) mri peak = 0.04055 (70) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (19256 voxels, overlap=0.959) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (19256 voxels, peak = 69), gca=69.0 gca peak = 0.09970 (69) mri peak = 0.04153 (70) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18457 voxels, overlap=0.951) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (18457 voxels, peak = 68), gca=68.0 gca peak = 0.22961 (78) mri peak = 0.10848 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (684 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.00 x + 0.0 (684 voxels, peak = 78), gca=78.0 gca peak = 0.12888 (75) mri peak = 0.12511 (80) Left_Caudate (11): linear fit = 1.01 x + 0.0 (547 voxels, overlap=0.880) Left_Caudate (11): linear fit = 1.01 x + 0.0 (547 voxels, peak = 76), gca=76.1 gca peak = 0.13179 (57) mri peak = 0.07049 (60) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (16691 voxels, overlap=0.965) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (16691 voxels, peak = 58), gca=58.4 gca peak = 0.14534 (57) mri peak = 0.06432 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (17418 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (17418 voxels, peak = 58), gca=58.4 gca peak = 0.15888 (90) mri peak = 0.10438 (88) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4035 voxels, overlap=0.959) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4035 voxels, peak = 89), gca=88.7 gca peak = 0.15228 (90) mri peak = 0.11771 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3827 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3827 voxels, peak = 90), gca=89.6 gca peak = 0.28722 (65) mri peak = 0.11818 (66) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (437 voxels, overlap=1.004) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (437 voxels, peak = 65), gca=65.0 gca peak = 0.29807 (64) mri peak = 0.10897 (63) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (312 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (312 voxels, peak = 64), gca=64.0 gca peak = 0.09953 (92) mri peak = 0.07506 (88) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (2690 voxels, overlap=0.989) Left_Thalamus (10): linear fit = 0.98 x + 0.0 (2690 voxels, peak = 90), gca=89.7 gca peak = 0.10688 (90) mri peak = 0.07758 (90) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (2618 voxels, overlap=0.929) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (2618 voxels, peak = 89), gca=88.7 gca peak = 0.09235 (77) mri peak = 0.08925 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1042 voxels, overlap=0.890) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1042 voxels, peak = 77), gca=77.0 gca peak = 0.10883 (78) mri peak = 0.08582 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1104 voxels, overlap=0.909) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1104 voxels, peak = 78), gca=78.0 gca peak = 0.07357 (86) mri peak = 0.07995 (86) Brain_Stem (16): linear fit = 1.01 x + 0.0 (8618 voxels, overlap=0.843) Brain_Stem (16): linear fit = 1.01 x + 0.0 (8618 voxels, peak = 87), gca=87.3 gca peak = 0.11812 (102) mri peak = 0.08284 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (875 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (875 voxels, peak = 102), gca=102.0 gca peak = 0.16586 (97) mri peak = 0.08686 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (994 voxels, overlap=0.882) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (994 voxels, peak = 97), gca=96.5 gca peak = 0.25345 (18) mri peak = 0.20219 (18) Third_Ventricle (14): linear fit = 1.08 x + 0.0 (364 voxels, overlap=0.866) Third_Ventricle (14): linear fit = 1.08 x + 0.0 (364 voxels, peak = 19), gca=19.4 gca peak = 0.19357 (13) mri peak = 0.16993 (16) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (190 voxels, overlap=0.791) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (190 voxels, peak = 13), gca=12.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16057 (30) gca peak = 0.36646 (104) gca peak CSF = 0.25869 (32) gca peak Left_Accumbens_area = 0.68543 (68) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (26) gca peak Right_Accumbens_area = 0.29771 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (28) gca peak WM_hypointensities = 0.08262 (78) gca peak non_WM_hypointensities = 0.11678 (56) gca peak Optic_Chiasm = 0.63186 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.03 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 37180 voxels changed in iteration 0 of unlikely voxel relabeling 213 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 30333 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 485 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 49123 changed. image ll: -2.078, PF=0.500 pass 2: 11818 changed. image ll: -2.077, PF=0.500 pass 3: 3404 changed. 25436 voxels changed in iteration 0 of unlikely voxel relabeling 239 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5166 voxels changed in iteration 0 of unlikely voxel relabeling 110 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4316 voxels changed in iteration 0 of unlikely voxel relabeling 47 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 3148 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 3 with volume 20879 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 622 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 116 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 2 with volume 18544 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 765 above threshold 100 - not erasing !!!!!!!!!! MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2327.164000 mri_ca_label stimesec 1.228000 mri_ca_label ru_maxrss 2102056 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 857490 mri_ca_label ru_majflt 33 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 152288 mri_ca_label ru_oublock 424 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 148 mri_ca_label ru_nivcsw 134221 auto-labeling took 39 minutes and 27 seconds. #-------------------------------------- #@# CC Seg 2018. 07. 09. (���) 16:35:45 KST mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/cc_up.lta 161019_x3DT1_SAG Could not set locale No such file or directory Could not set locale No such file or directory will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/transforms/cc_up.lta reading aseg from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.auto_noCCseg.mgz reading norm from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/norm.mgz 15644 voxels in left wm, 11407 in right wm, xrange [124, 129] searching rotation angles z=[-6 8], y=[-7 7] searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 global minimum found at slice 125.7, rotations (-0.24, 0.95) final transformation (x=125.7, yr=-0.237, zr=0.955): 0.99985 -0.01666 -0.00413 4.49499; 0.01666 0.99986 -0.00007 20.92754; 0.00413 -0.00000 0.99999 21.48192; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 127 cc center is found at 127 105 106 eigenvectors: 0.00200 0.00449 0.99999; 0.09444 -0.99552 0.00428; 0.99553 0.09443 -0.00242; error in mid anterior detected - correcting... writing aseg with callosum to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg 2018. 07. 09. (���) 16:36:08 KST cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 2018. 07. 09. (���) 16:36:08 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz Could not set locale No such file or directory Could not set locale setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 219 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction 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 109 gm peak at 72 (72), valley at 45 (45) csf peak at 17, setting threshold to 53 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 72 (72), valley at 44 (44) csf peak at 17, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 34 seconds. #-------------------------------------------- #@# Mask BFS 2018. 07. 09. (���) 16:38:45 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz Could not set locale No such file or directory Could not set locale threshold mask volume at 5 DoAbs = 0 Found 1279635 voxels in mask (pct= 7.63) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation 2018. 07. 09. (���) 16:38:46 KST mri_segment -mprage brain.mgz wm.seg.mgz Could not set locale No such file or directory Could not set locale No such file or directory doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 104.1 +- 5.2 [79.0 --> 125.0] GM (72.0) : 69.1 +- 11.1 [30.0 --> 95.0] setting bottom of white matter range to 80.1 setting top of gray matter range to 91.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 2437 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3277 filled 384 bright non-wm voxels segmented. 1508 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz Could not set locale No such file or directory Could not set locale No such file or directory preserving editing changes in input volume... auto filling took 0.52 minutes reading wm segmentation from wm.seg.mgz... 640 voxels added to wm to prevent paths from MTL structures to cortex 3906 additional wm voxels added 0 additional wm voxels added SEG EDIT: 79216 voxels turned on, 23634 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 107 new 107 115,126,128 old 107 new 107 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 14 found - 14 modified | TOTAL: 31 pass 2 (xy-): 0 found - 14 modified | TOTAL: 31 pass 1 (yz+): 15 found - 15 modified | TOTAL: 46 pass 2 (yz+): 0 found - 15 modified | TOTAL: 46 pass 1 (yz-): 10 found - 10 modified | TOTAL: 56 pass 2 (yz-): 0 found - 10 modified | TOTAL: 56 pass 1 (xz+): 15 found - 15 modified | TOTAL: 71 pass 2 (xz+): 0 found - 15 modified | TOTAL: 71 pass 1 (xz-): 20 found - 20 modified | TOTAL: 91 pass 2 (xz-): 0 found - 20 modified | TOTAL: 91 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 56 found - 56 modified | TOTAL: 56 pass 2 (++): 0 found - 56 modified | TOTAL: 56 pass 1 (+-): 60 found - 60 modified | TOTAL: 116 pass 2 (+-): 0 found - 60 modified | TOTAL: 116 pass 1 (--): 35 found - 35 modified | TOTAL: 151 pass 2 (--): 0 found - 35 modified | TOTAL: 151 pass 1 (-+): 50 found - 50 modified | TOTAL: 201 pass 2 (-+): 0 found - 50 modified | TOTAL: 201 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 307 (out of 450339: 0.068171) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill 2018. 07. 09. (���) 16:40:21 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz wm.mgz filled.mgz Could not set locale No such file or directory Could not set locale No such file or directory logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.10983 -0.03579 0.02776 -13.39636; 0.04296 1.17169 0.07571 -37.29089; -0.02909 -0.07417 1.14582 -11.91005; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.10983 -0.03579 0.02776 -13.39636; 0.04296 1.17169 0.07571 -37.29089; -0.02909 -0.07417 1.14582 -11.91005; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1653 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using seed (124, 113, 88), TAL = (4.0, -40.0, 15.0) talairach voxel to voxel transform 0.89942 0.02599 -0.02351 12.73808; -0.03431 0.84892 -0.05526 30.53935; 0.02061 0.05561 0.86856 12.69456; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 113, 88) --> (4.0, -40.0, 15.0) done. writing output to filled.mgz... filling took 1.7 minutes talairach cc position changed to (4.00, -40.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -40.00, 15.00) SRC: (108.94, 117.97, 97.60) search lh wm seed point around talairach space (-14.00, -40.00, 15.00), SRC: (141.32, 116.73, 98.34) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh 2018. 07. 09. (���) 16:42:03 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 12 found - 12 modified | TOTAL: 13 pass 2 (yz+): 0 found - 12 modified | TOTAL: 13 pass 1 (yz-): 8 found - 8 modified | TOTAL: 21 pass 2 (yz-): 0 found - 8 modified | TOTAL: 21 pass 1 (xz+): 0 found - 0 modified | TOTAL: 21 pass 1 (xz-): 1 found - 1 modified | TOTAL: 22 pass 2 (xz-): 0 found - 1 modified | TOTAL: 22 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 2 found - 2 modified | TOTAL: 2 pass 2 (--): 0 found - 2 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 26 (out of 221846: 0.011720) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix Could not set locale No such file or directory Could not set locale No such file or directory $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 50: 609 vertices, 684 faces slice 60: 5072 vertices, 5282 faces slice 70: 12742 vertices, 13042 faces slice 80: 22072 vertices, 22404 faces slice 90: 31310 vertices, 31583 faces slice 100: 41068 vertices, 41431 faces slice 110: 51630 vertices, 52010 faces slice 120: 62285 vertices, 62652 faces slice 130: 72869 vertices, 73286 faces slice 140: 82600 vertices, 82957 faces slice 150: 90295 vertices, 90555 faces slice 160: 96978 vertices, 97244 faces slice 170: 102872 vertices, 103125 faces slice 180: 107600 vertices, 107789 faces slice 190: 110465 vertices, 110558 faces slice 200: 110678 vertices, 110720 faces slice 210: 110678 vertices, 110720 faces slice 220: 110678 vertices, 110720 faces slice 230: 110678 vertices, 110720 faces slice 240: 110678 vertices, 110720 faces slice 250: 110678 vertices, 110720 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 110666 voxel in cpt #1: X=-44 [v=110666,e=332130,f=221420] located at (-23.839310, -14.407234, 13.839562) 12 voxel in cpt #2: X=2 [v=12,e=30,f=20] located at (2.000000, 23.000000, 13.500000) For the whole surface: X=-42 [v=110678,e=332160,f=221440] 2 components have been found keeping component #1 with 110666 vertices done #-------------------------------------------- #@# Tessellate rh 2018. 07. 09. (���) 16:42:08 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 11 found - 11 modified | TOTAL: 13 pass 2 (yz+): 0 found - 11 modified | TOTAL: 13 pass 1 (yz-): 9 found - 9 modified | TOTAL: 22 pass 2 (yz-): 0 found - 9 modified | TOTAL: 22 pass 1 (xz+): 2 found - 2 modified | TOTAL: 24 pass 2 (xz+): 0 found - 2 modified | TOTAL: 24 pass 1 (xz-): 0 found - 0 modified | TOTAL: 24 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 0 found - 0 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 34 (out of 214901: 0.015821) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix Could not set locale No such file or directory Could not set locale No such file or directory $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 50: 374 vertices, 416 faces slice 60: 4817 vertices, 5020 faces slice 70: 12474 vertices, 12803 faces slice 80: 22448 vertices, 22772 faces slice 90: 31849 vertices, 32116 faces slice 100: 41656 vertices, 41994 faces slice 110: 52119 vertices, 52482 faces slice 120: 62950 vertices, 63303 faces slice 130: 72751 vertices, 73118 faces slice 140: 81792 vertices, 82109 faces slice 150: 89178 vertices, 89444 faces slice 160: 95746 vertices, 95991 faces slice 170: 101340 vertices, 101583 faces slice 180: 106017 vertices, 106195 faces slice 190: 108983 vertices, 109052 faces slice 200: 109080 vertices, 109114 faces slice 210: 109080 vertices, 109114 faces slice 220: 109080 vertices, 109114 faces slice 230: 109080 vertices, 109114 faces slice 240: 109080 vertices, 109114 faces slice 250: 109080 vertices, 109114 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 109080 voxel in cpt #1: X=-34 [v=109080,e=327342,f=218228] located at (27.331537, -15.062541, 12.073606) For the whole surface: X=-34 [v=109080,e=327342,f=218228] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh 2018. 07. 09. (���) 16:42:13 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh 2018. 07. 09. (���) 16:42:16 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh 2018. 07. 09. (���) 16:42:19 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Could not set locale No such file or directory Could not set locale Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.3 mm, total surface area = 57947 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.041 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.037 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.036 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 22.960000 mris_inflate stimesec 0.164000 mris_inflate ru_maxrss 161044 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 143592 mris_inflate ru_majflt 28 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8064 mris_inflate ru_oublock 7800 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 32 mris_inflate ru_nivcsw 1447 #-------------------------------------------- #@# Inflation1 rh 2018. 07. 09. (���) 16:42:42 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Could not set locale No such file or directory Could not set locale Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.0 mm, total surface area = 57051 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.086 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.037 (target=0.015) step 055: RMS=0.036 (target=0.015) step 060: RMS=0.036 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 21.856000 mris_inflate stimesec 0.124000 mris_inflate ru_maxrss 158708 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 141546 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 7688 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 740 #-------------------------------------------- #@# QSphere lh 2018. 07. 09. (���) 16:43:05 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix Could not set locale No such file or directory Could not set locale doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.11 +- 0.59 (0.00-->6.86) (max @ vno 84216 --> 85045) face area 0.03 +- 0.04 (-0.09-->0.86) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.364... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.620, avgs=0 005/300: dt: 0.9000, rms radial error=175.363, avgs=0 010/300: dt: 0.9000, rms radial error=174.810, avgs=0 015/300: dt: 0.9000, rms radial error=174.084, avgs=0 020/300: dt: 0.9000, rms radial error=173.257, avgs=0 025/300: dt: 0.9000, rms radial error=172.373, avgs=0 030/300: dt: 0.9000, rms radial error=171.457, avgs=0 035/300: dt: 0.9000, rms radial error=170.524, avgs=0 040/300: dt: 0.9000, rms radial error=169.585, avgs=0 045/300: dt: 0.9000, rms radial error=168.646, avgs=0 050/300: dt: 0.9000, rms radial error=167.707, avgs=0 055/300: dt: 0.9000, rms radial error=166.771, avgs=0 060/300: dt: 0.9000, rms radial error=165.840, avgs=0 065/300: dt: 0.9000, rms radial error=164.913, avgs=0 070/300: dt: 0.9000, rms radial error=163.990, avgs=0 075/300: dt: 0.9000, rms radial error=163.072, avgs=0 080/300: dt: 0.9000, rms radial error=162.159, avgs=0 085/300: dt: 0.9000, rms radial error=161.250, avgs=0 090/300: dt: 0.9000, rms radial error=160.346, avgs=0 095/300: dt: 0.9000, rms radial error=159.447, avgs=0 100/300: dt: 0.9000, rms radial error=158.553, avgs=0 105/300: dt: 0.9000, rms radial error=157.663, avgs=0 110/300: dt: 0.9000, rms radial error=156.779, avgs=0 115/300: dt: 0.9000, rms radial error=155.898, avgs=0 120/300: dt: 0.9000, rms radial error=155.023, avgs=0 125/300: dt: 0.9000, rms radial error=154.152, avgs=0 130/300: dt: 0.9000, rms radial error=153.286, avgs=0 135/300: dt: 0.9000, rms radial error=152.425, avgs=0 140/300: dt: 0.9000, rms radial error=151.569, avgs=0 145/300: dt: 0.9000, rms radial error=150.717, avgs=0 150/300: dt: 0.9000, rms radial error=149.870, avgs=0 155/300: dt: 0.9000, rms radial error=149.028, avgs=0 160/300: dt: 0.9000, rms radial error=148.190, avgs=0 165/300: dt: 0.9000, rms radial error=147.357, avgs=0 170/300: dt: 0.9000, rms radial error=146.528, avgs=0 175/300: dt: 0.9000, rms radial error=145.704, avgs=0 180/300: dt: 0.9000, rms radial error=144.884, avgs=0 185/300: dt: 0.9000, rms radial error=144.069, avgs=0 190/300: dt: 0.9000, rms radial error=143.258, avgs=0 195/300: dt: 0.9000, rms radial error=142.451, avgs=0 200/300: dt: 0.9000, rms radial error=141.649, avgs=0 205/300: dt: 0.9000, rms radial error=140.852, avgs=0 210/300: dt: 0.9000, rms radial error=140.059, avgs=0 215/300: dt: 0.9000, rms radial error=139.270, avgs=0 220/300: dt: 0.9000, rms radial error=138.486, avgs=0 225/300: dt: 0.9000, rms radial error=137.706, avgs=0 230/300: dt: 0.9000, rms radial error=136.931, avgs=0 235/300: dt: 0.9000, rms radial error=136.159, avgs=0 240/300: dt: 0.9000, rms radial error=135.392, avgs=0 245/300: dt: 0.9000, rms radial error=134.630, avgs=0 250/300: dt: 0.9000, rms radial error=133.871, avgs=0 255/300: dt: 0.9000, rms radial error=133.117, avgs=0 260/300: dt: 0.9000, rms radial error=132.367, avgs=0 265/300: dt: 0.9000, rms radial error=131.621, avgs=0 270/300: dt: 0.9000, rms radial error=130.879, avgs=0 275/300: dt: 0.9000, rms radial error=130.142, avgs=0 280/300: dt: 0.9000, rms radial error=129.408, avgs=0 285/300: dt: 0.9000, rms radial error=128.679, avgs=0 290/300: dt: 0.9000, rms radial error=127.953, avgs=0 295/300: dt: 0.9000, rms radial error=127.232, avgs=0 300/300: dt: 0.9000, rms radial error=126.515, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12172.82 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00046 epoch 2 (K=40.0), pass 1, starting sse = 1724.93 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00127 epoch 3 (K=160.0), pass 1, starting sse = 120.08 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/16 = 0.00903 epoch 4 (K=640.0), pass 1, starting sse = 5.46 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/17 = 0.00484 final distance error %19.26 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0365 hours mris_sphere utimesec 129.572000 mris_sphere stimesec 0.224000 mris_sphere ru_maxrss 161744 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 175686 mris_sphere ru_majflt 32 mris_sphere ru_nswap 0 mris_sphere ru_inblock 8928 mris_sphere ru_oublock 7800 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 36 mris_sphere ru_nivcsw 12897 FSRUNTIME@ mris_sphere 0.0365 hours 1 threads #-------------------------------------------- #@# QSphere rh 2018. 07. 09. (���) 16:45:16 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Could not set locale No such file or directory Could not set locale doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.11 +- 0.60 (0.00-->7.04) (max @ vno 81533 --> 81534) face area 0.03 +- 0.04 (-0.05-->0.71) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.364... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.734, avgs=0 005/300: dt: 0.9000, rms radial error=175.477, avgs=0 010/300: dt: 0.9000, rms radial error=174.924, avgs=0 015/300: dt: 0.9000, rms radial error=174.200, avgs=0 020/300: dt: 0.9000, rms radial error=173.377, avgs=0 025/300: dt: 0.9000, rms radial error=172.499, avgs=0 030/300: dt: 0.9000, rms radial error=171.590, avgs=0 035/300: dt: 0.9000, rms radial error=170.663, avgs=0 040/300: dt: 0.9000, rms radial error=169.729, avgs=0 045/300: dt: 0.9000, rms radial error=168.792, avgs=0 050/300: dt: 0.9000, rms radial error=167.855, avgs=0 055/300: dt: 0.9000, rms radial error=166.921, avgs=0 060/300: dt: 0.9000, rms radial error=165.990, avgs=0 065/300: dt: 0.9000, rms radial error=165.063, avgs=0 070/300: dt: 0.9000, rms radial error=164.141, avgs=0 075/300: dt: 0.9000, rms radial error=163.224, avgs=0 080/300: dt: 0.9000, rms radial error=162.311, avgs=0 085/300: dt: 0.9000, rms radial error=161.403, avgs=0 090/300: dt: 0.9000, rms radial error=160.500, avgs=0 095/300: dt: 0.9000, rms radial error=159.601, avgs=0 100/300: dt: 0.9000, rms radial error=158.707, avgs=0 105/300: dt: 0.9000, rms radial error=157.819, avgs=0 110/300: dt: 0.9000, rms radial error=156.935, avgs=0 115/300: dt: 0.9000, rms radial error=156.055, avgs=0 120/300: dt: 0.9000, rms radial error=155.181, avgs=0 125/300: dt: 0.9000, rms radial error=154.311, avgs=0 130/300: dt: 0.9000, rms radial error=153.446, avgs=0 135/300: dt: 0.9000, rms radial error=152.585, avgs=0 140/300: dt: 0.9000, rms radial error=151.730, avgs=0 145/300: dt: 0.9000, rms radial error=150.879, avgs=0 150/300: dt: 0.9000, rms radial error=150.032, avgs=0 155/300: dt: 0.9000, rms radial error=149.191, avgs=0 160/300: dt: 0.9000, rms radial error=148.354, avgs=0 165/300: dt: 0.9000, rms radial error=147.521, avgs=0 170/300: dt: 0.9000, rms radial error=146.693, avgs=0 175/300: dt: 0.9000, rms radial error=145.869, avgs=0 180/300: dt: 0.9000, rms radial error=145.050, avgs=0 185/300: dt: 0.9000, rms radial error=144.235, avgs=0 190/300: dt: 0.9000, rms radial error=143.424, avgs=0 195/300: dt: 0.9000, rms radial error=142.618, avgs=0 200/300: dt: 0.9000, rms radial error=141.817, avgs=0 205/300: dt: 0.9000, rms radial error=141.019, avgs=0 210/300: dt: 0.9000, rms radial error=140.226, avgs=0 215/300: dt: 0.9000, rms radial error=139.438, avgs=0 220/300: dt: 0.9000, rms radial error=138.654, avgs=0 225/300: dt: 0.9000, rms radial error=137.874, avgs=0 230/300: dt: 0.9000, rms radial error=137.098, avgs=0 235/300: dt: 0.9000, rms radial error=136.327, avgs=0 240/300: dt: 0.9000, rms radial error=135.560, avgs=0 245/300: dt: 0.9000, rms radial error=134.797, avgs=0 250/300: dt: 0.9000, rms radial error=134.039, avgs=0 255/300: dt: 0.9000, rms radial error=133.284, avgs=0 260/300: dt: 0.9000, rms radial error=132.534, avgs=0 265/300: dt: 0.9000, rms radial error=131.788, avgs=0 270/300: dt: 0.9000, rms radial error=131.046, avgs=0 275/300: dt: 0.9000, rms radial error=130.309, avgs=0 280/300: dt: 0.9000, rms radial error=129.575, avgs=0 285/300: dt: 0.9000, rms radial error=128.846, avgs=0 290/300: dt: 0.9000, rms radial error=128.120, avgs=0 295/300: dt: 0.9000, rms radial error=127.399, avgs=0 300/300: dt: 0.9000, rms radial error=126.681, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12017.71 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00046 epoch 2 (K=40.0), pass 1, starting sse = 1719.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00120 epoch 3 (K=160.0), pass 1, starting sse = 120.32 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.24/22 = 0.01069 epoch 4 (K=640.0), pass 1, starting sse = 4.35 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/19 = 0.00412 final distance error %19.01 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0380 hours mris_sphere utimesec 136.568000 mris_sphere stimesec 0.248000 mris_sphere ru_maxrss 159256 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 185816 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 7696 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 2474 FSRUNTIME@ mris_sphere 0.0380 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh 2018. 07. 09. (���) 16:47:33 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh 2018. 07. 09. (���) 16:47:33 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh 2018. 07. 09. (���) 16:47:33 KST mris_fix_topology -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 161019_x3DT1_SAG lh Could not set locale No such file or directory Could not set locale reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ $Id$ before topology correction, eno=-44 (nv=110666, nf=221420, ne=332130, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 2438 ambiguous faces found in tessellation segmenting defects... 29 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 29 defects to be corrected 0 vertices coincident reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1276 (-4.5638) -vertex loglikelihood: -6.4046 (-3.2023) -normal dot loglikelihood: -3.5985 (-3.5985) -quad curv loglikelihood: -6.4717 (-3.2358) Total Loglikelihood : -25.6023 CORRECTING DEFECT 0 (vertices=27, convex hull=62, v0=4053) After retessellation of defect 0 (v0=4053), euler #=-26 (109130,326638,217482) : difference with theory (-26) = 0 CORRECTING DEFECT 1 (vertices=25, convex hull=64, v0=4478) After retessellation of defect 1 (v0=4478), euler #=-25 (109139,326691,217527) : difference with theory (-25) = 0 CORRECTING DEFECT 2 (vertices=32, convex hull=81, v0=5689) After retessellation of defect 2 (v0=5689), euler #=-24 (109159,326780,217597) : difference with theory (-24) = 0 CORRECTING DEFECT 3 (vertices=30, convex hull=76, v0=13559) After retessellation of defect 3 (v0=13559), euler #=-23 (109173,326853,217657) : difference with theory (-23) = 0 CORRECTING DEFECT 4 (vertices=46, convex hull=87, v0=18581) After retessellation of defect 4 (v0=18581), euler #=-22 (109192,326947,217733) : difference with theory (-22) = 0 CORRECTING DEFECT 5 (vertices=45, convex hull=67, v0=20605) After retessellation of defect 5 (v0=20605), euler #=-21 (109216,327048,217811) : difference with theory (-21) = 0 CORRECTING DEFECT 6 (vertices=29, convex hull=32, v0=20751) After retessellation of defect 6 (v0=20751), euler #=-20 (109220,327072,217832) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=30, convex hull=35, v0=31849) After retessellation of defect 7 (v0=31849), euler #=-19 (109228,327110,217863) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=29, convex hull=68, v0=32973) After retessellation of defect 8 (v0=32973), euler #=-18 (109244,327186,217924) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=48, convex hull=67, v0=33695) After retessellation of defect 9 (v0=33695), euler #=-17 (109269,327290,218004) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=24, convex hull=24, v0=37788) After retessellation of defect 10 (v0=37788), euler #=-16 (109273,327307,218018) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=24, convex hull=58, v0=39594) After retessellation of defect 11 (v0=39594), euler #=-15 (109284,327361,218062) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=90, convex hull=68, v0=51345) After retessellation of defect 12 (v0=51345), euler #=-14 (109305,327451,218132) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=22, convex hull=46, v0=67164) After retessellation of defect 13 (v0=67164), euler #=-13 (109314,327494,218167) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=47, convex hull=67, v0=67542) After retessellation of defect 14 (v0=67542), euler #=-12 (109336,327586,218238) : difference with theory (-12) = 0 CORRECTING DEFECT 15 (vertices=103, convex hull=52, v0=70367) After retessellation of defect 15 (v0=70367), euler #=-11 (109346,327636,218279) : difference with theory (-11) = 0 CORRECTING DEFECT 16 (vertices=8, convex hull=28, v0=71360) After retessellation of defect 16 (v0=71360), euler #=-10 (109347,327648,218291) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=52, convex hull=73, v0=74991) After retessellation of defect 17 (v0=74991), euler #=-9 (109373,327755,218373) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=84, convex hull=91, v0=75680) After retessellation of defect 18 (v0=75680), euler #=-8 (109388,327838,218442) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=264, convex hull=49, v0=78582) After retessellation of defect 19 (v0=78582), euler #=-7 (109404,327909,218498) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=5, convex hull=18, v0=81649) After retessellation of defect 20 (v0=81649), euler #=-6 (109405,327915,218504) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=20, convex hull=52, v0=84988) After retessellation of defect 21 (v0=84988), euler #=-5 (109417,327970,218548) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=32, convex hull=69, v0=85842) After retessellation of defect 22 (v0=85842), euler #=-4 (109436,328054,218614) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=119, convex hull=120, v0=92177) After retessellation of defect 23 (v0=92177), euler #=-3 (109471,328214,218740) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=109, convex hull=119, v0=92764) After retessellation of defect 24 (v0=92764), euler #=-2 (109518,328405,218885) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=158, convex hull=204, v0=93361) After retessellation of defect 25 (v0=93361), euler #=-1 (109616,328799,219182) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=21, convex hull=56, v0=95713) After retessellation of defect 26 (v0=95713), euler #=0 (109630,328863,219233) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=5, convex hull=19, v0=99873) After retessellation of defect 27 (v0=99873), euler #=1 (109632,328875,219244) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=25, convex hull=35, v0=108912) After retessellation of defect 28 (v0=108912), euler #=2 (109637,328905,219270) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.12-->7.46) (max @ vno 92363 --> 94314) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.12-->7.46) (max @ vno 92363 --> 94314) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 63 mutations (27.2%), 169 crossovers (72.8%), 68 vertices were eliminated building final representation... 1029 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=109637, nf=219270, ne=328905, g=0) writing corrected surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 1.7 minutes removing intersecting faces 000: 129 intersecting 001: 8 intersecting 002: 2 intersecting step 1 with no progress (num=2, old_num=2) 003: 2 intersecting step 2 with no progress (num=2, old_num=2) 004: 2 intersecting step 3 with no progress (num=2, old_num=2) 005: 2 intersecting step 4 with no progress (num=2, old_num=2) 006: 2 intersecting step 5 with no progress (num=2, old_num=2) 007: 2 intersecting step 6 with no progress (num=2, old_num=2) 008: 2 intersecting step 7 with no progress (num=2, old_num=2) 009: 2 intersecting step 8 with no progress (num=2, old_num=2) 010: 2 intersecting step 9 with no progress (num=2, old_num=2) 011: 2 intersecting step 10 with no progress (num=2, old_num=2) 012: 2 intersecting step 11 with no progress (num=2, old_num=2) 013: 2 intersecting step 12 with no progress (num=2, old_num=2) 014: 2 intersecting step 13 with no progress (num=2, old_num=2) 015: 2 intersecting step 14 with no progress (num=2, old_num=2) 016: 2 intersecting step 15 with no progress (num=2, old_num=2) 017: 2 intersecting step 16 with no progress (num=2, old_num=2) terminating search with 2 intersecting mris_fix_topology utimesec 99.004000 mris_fix_topology stimesec 0.216000 mris_fix_topology ru_maxrss 706348 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 188714 mris_fix_topology ru_majflt 36 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 9160 mris_fix_topology ru_oublock 10344 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 42 mris_fix_topology ru_nivcsw 15264 FSRUNTIME@ mris_fix_topology lh 0.0281 hours 1 threads #@# Fix Topology rh 2018. 07. 09. (���) 16:49:15 KST mris_fix_topology -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 161019_x3DT1_SAG rh Could not set locale No such file or directory Could not set locale reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ $Id$ before topology correction, eno=-34 (nv=109080, nf=218228, ne=327342, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 2040 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 21 defects to be corrected 0 vertices coincident reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1820 (-4.5910) -vertex loglikelihood: -6.4097 (-3.2048) -normal dot loglikelihood: -3.6643 (-3.6643) -quad curv loglikelihood: -6.3461 (-3.1730) Total Loglikelihood : -25.6020 CORRECTING DEFECT 0 (vertices=52, convex hull=104, v0=7430) After retessellation of defect 0 (v0=7430), euler #=-18 (107847,323012,215147) : difference with theory (-18) = 0 CORRECTING DEFECT 1 (vertices=59, convex hull=74, v0=9881) After retessellation of defect 1 (v0=9881), euler #=-17 (107873,323123,215233) : difference with theory (-17) = 0 CORRECTING DEFECT 2 (vertices=67, convex hull=90, v0=15263) After retessellation of defect 2 (v0=15263), euler #=-16 (107912,323281,215353) : difference with theory (-16) = 0 CORRECTING DEFECT 3 (vertices=22, convex hull=71, v0=29359) After retessellation of defect 3 (v0=29359), euler #=-15 (107925,323348,215408) : difference with theory (-15) = 0 CORRECTING DEFECT 4 (vertices=95, convex hull=139, v0=45549) After retessellation of defect 4 (v0=45549), euler #=-14 (107959,323515,215542) : difference with theory (-14) = 0 CORRECTING DEFECT 5 (vertices=33, convex hull=69, v0=45843) After retessellation of defect 5 (v0=45843), euler #=-13 (107979,323604,215612) : difference with theory (-13) = 0 CORRECTING DEFECT 6 (vertices=47, convex hull=68, v0=47668) After retessellation of defect 6 (v0=47668), euler #=-12 (108001,323697,215684) : difference with theory (-12) = 0 CORRECTING DEFECT 7 (vertices=18, convex hull=24, v0=64559) After retessellation of defect 7 (v0=64559), euler #=-11 (108004,323714,215699) : difference with theory (-11) = 0 CORRECTING DEFECT 8 (vertices=24, convex hull=56, v0=64900) After retessellation of defect 8 (v0=64900), euler #=-10 (108013,323758,215735) : difference with theory (-10) = 0 CORRECTING DEFECT 9 (vertices=18, convex hull=28, v0=68450) After retessellation of defect 9 (v0=68450), euler #=-9 (108018,323783,215756) : difference with theory (-9) = 0 CORRECTING DEFECT 10 (vertices=146, convex hull=64, v0=68670) After retessellation of defect 10 (v0=68670), euler #=-8 (108032,323848,215808) : difference with theory (-8) = 0 CORRECTING DEFECT 11 (vertices=38, convex hull=79, v0=73647) After retessellation of defect 11 (v0=73647), euler #=-7 (108041,323904,215856) : difference with theory (-7) = 0 CORRECTING DEFECT 12 (vertices=38, convex hull=67, v0=73701) After retessellation of defect 12 (v0=73701), euler #=-6 (108054,323968,215908) : difference with theory (-6) = 0 CORRECTING DEFECT 13 (vertices=72, convex hull=27, v0=75638) After retessellation of defect 13 (v0=75638), euler #=-5 (108058,323991,215928) : difference with theory (-5) = 0 CORRECTING DEFECT 14 (vertices=274, convex hull=49, v0=78178) After retessellation of defect 14 (v0=78178), euler #=-4 (108069,324046,215973) : difference with theory (-4) = 0 CORRECTING DEFECT 15 (vertices=44, convex hull=52, v0=85112) After retessellation of defect 15 (v0=85112), euler #=-3 (108093,324140,216044) : difference with theory (-3) = 0 CORRECTING DEFECT 16 (vertices=49, convex hull=61, v0=91637) After retessellation of defect 16 (v0=91637), euler #=-2 (108106,324203,216095) : difference with theory (-2) = 0 CORRECTING DEFECT 17 (vertices=38, convex hull=71, v0=99127) After retessellation of defect 17 (v0=99127), euler #=-1 (108133,324311,216177) : difference with theory (-1) = 0 CORRECTING DEFECT 18 (vertices=38, convex hull=62, v0=100878) After retessellation of defect 18 (v0=100878), euler #=0 (108152,324396,216244) : difference with theory (0) = 0 CORRECTING DEFECT 19 (vertices=27, convex hull=56, v0=101086) After retessellation of defect 19 (v0=101086), euler #=1 (108164,324450,216287) : difference with theory (1) = 0 CORRECTING DEFECT 20 (vertices=62, convex hull=87, v0=101108) After retessellation of defect 20 (v0=101108), euler #=2 (108203,324603,216402) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.12-->8.81) (max @ vno 71091 --> 73925) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.12-->8.81) (max @ vno 71091 --> 73925) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 61 mutations (31.1%), 135 crossovers (68.9%), 70 vertices were eliminated building final representation... 877 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=108203, nf=216402, ne=324603, g=0) writing corrected surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 1.2 minutes removing intersecting faces 000: 124 intersecting 001: 4 intersecting terminating search with 0 intersecting mris_fix_topology utimesec 68.144000 mris_fix_topology stimesec 0.156000 mris_fix_topology ru_maxrss 704764 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 188239 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 10200 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 0 mris_fix_topology ru_nivcsw 3862 FSRUNTIME@ mris_fix_topology rh 0.0193 hours 1 threads mris_euler_number ../surf/lh.orig Could not set locale No such file or directory Could not set locale euler # = v-e+f = 2g-2: 109637 - 328905 + 219270 = 2 --> 0 holes F =2V-4: 219270 = 219274-4 (0) 2E=3F: 657810 = 657810 (0) total defect index = 0 mris_euler_number ../surf/rh.orig Could not set locale No such file or directory Could not set locale euler # = v-e+f = 2g-2: 108203 - 324603 + 216402 = 2 --> 0 holes F =2V-4: 216402 = 216406-4 (0) 2E=3F: 649206 = 649206 (0) total defect index = 0 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig Could not set locale No such file or directory Could not set locale intersection removal took 0.00 hours removing intersecting faces 000: 26 intersecting terminating search with 0 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig Could not set locale No such file or directory Could not set locale intersection removal took 0.00 hours removing intersecting faces 000: 18 intersecting 001: 4 intersecting terminating search with 0 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh 2018. 07. 09. (���) 16:50:31 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 161019_x3DT1_SAG lh Could not set locale No such file or directory Could not set locale Could not set locale using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ $Id$ reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/filled.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/brain.finalsurfs.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/../mri/aseg.presurf.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... 13593 bright wm thresholded. 600 bright non-wm voxels segmented. reading original surface position from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.orig... computing class statistics... border white: 206272 voxels (1.23%) border gray 224126 voxels (1.34%) WM (96.0): 97.0 +- 7.9 [70.0 --> 110.0] GM (74.0) : 71.8 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.5 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.1 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->3.76) (max @ vno 96716 --> 109476) face area 0.28 +- 0.12 (0.00-->3.01) mean absolute distance = 0.90 +- 1.12 3476 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-6.1, GM=70+-8.7 mean inside = 92.1, mean outside = 75.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=80.5, 286 (286) missing vertices, mean dist 0.2 [0.9 (%37.5)->0.9 (%62.5))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %36 local maxima, %58 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.03-->3.60) (max @ vno 96716 --> 109476) face area 0.28 +- 0.13 (0.00-->2.96) mean absolute distance = 0.43 +- 0.85 3457 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2662524.8, rms=10.331 001: dt: 0.5000, sse=1524235.2, rms=7.271 (29.622%) 002: dt: 0.5000, sse=1010768.4, rms=5.312 (26.944%) 003: dt: 0.5000, sse=783539.1, rms=4.138 (22.098%) 004: dt: 0.5000, sse=678338.1, rms=3.444 (16.778%) 005: dt: 0.5000, sse=649676.4, rms=3.118 (9.450%) 006: dt: 0.5000, sse=636402.1, rms=2.949 (5.437%) 007: dt: 0.5000, sse=609394.8, rms=2.891 (1.973%) rms = 2.84, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=605550.7, rms=2.843 (1.644%) 009: dt: 0.2500, sse=513570.3, rms=1.739 (38.824%) 010: dt: 0.2500, sse=491092.5, rms=1.500 (13.731%) rms = 1.45, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=491102.6, rms=1.445 (3.680%) rms = 1.40, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=490132.7, rms=1.402 (2.992%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=82.7, 228 (153) missing vertices, mean dist -0.3 [0.5 (%63.6)->0.2 (%36.4))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %45 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.04-->3.61) (max @ vno 92363 --> 94314) face area 0.36 +- 0.16 (0.00-->3.95) mean absolute distance = 0.33 +- 0.52 2365 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=897358.4, rms=3.954 013: dt: 0.5000, sse=720886.0, rms=2.605 (34.132%) 014: dt: 0.5000, sse=688928.1, rms=2.380 (8.615%) 015: dt: 0.5000, sse=676957.4, rms=2.328 (2.200%) rms = 2.53, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=628263.6, rms=1.636 (29.725%) 017: dt: 0.2500, sse=610245.4, rms=1.302 (20.438%) 018: dt: 0.2500, sse=608479.6, rms=1.225 (5.864%) rms = 1.21, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=612324.4, rms=1.212 (1.106%) rms = 1.18, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=604258.8, rms=1.184 (2.301%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=85.2, 219 (126) missing vertices, mean dist -0.2 [0.4 (%67.9)->0.2 (%32.1))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.03-->3.46) (max @ vno 52954 --> 53917) face area 0.35 +- 0.16 (0.00-->3.86) mean absolute distance = 0.26 +- 0.39 2587 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=811052.6, rms=3.500 021: dt: 0.5000, sse=655345.2, rms=2.073 (40.780%) rms = 2.12, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=618665.8, rms=1.555 (24.964%) 023: dt: 0.2500, sse=602147.3, rms=1.193 (23.310%) 024: dt: 0.2500, sse=588849.9, rms=1.107 (7.166%) rms = 1.10, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=584451.9, rms=1.099 (0.787%) rms = 1.08, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=585175.3, rms=1.075 (2.118%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=86.4, 237 (122) missing vertices, mean dist -0.1 [0.3 (%59.3)->0.2 (%40.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=620090.1, rms=1.888 027: dt: 0.5000, sse=589393.1, rms=1.470 (22.127%) rms = 1.86, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=565155.8, rms=1.031 (29.878%) 029: dt: 0.2500, sse=561509.4, rms=0.910 (11.712%) rms = 0.87, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=567949.8, rms=0.868 (4.618%) rms = 0.86, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=554938.9, rms=0.863 (0.609%) positioning took 0.3 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7446 vertices erasing segment 1 (vno[0] = 42365) erasing segment 2 (vno[0] = 43124) erasing segment 3 (vno[0] = 67763) erasing segment 4 (vno[0] = 77851) erasing segment 5 (vno[0] = 78706) erasing segment 6 (vno[0] = 78770) erasing segment 7 (vno[0] = 79665) erasing segment 8 (vno[0] = 81460) erasing segment 9 (vno[0] = 82357) erasing segment 10 (vno[0] = 83282) erasing segment 11 (vno[0] = 85553) erasing segment 12 (vno[0] = 86316) writing cortex label to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label... writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.area vertex spacing 0.89 +- 0.25 (0.03-->3.62) (max @ vno 92363 --> 94314) face area 0.34 +- 0.16 (0.00-->3.47) refinement took 2.6 minutes #-------------------------------------------- #@# Make White Surf rh 2018. 07. 09. (���) 16:53:08 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 161019_x3DT1_SAG rh Could not set locale No such file or directory Could not set locale Could not set locale using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ $Id$ reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/filled.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/brain.finalsurfs.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/../mri/aseg.presurf.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... 13593 bright wm thresholded. 600 bright non-wm voxels segmented. reading original surface position from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.orig... computing class statistics... border white: 206272 voxels (1.23%) border gray 224126 voxels (1.34%) WM (96.0): 97.0 +- 7.9 [70.0 --> 110.0] GM (74.0) : 71.8 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.1 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.04-->2.57) (max @ vno 48476 --> 53571) face area 0.28 +- 0.12 (0.00-->1.50) mean absolute distance = 0.96 +- 1.16 3558 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.0, GM=67+-10.4 mean inside = 91.8, mean outside = 74.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=79.1, 79 (79) missing vertices, mean dist 0.3 [1.0 (%34.0)->1.0 (%66.0))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %43 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.03-->4.11) (max @ vno 45435 --> 45428) face area 0.28 +- 0.13 (0.00-->1.59) mean absolute distance = 0.46 +- 0.87 3387 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2816019.0, rms=10.788 001: dt: 0.5000, sse=1656710.2, rms=7.777 (27.906%) 002: dt: 0.5000, sse=1104835.4, rms=5.803 (25.378%) 003: dt: 0.5000, sse=849800.0, rms=4.532 (21.908%) 004: dt: 0.5000, sse=722503.2, rms=3.730 (17.690%) 005: dt: 0.5000, sse=651956.9, rms=3.307 (11.358%) 006: dt: 0.5000, sse=621725.4, rms=3.083 (6.764%) 007: dt: 0.5000, sse=620366.5, rms=2.988 (3.081%) 008: dt: 0.5000, sse=618186.9, rms=2.932 (1.877%) rms = 2.91, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=612501.3, rms=2.911 (0.716%) 010: dt: 0.2500, sse=517276.2, rms=1.782 (38.789%) 011: dt: 0.2500, sse=494601.3, rms=1.526 (14.357%) 012: dt: 0.2500, sse=485967.2, rms=1.468 (3.784%) rms = 1.45, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=482875.6, rms=1.445 (1.557%) rms = 1.41, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=482555.0, rms=1.410 (2.461%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group in thread:0 removing 3 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=81.2, 52 (11) missing vertices, mean dist -0.3 [0.6 (%61.6)->0.3 (%38.4))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.25 (0.03-->4.34) (max @ vno 45435 --> 45428) face area 0.36 +- 0.17 (0.00-->2.41) mean absolute distance = 0.37 +- 0.55 2811 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=920857.1, rms=4.127 015: dt: 0.5000, sse=734226.0, rms=2.777 (32.706%) 016: dt: 0.5000, sse=695955.9, rms=2.539 (8.572%) 017: dt: 0.5000, sse=685728.4, rms=2.454 (3.346%) rms = 2.64, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=628569.1, rms=1.730 (29.513%) 019: dt: 0.2500, sse=608491.1, rms=1.370 (20.811%) 020: dt: 0.2500, sse=601160.2, rms=1.277 (6.765%) rms = 1.25, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=600307.2, rms=1.251 (2.043%) rms = 1.22, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=599808.8, rms=1.216 (2.809%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 removing 2 vertex label from ripped group in thread:0 removing 1 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=83.8, 55 (6) missing vertices, mean dist -0.2 [0.4 (%67.3)->0.2 (%32.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.91 +- 0.25 (0.04-->4.36) (max @ vno 45435 --> 45428) face area 0.35 +- 0.16 (0.00-->2.62) mean absolute distance = 0.30 +- 0.42 2854 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=838742.9, rms=3.732 023: dt: 0.5000, sse=665119.2, rms=2.225 (40.378%) rms = 2.24, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=618304.2, rms=1.689 (24.076%) 025: dt: 0.2500, sse=594598.4, rms=1.260 (25.425%) rms = 1.14, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=598279.8, rms=1.142 (9.373%) rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=579516.1, rms=1.099 (3.703%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 removing 2 vertex label from ripped group in thread:0 removing 1 vertex label from ripped group in thread:0 NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=85.2, 74 (5) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=629297.4, rms=2.103 028: dt: 0.5000, sse=618480.6, rms=1.568 (25.417%) rms = 1.96, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=573801.4, rms=1.082 (31.030%) 030: dt: 0.2500, sse=559518.9, rms=0.931 (13.896%) rms = 0.88, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=556833.9, rms=0.883 (5.173%) rms = 0.87, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=554167.3, rms=0.868 (1.761%) positioning took 0.3 minutes generating cortex label... 15 non-cortical segments detected only using segment with 7399 vertices erasing segment 0 (vno[0] = 26872) erasing segment 2 (vno[0] = 45196) erasing segment 3 (vno[0] = 67435) erasing segment 4 (vno[0] = 76453) erasing segment 5 (vno[0] = 79046) erasing segment 6 (vno[0] = 79053) erasing segment 7 (vno[0] = 80666) erasing segment 8 (vno[0] = 80724) erasing segment 9 (vno[0] = 80753) erasing segment 10 (vno[0] = 80756) erasing segment 11 (vno[0] = 81524) erasing segment 12 (vno[0] = 83165) erasing segment 13 (vno[0] = 84715) erasing segment 14 (vno[0] = 86000) writing cortex label to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label... writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.area vertex spacing 0.90 +- 0.26 (0.04-->4.48) (max @ vno 45428 --> 45435) face area 0.34 +- 0.16 (0.00-->2.61) refinement took 2.7 minutes #-------------------------------------------- #@# Smooth2 lh 2018. 07. 09. (���) 16:55:50 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm Could not set locale No such file or directory Could not set locale smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh 2018. 07. 09. (���) 16:55:53 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Could not set locale No such file or directory Could not set locale smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh 2018. 07. 09. (���) 16:55:56 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_inflate -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Could not set locale No such file or directory Could not set locale Reading ../surf/lh.smoothwm avg radius = 43.5 mm, total surface area = 66121 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 22.380000 mris_inflate stimesec 0.092000 mris_inflate ru_maxrss 156924 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 110106 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 256 mris_inflate ru_oublock 8592 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1 mris_inflate ru_nivcsw 4223 #-------------------------------------------- #@# Inflation2 rh 2018. 07. 09. (���) 16:56:19 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_inflate -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Could not set locale No such file or directory Could not set locale Reading ../surf/rh.smoothwm avg radius = 43.2 mm, total surface area = 65878 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.180 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 21.776000 mris_inflate stimesec 0.096000 mris_inflate ru_maxrss 154948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 108608 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8472 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 2000 #-------------------------------------------- #@# Curv .H and .K lh 2018. 07. 09. (���) 16:56:41 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_curvature -w -seed 1234 lh.white.preaparc Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 total integrated curvature = 2.534*4pi (31.840) --> -2 handles ICI = 139.2, FI = 1377.4, variation=21949.461 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 179 vertices thresholded to be in k1 ~ [-0.17 0.35], k2 ~ [-0.11 0.06] total integrated curvature = 0.646*4pi (8.124) --> 0 handles ICI = 1.3, FI = 6.9, variation=123.615 106 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 122 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.018, std = 0.021 done. #-------------------------------------------- #@# Curv .H and .K rh 2018. 07. 09. (���) 16:57:25 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_curvature -w -seed 1234 rh.white.preaparc Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 total integrated curvature = 7.623*4pi (95.800) --> -7 handles ICI = 144.4, FI = 1358.1, variation=21823.281 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 114 vertices thresholded to be in k1 ~ [-0.24 6.81], k2 ~ [-0.10 0.09] total integrated curvature = 0.607*4pi (7.633) --> 0 handles ICI = 1.3, FI = 7.0, variation=122.356 82 vertices thresholded to be in [-0.06 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 110 vertices thresholded to be in [-0.13 2.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh 2018. 07. 09. (���) 16:58:07 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 161019_x3DT1_SAG lh curv sulc Could not set locale No such file or directory Could not set locale Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ 161019_x3DT1_SAG/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 198 ] Gb_filter = 0 WARN: S lookup min: -0.525741 WARN: S explicit min: 0.000000 vertex = 455 #----------------------------------------- #@# Curvature Stats rh 2018. 07. 09. (���) 16:58:10 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 161019_x3DT1_SAG rh curv sulc Could not set locale No such file or directory Could not set locale Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ 161019_x3DT1_SAG/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 196 ] Gb_filter = 0 WARN: S lookup min: -0.141157 WARN: S explicit min: 0.000000 vertex = 37 #-------------------------------------------- #@# Sphere lh 2018. 07. 09. (���) 16:58:12 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_sphere -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere Could not set locale No such file or directory Could not set locale setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.339... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.11 pass 1: epoch 2 of 3 starting distance error %18.12 unfolding complete - removing small folds... starting distance error %18.09 removing remaining folds... final distance error %18.09 MRISunfold() return, current seed 1234 -01: dt=0.0000, 348 negative triangles 107: dt=0.9900, 348 negative triangles 108: dt=0.9900, 103 negative triangles 109: dt=0.9900, 69 negative triangles 110: dt=0.9900, 56 negative triangles 111: dt=0.9900, 35 negative triangles 112: dt=0.9900, 34 negative triangles 113: dt=0.9900, 35 negative triangles 114: dt=0.9900, 33 negative triangles 115: dt=0.9900, 30 negative triangles 116: dt=0.9900, 29 negative triangles 117: dt=0.9900, 26 negative triangles 118: dt=0.9900, 19 negative triangles 119: dt=0.9900, 23 negative triangles 120: dt=0.9900, 21 negative triangles 121: dt=0.9900, 16 negative triangles 122: dt=0.9900, 20 negative triangles 123: dt=0.9900, 22 negative triangles 124: dt=0.9900, 16 negative triangles 125: dt=0.9900, 12 negative triangles 126: dt=0.9900, 12 negative triangles 127: dt=0.9900, 11 negative triangles 128: dt=0.9900, 11 negative triangles 129: dt=0.9900, 9 negative triangles 130: dt=0.9900, 14 negative triangles 131: dt=0.9900, 11 negative triangles 132: dt=0.9900, 8 negative triangles 133: dt=0.9900, 9 negative triangles 134: dt=0.9900, 9 negative triangles 135: dt=0.9900, 7 negative triangles 136: dt=0.9900, 5 negative triangles 137: dt=0.9900, 7 negative triangles 138: dt=0.9900, 5 negative triangles 139: dt=0.9900, 7 negative triangles 140: dt=0.9900, 4 negative triangles 141: dt=0.9900, 4 negative triangles 142: dt=0.9900, 2 negative triangles 143: dt=0.9900, 1 negative triangles 144: dt=0.9900, 3 negative triangles 145: dt=0.9900, 1 negative triangles 146: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1315 hours mris_sphere utimesec 463.368000 mris_sphere stimesec 0.316000 mris_sphere ru_maxrss 216000 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 191181 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 8 mris_sphere ru_oublock 7736 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1 mris_sphere ru_nivcsw 32138 FSRUNTIME@ mris_sphere 0.1315 hours 1 threads #-------------------------------------------- #@# Sphere rh 2018. 07. 09. (���) 17:06:05 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_sphere -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Could not set locale No such file or directory Could not set locale setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.339... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %40.16 pass 1: epoch 2 of 3 starting distance error %18.56 unfolding complete - removing small folds... starting distance error %18.45 removing remaining folds... final distance error %18.47 MRISunfold() return, current seed 1234 -01: dt=0.0000, 97 negative triangles 123: dt=0.9900, 97 negative triangles 124: dt=0.9900, 52 negative triangles 125: dt=0.9900, 40 negative triangles 126: dt=0.9900, 24 negative triangles 127: dt=0.9900, 20 negative triangles 128: dt=0.9900, 24 negative triangles 129: dt=0.9900, 22 negative triangles 130: dt=0.9900, 22 negative triangles 131: dt=0.9900, 21 negative triangles 132: dt=0.9900, 17 negative triangles 133: dt=0.9900, 17 negative triangles 134: dt=0.9900, 15 negative triangles 135: dt=0.9900, 17 negative triangles 136: dt=0.9900, 12 negative triangles 137: dt=0.9900, 19 negative triangles 138: dt=0.9900, 11 negative triangles 139: dt=0.9900, 14 negative triangles 140: dt=0.9900, 15 negative triangles 141: dt=0.9900, 17 negative triangles 142: dt=0.9900, 16 negative triangles 143: dt=0.9900, 10 negative triangles 144: dt=0.9900, 4 negative triangles 145: dt=0.9900, 10 negative triangles 146: dt=0.9900, 4 negative triangles 147: dt=0.9900, 5 negative triangles 148: dt=0.9900, 4 negative triangles 149: dt=0.9900, 5 negative triangles 150: dt=0.9900, 3 negative triangles 151: dt=0.9900, 1 negative triangles 152: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1072 hours mris_sphere utimesec 377.256000 mris_sphere stimesec 0.360000 mris_sphere ru_maxrss 213088 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 220479 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 7632 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 22251 FSRUNTIME@ mris_sphere 0.1072 hours 1 threads #-------------------------------------------- #@# Surf Reg lh 2018. 07. 09. (���) 17:12:31 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_register -curv -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/kt/Downloads/freesurferDev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg Could not set locale No such file or directory Could not set locale using smoothwm curvature for final alignment cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts cmdline mris_register -curv -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /home/kt/Downloads/freesurferDev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ $Id$ reading surface from ../surf/lh.sphere... reading template parameterization from /home/kt/Downloads/freesurferDev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.351 curvature mean = 0.019, std = 0.823 curvature mean = 0.022, std = 0.880 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (3.50, -5.50, 6.50) sse = 144225.9, elapsed since starting=0.3818 min MRISrigidBodyAlignGlobal() done 0.38 min curvature mean = -0.001, std = 0.854 curvature mean = 0.008, std = 0.955 curvature mean = -0.002, std = 0.867 curvature mean = 0.003, std = 0.983 curvature mean = -0.002, std = 0.870 curvature mean = 0.001, std = 0.994 2 Reading smoothwm curvature mean = -0.028, std = 0.282 curvature mean = 0.037, std = 0.253 curvature mean = 0.064, std = 0.380 curvature mean = 0.034, std = 0.312 curvature mean = 0.027, std = 0.586 curvature mean = 0.034, std = 0.339 curvature mean = 0.014, std = 0.723 curvature mean = 0.034, std = 0.350 curvature mean = 0.005, std = 0.818 MRISregister() return, current seed 0 -01: dt=0.0000, 12 negative triangles 090: dt=0.9900, 12 negative triangles expanding nbhd size to 1 091: dt=0.9900, 17 negative triangles 092: dt=0.9900, 11 negative triangles 093: dt=0.9900, 13 negative triangles 094: dt=0.9900, 13 negative triangles 095: dt=0.9900, 15 negative triangles 096: dt=0.9900, 14 negative triangles 097: dt=0.9900, 12 negative triangles 098: dt=0.9900, 12 negative triangles 099: dt=0.9900, 12 negative triangles 100: dt=0.9900, 12 negative triangles 101: dt=0.9900, 9 negative triangles 102: dt=0.9900, 9 negative triangles 103: dt=0.9900, 9 negative triangles 104: dt=0.9900, 10 negative triangles 105: dt=0.9900, 10 negative triangles 106: dt=0.9900, 8 negative triangles 107: dt=0.9900, 8 negative triangles 108: dt=0.9900, 8 negative triangles 109: dt=0.9900, 9 negative triangles 110: dt=0.9900, 10 negative triangles 111: dt=0.9900, 6 negative triangles 112: dt=0.9900, 4 negative triangles 113: dt=0.9900, 4 negative triangles 114: dt=0.9900, 4 negative triangles 115: dt=0.9900, 3 negative triangles 116: dt=0.9900, 3 negative triangles 117: dt=0.9900, 3 negative triangles 118: dt=0.9900, 4 negative triangles 119: dt=0.9900, 3 negative triangles 120: dt=0.9900, 3 negative triangles 121: dt=0.9900, 2 negative triangles 122: dt=0.9900, 3 negative triangles 123: dt=0.9900, 2 negative triangles 124: dt=0.9900, 3 negative triangles 125: dt=0.9900, 2 negative triangles 126: dt=0.9900, 2 negative triangles 127: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.09 hours mris_register utimesec 328.716000 mris_register stimesec 0.272000 mris_register ru_maxrss 209016 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 77730 mris_register ru_majflt 34 mris_register ru_nswap 0 mris_register ru_inblock 15096 mris_register ru_oublock 7736 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 62 mris_register ru_nivcsw 18300 FSRUNTIME@ mris_register 0.0923 hours 1 threads #-------------------------------------------- #@# Surf Reg rh 2018. 07. 09. (���) 17:18:04 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_register -curv -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/kt/Downloads/freesurferDev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Could not set locale No such file or directory Could not set locale using smoothwm curvature for final alignment cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts cmdline mris_register -curv -rusage /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /home/kt/Downloads/freesurferDev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ $Id$ reading surface from ../surf/rh.sphere... reading template parameterization from /home/kt/Downloads/freesurferDev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host=kt-B8, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = -0.000, std = 5.304 curvature mean = 0.033, std = 0.809 curvature mean = 0.016, std = 0.883 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (6.00, -6.50, 10.50) sse = 157158.0, elapsed since starting=0.3649 min MRISrigidBodyAlignGlobal() done 0.37 min curvature mean = 0.008, std = 0.839 curvature mean = 0.005, std = 0.957 curvature mean = 0.007, std = 0.852 curvature mean = 0.002, std = 0.984 curvature mean = 0.006, std = 0.855 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.027, std = 0.283 curvature mean = 0.036, std = 0.247 curvature mean = 0.049, std = 0.393 curvature mean = 0.028, std = 0.306 curvature mean = 0.025, std = 0.588 curvature mean = 0.027, std = 0.334 curvature mean = 0.012, std = 0.723 curvature mean = 0.027, std = 0.347 curvature mean = 0.003, std = 0.822 MRISregister() return, current seed 0 -01: dt=0.0000, 15 negative triangles 098: dt=0.9900, 15 negative triangles expanding nbhd size to 1 099: dt=0.9900, 28 negative triangles 100: dt=0.9405, 16 negative triangles 101: dt=0.9405, 12 negative triangles 102: dt=0.9405, 17 negative triangles 103: dt=0.9405, 11 negative triangles 104: dt=0.9405, 11 negative triangles 105: dt=0.9405, 5 negative triangles 106: dt=0.9405, 3 negative triangles 107: dt=0.9405, 5 negative triangles 108: dt=0.9405, 3 negative triangles 109: dt=0.9405, 2 negative triangles 110: dt=0.9405, 2 negative triangles 111: dt=0.9405, 1 negative triangles 112: dt=0.9405, 1 negative triangles 113: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.10 hours mris_register utimesec 339.948000 mris_register stimesec 0.240000 mris_register ru_maxrss 204512 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 53230 mris_register ru_majflt 61 mris_register ru_nswap 0 mris_register ru_inblock 18912 mris_register ru_oublock 7632 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 106 mris_register ru_nivcsw 12547 FSRUNTIME@ mris_register 0.0955 hours 1 threads #-------------------------------------------- #@# Jacobian white lh 2018. 07. 09. (���) 17:23:48 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white Could not set locale No such file or directory Could not set locale reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh 2018. 07. 09. (���) 17:23:50 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Could not set locale No such file or directory Could not set locale reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh 2018. 07. 09. (���) 17:23:51 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mrisp_paint -a 5 /home/kt/Downloads/freesurferDev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv Could not set locale No such file or directory Could not set locale averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /home/kt/Downloads/freesurferDev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh 2018. 07. 09. (���) 17:23:52 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mrisp_paint -a 5 /home/kt/Downloads/freesurferDev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Could not set locale No such file or directory Could not set locale averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /home/kt/Downloads/freesurferDev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh 2018. 07. 09. (���) 17:23:53 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG lh ../surf/lh.sphere.reg /home/kt/Downloads/freesurferDev/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 957 labels changed using aseg relabeling using gibbs priors... 000: 2577 changed, 109637 examined... 001: 593 changed, 11053 examined... 002: 123 changed, 3310 examined... 003: 32 changed, 741 examined... 004: 5 changed, 183 examined... 005: 3 changed, 30 examined... 006: 1 changed, 18 examined... 007: 0 changed, 6 examined... 220 labels changed using aseg 000: 104 total segments, 59 labels (121 vertices) changed 001: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1680 vertices marked for relabeling... 1680 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 34 seconds. #----------------------------------------- #@# Cortical Parc rh 2018. 07. 09. (���) 17:24:36 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG rh ../surf/rh.sphere.reg /home/kt/Downloads/freesurferDev/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 940 labels changed using aseg relabeling using gibbs priors... 000: 2320 changed, 108203 examined... 001: 532 changed, 10309 examined... 002: 104 changed, 3009 examined... 003: 30 changed, 634 examined... 004: 9 changed, 185 examined... 005: 4 changed, 51 examined... 006: 0 changed, 18 examined... 141 labels changed using aseg 000: 87 total segments, 48 labels (104 vertices) changed 001: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1473 vertices marked for relabeling... 1473 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 28 seconds. #-------------------------------------------- #@# Make Pial Surf lh 2018. 07. 09. (���) 17:25:19 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 161019_x3DT1_SAG lh Could not set locale No such file or directory Could not set locale Could not set locale using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ $Id$ reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/filled.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/brain.finalsurfs.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/../mri/aseg.presurf.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... 13593 bright wm thresholded. 600 bright non-wm voxels segmented. reading original surface position from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.orig... computing class statistics... border white: 206272 voxels (1.23%) border gray 224126 voxels (1.34%) WM (96.0): 97.0 +- 7.9 [70.0 --> 110.0] GM (74.0) : 71.8 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.5 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.1 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-6.1, GM=70+-8.7 mean inside = 92.1, mean outside = 75.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.03-->3.62) (max @ vno 92363 --> 94314) face area 0.33 +- 0.16 (0.00-->3.42) mean absolute distance = 0.76 +- 1.07 3046 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 2 with 172 points - only 0.00% unknown removing 4 vertex label from ripped group in thread:0 deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 5 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group in thread:0 deleting segment 6 with 2 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=80.7, 295 (295) missing vertices, mean dist 0.3 [1.3 (%16.9)->0.6 (%83.1))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %36 local maxima, %59 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.01-->3.92) (max @ vno 82420 --> 83323) face area 0.33 +- 0.16 (0.00-->3.44) mean absolute distance = 0.42 +- 0.84 3250 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1679852.4, rms=7.391 001: dt: 0.5000, sse=996971.4, rms=4.716 (36.183%) 002: dt: 0.5000, sse=759996.0, rms=3.278 (30.492%) 003: dt: 0.5000, sse=697967.2, rms=2.853 (12.967%) 004: dt: 0.5000, sse=665499.4, rms=2.621 (8.142%) rms = 2.71, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=603767.4, rms=1.900 (27.500%) 006: dt: 0.2500, sse=583364.5, rms=1.535 (19.192%) rms = 1.44, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=590325.2, rms=1.441 (6.133%) rms = 1.40, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=577357.1, rms=1.403 (2.678%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 34 points - only 0.00% unknown deleting segment 4 with 25 points - only 0.00% unknown removing 4 vertex label from ripped group in thread:0 deleting segment 6 with 4 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=82.7, 216 (167) missing vertices, mean dist -0.2 [0.5 (%59.4)->0.2 (%40.6))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %45 local maxima, %49 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.02-->4.07) (max @ vno 52954 --> 53917) face area 0.36 +- 0.17 (0.00-->3.87) mean absolute distance = 0.34 +- 0.53 2587 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=837057.1, rms=3.549 009: dt: 0.5000, sse=697153.2, rms=2.327 (34.422%) 010: dt: 0.5000, sse=678860.9, rms=2.137 (8.185%) rms = 2.21, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=648642.8, rms=1.591 (25.547%) 012: dt: 0.2500, sse=614898.4, rms=1.256 (21.059%) rms = 1.19, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=636650.8, rms=1.188 (5.419%) rms = 1.16, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=620891.8, rms=1.156 (2.694%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 deleting segment 0 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group in thread:0 deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 39 points - only 0.00% unknown removing 2 vertex label from ripped group in thread:0 deleting segment 5 with 2 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=85.2, 221 (146) missing vertices, mean dist -0.2 [0.4 (%68.1)->0.2 (%31.9))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.03-->4.54) (max @ vno 82420 --> 83323) face area 0.35 +- 0.17 (0.00-->3.72) mean absolute distance = 0.26 +- 0.39 2665 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=833117.7, rms=3.513 015: dt: 0.5000, sse=685231.1, rms=2.070 (41.061%) rms = 2.10, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=633973.8, rms=1.555 (24.897%) 017: dt: 0.2500, sse=617672.8, rms=1.184 (23.868%) 018: dt: 0.2500, sse=606237.9, rms=1.095 (7.504%) rms = 1.08, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=605441.1, rms=1.084 (1.027%) rms = 1.06, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=602672.8, rms=1.064 (1.865%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group in thread:0 deleting segment 0 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 86 points - only 0.00% unknown removing 2 vertex label from ripped group in thread:0 deleting segment 3 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 4 with 1 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=86.4, 241 (145) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=637277.4, rms=1.883 021: dt: 0.5000, sse=620203.6, rms=1.463 (22.300%) rms = 1.85, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=592366.6, rms=1.029 (29.689%) 023: dt: 0.2500, sse=584628.1, rms=0.910 (11.535%) rms = 0.86, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=570343.1, rms=0.865 (4.981%) rms = 0.86, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=581037.9, rms=0.861 (0.403%) positioning took 0.3 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7409 vertices erasing segment 1 (vno[0] = 42365) erasing segment 2 (vno[0] = 43124) erasing segment 3 (vno[0] = 66780) erasing segment 4 (vno[0] = 77851) erasing segment 5 (vno[0] = 78706) erasing segment 6 (vno[0] = 78770) erasing segment 7 (vno[0] = 79665) erasing segment 8 (vno[0] = 81414) erasing segment 9 (vno[0] = 81459) erasing segment 10 (vno[0] = 83282) erasing segment 11 (vno[0] = 85553) erasing segment 12 (vno[0] = 86316) erasing segment 13 (vno[0] = 109376) writing cortex label to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label... writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.area vertex spacing 0.89 +- 0.26 (0.04-->4.59) (max @ vno 82420 --> 83323) face area 0.34 +- 0.16 (0.00-->3.39) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group in thread:0 deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 15 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=55.4, 188 (188) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.3 (%100.0))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %25 local maxima, %53 large gradients and %17 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21079992.0, rms=31.436 001: dt: 0.5000, sse=15636567.0, rms=26.956 (14.253%) 002: dt: 0.5000, sse=11372235.0, rms=22.837 (15.279%) 003: dt: 0.5000, sse=8253613.0, rms=19.272 (15.610%) 004: dt: 0.5000, sse=6175026.0, rms=16.469 (14.547%) 005: dt: 0.5000, sse=4774636.5, rms=14.271 (13.347%) 006: dt: 0.5000, sse=3696227.8, rms=12.311 (13.732%) 007: dt: 0.5000, sse=2860279.5, rms=10.540 (14.382%) 008: dt: 0.5000, sse=2207640.5, rms=8.914 (15.432%) 009: dt: 0.5000, sse=1749138.2, rms=7.562 (15.166%) 010: dt: 0.5000, sse=1437846.6, rms=6.485 (14.244%) 011: dt: 0.5000, sse=1255493.1, rms=5.758 (11.206%) 012: dt: 0.5000, sse=1141971.6, rms=5.255 (8.734%) 013: dt: 0.5000, sse=1081303.0, rms=4.963 (5.558%) 014: dt: 0.5000, sse=1038121.8, rms=4.746 (4.376%) 015: dt: 0.5000, sse=1014360.7, rms=4.620 (2.657%) 016: dt: 0.5000, sse=993638.6, rms=4.511 (2.363%) 017: dt: 0.5000, sse=982714.3, rms=4.448 (1.385%) 018: dt: 0.5000, sse=970868.3, rms=4.384 (1.437%) rms = 4.34, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=964411.9, rms=4.345 (0.897%) 020: dt: 0.2500, sse=786694.3, rms=3.123 (28.129%) 021: dt: 0.2500, sse=745175.0, rms=2.774 (11.184%) 022: dt: 0.2500, sse=735006.8, rms=2.680 (3.375%) 023: dt: 0.2500, sse=729290.2, rms=2.628 (1.940%) rms = 2.61, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=727507.9, rms=2.610 (0.672%) 025: dt: 0.1250, sse=714016.1, rms=2.474 (5.227%) rms = 2.46, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=712289.2, rms=2.456 (0.710%) positioning took 1.4 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=53.3, 397 (10) missing vertices, mean dist 0.1 [0.1 (%43.3)->0.4 (%56.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %46 local maxima, %37 large gradients and %12 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1085816.4, rms=4.308 027: dt: 0.5000, sse=993663.9, rms=3.747 (13.019%) rms = 4.13, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=883693.9, rms=2.952 (21.230%) 029: dt: 0.2500, sse=846831.5, rms=2.648 (10.296%) 030: dt: 0.2500, sse=837121.9, rms=2.559 (3.360%) rms = 2.52, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=833069.8, rms=2.524 (1.359%) 032: dt: 0.1250, sse=822279.8, rms=2.410 (4.531%) rms = 2.39, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=820231.8, rms=2.389 (0.850%) positioning took 0.4 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=51.8, 523 (6) missing vertices, mean dist 0.1 [0.1 (%42.3)->0.3 (%57.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %59 local maxima, %24 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=920955.9, rms=3.163 rms = 3.84, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=855346.2, rms=2.604 (17.657%) 035: dt: 0.2500, sse=839458.2, rms=2.448 (5.998%) rms = 2.40, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=833574.6, rms=2.401 (1.929%) 037: dt: 0.1250, sse=825527.8, rms=2.313 (3.672%) rms = 2.30, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=823921.9, rms=2.299 (0.613%) positioning took 0.3 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=50.9, 1234 (5) missing vertices, mean dist 0.1 [0.1 (%47.0)->0.2 (%53.0))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %64 local maxima, %19 large gradients and %11 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=850967.2, rms=2.569 rms = 3.28, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=826561.6, rms=2.319 (9.763%) rms = 2.27, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=821444.4, rms=2.272 (2.019%) 041: dt: 0.1250, sse=816328.2, rms=2.214 (2.523%) rms = 2.19, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=813400.5, rms=2.188 (1.211%) positioning took 0.3 minutes writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.area.pial vertex spacing 1.00 +- 0.41 (0.01-->5.21) (max @ vno 78717 --> 77789) face area 0.40 +- 0.29 (0.00-->5.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 109637 vertices processed 25000 of 109637 vertices processed 50000 of 109637 vertices processed 75000 of 109637 vertices processed 100000 of 109637 vertices processed 0 of 109637 vertices processed 25000 of 109637 vertices processed 50000 of 109637 vertices processed 75000 of 109637 vertices processed 100000 of 109637 vertices processed thickness calculation complete, 92:625 truncations. 36502 vertices at 0 distance 89255 vertices at 1 distance 57117 vertices at 2 distance 18100 vertices at 3 distance 4878 vertices at 4 distance 1519 vertices at 5 distance 548 vertices at 6 distance 211 vertices at 7 distance 94 vertices at 8 distance 50 vertices at 9 distance 39 vertices at 10 distance 28 vertices at 11 distance 17 vertices at 12 distance 8 vertices at 13 distance 3 vertices at 14 distance 9 vertices at 15 distance 7 vertices at 16 distance 5 vertices at 17 distance 0 vertices at 18 distance 1 vertices at 19 distance 7 vertices at 20 distance writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.thickness positioning took 5.9 minutes #-------------------------------------------- #@# Make Pial Surf rh 2018. 07. 09. (���) 17:31:20 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 161019_x3DT1_SAG rh Could not set locale No such file or directory Could not set locale Could not set locale using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ $Id$ reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/filled.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/brain.finalsurfs.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/../mri/aseg.presurf.mgz... reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... 13593 bright wm thresholded. 600 bright non-wm voxels segmented. reading original surface position from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.orig... computing class statistics... border white: 206272 voxels (1.23%) border gray 224126 voxels (1.34%) WM (96.0): 97.0 +- 7.9 [70.0 --> 110.0] GM (74.0) : 71.8 +- 11.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 55.5 (was 70) setting MAX_BORDER_WHITE to 108.9 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 44.1 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.6 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101+-7.0, GM=67+-10.4 mean inside = 91.8, mean outside = 74.8 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.26 (0.04-->4.48) (max @ vno 45428 --> 45435) face area 0.34 +- 0.16 (0.00-->2.57) mean absolute distance = 0.81 +- 1.12 3189 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group in thread:0 deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 243 points - only 0.00% unknown deleting segment 3 with 67 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 4 with 1 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=79.2, 106 (106) missing vertices, mean dist 0.3 [1.4 (%17.7)->0.7 (%82.3))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %42 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.02-->4.60) (max @ vno 45435 --> 45428) face area 0.34 +- 0.16 (0.00-->2.08) mean absolute distance = 0.45 +- 0.88 3279 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1776853.4, rms=7.803 001: dt: 0.5000, sse=1073264.2, rms=5.120 (34.385%) 002: dt: 0.5000, sse=804638.4, rms=3.666 (28.392%) 003: dt: 0.5000, sse=722858.7, rms=3.125 (14.764%) 004: dt: 0.5000, sse=695485.2, rms=2.833 (9.352%) rms = 2.84, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=617099.8, rms=2.101 (25.833%) 006: dt: 0.2500, sse=588586.2, rms=1.698 (19.184%) 007: dt: 0.2500, sse=584783.3, rms=1.573 (7.338%) rms = 1.53, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=581169.2, rms=1.528 (2.863%) rms = 1.49, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=577278.6, rms=1.488 (2.622%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 23 points - only 0.00% unknown deleting segment 1 with 48 points - only 0.00% unknown deleting segment 2 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group in thread:0 deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 61 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=81.2, 75 (23) missing vertices, mean dist -0.2 [0.6 (%57.8)->0.2 (%42.2))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %49 local maxima, %46 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.92 +- 0.26 (0.02-->4.69) (max @ vno 45435 --> 45428) face area 0.36 +- 0.17 (0.00-->2.39) mean absolute distance = 0.38 +- 0.56 2913 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=866294.8, rms=3.778 010: dt: 0.5000, sse=718699.9, rms=2.582 (31.654%) 011: dt: 0.5000, sse=685365.2, rms=2.362 (8.507%) rms = 2.39, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=642255.9, rms=1.791 (24.160%) 013: dt: 0.2500, sse=618260.9, rms=1.407 (21.439%) 014: dt: 0.2500, sse=611539.8, rms=1.299 (7.728%) rms = 1.27, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=602966.6, rms=1.266 (2.547%) rms = 1.23, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=600755.8, rms=1.232 (2.618%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 2 with 73 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 63 points - only 0.00% unknown deleting segment 5 with 47 points - only 12.77% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=83.8, 73 (12) missing vertices, mean dist -0.2 [0.5 (%67.5)->0.2 (%32.5))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.06-->4.74) (max @ vno 45435 --> 45428) face area 0.35 +- 0.17 (0.00-->2.94) mean absolute distance = 0.29 +- 0.43 2865 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=843947.5, rms=3.764 017: dt: 0.5000, sse=669692.9, rms=2.249 (40.243%) rms = 2.22, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=663389.5, rms=2.225 (1.090%) 019: dt: 0.2500, sse=601687.3, rms=1.321 (40.602%) 020: dt: 0.2500, sse=591352.3, rms=1.179 (10.753%) rms = 1.16, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=595261.8, rms=1.157 (1.870%) rms = 1.11, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=590685.8, rms=1.110 (4.089%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 82 points - only 0.00% unknown removing 3 vertex label from ripped group in thread:0 deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 63 points - only 0.00% unknown deleting segment 4 with 25 points - only 24.00% unknown deleting segment 5 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group in thread:0 deleting segment 6 with 3 points - only 0.00% unknown NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=85.2, 91 (9) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.2 (%39.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=637254.4, rms=2.088 023: dt: 0.5000, sse=606829.7, rms=1.575 (24.602%) rms = 1.97, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=579366.0, rms=1.088 (30.895%) 025: dt: 0.2500, sse=567933.4, rms=0.952 (12.529%) rms = 0.90, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=574691.6, rms=0.901 (5.287%) rms = 0.88, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=568393.9, rms=0.884 (1.971%) positioning took 0.3 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7400 vertices erasing segment 0 (vno[0] = 25789) erasing segment 1 (vno[0] = 26872) erasing segment 2 (vno[0] = 26901) erasing segment 4 (vno[0] = 43367) erasing segment 5 (vno[0] = 45196) erasing segment 6 (vno[0] = 76453) erasing segment 7 (vno[0] = 80666) erasing segment 8 (vno[0] = 80724) erasing segment 9 (vno[0] = 80756) erasing segment 10 (vno[0] = 81524) erasing segment 11 (vno[0] = 82341) erasing segment 12 (vno[0] = 84715) erasing segment 13 (vno[0] = 86000) writing cortex label to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label... writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.area vertex spacing 0.89 +- 0.26 (0.02-->4.79) (max @ vno 45428 --> 45435) face area 0.34 +- 0.17 (0.00-->2.99) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 1 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group in thread:0 deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 18 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=53.2, 102 (102) missing vertices, mean dist 1.9 [0.5 (%0.0)->2.4 (%100.0))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %21 local maxima, %53 large gradients and %22 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kt-B8, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=22119790.0, rms=32.450 001: dt: 0.5000, sse=16560664.0, rms=27.963 (13.825%) 002: dt: 0.5000, sse=12160340.0, rms=23.818 (14.823%) 003: dt: 0.5000, sse=8906414.0, rms=20.210 (15.148%) 004: dt: 0.5000, sse=6701907.5, rms=17.340 (14.202%) 005: dt: 0.5000, sse=5175471.5, rms=15.032 (13.307%) 006: dt: 0.5000, sse=3983880.2, rms=12.946 (13.883%) 007: dt: 0.5000, sse=3059480.5, rms=11.056 (14.596%) 008: dt: 0.5000, sse=2336046.2, rms=9.310 (15.791%) 009: dt: 0.5000, sse=1832975.4, rms=7.869 (15.478%) 010: dt: 0.5000, sse=1491511.1, rms=6.715 (14.664%) 011: dt: 0.5000, sse=1297915.5, rms=5.962 (11.219%) 012: dt: 0.5000, sse=1173704.2, rms=5.422 (9.062%) 013: dt: 0.5000, sse=1110058.6, rms=5.122 (5.534%) 014: dt: 0.5000, sse=1061478.0, rms=4.879 (4.735%) 015: dt: 0.5000, sse=1040838.2, rms=4.772 (2.200%) 016: dt: 0.5000, sse=1015071.2, rms=4.635 (2.857%) rms = 4.60, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=1008112.3, rms=4.598 (0.813%) 018: dt: 0.2500, sse=835449.7, rms=3.478 (24.346%) 019: dt: 0.2500, sse=792543.2, rms=3.153 (9.353%) 020: dt: 0.2500, sse=780514.6, rms=3.055 (3.123%) 021: dt: 0.2500, sse=773008.6, rms=2.993 (2.015%) rms = 2.96, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=769210.1, rms=2.961 (1.069%) 023: dt: 0.1250, sse=757779.1, rms=2.857 (3.504%) rms = 2.84, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=756054.0, rms=2.842 (0.542%) positioning took 1.4 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=51.6, 560 (6) missing vertices, mean dist 0.1 [0.1 (%45.7)->0.4 (%54.3))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %39 local maxima, %40 large gradients and %15 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kt-B8, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1032384.2, rms=4.056 025: dt: 0.5000, sse=992157.6, rms=3.801 (6.294%) rms = 4.24, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=898811.7, rms=3.136 (17.482%) 027: dt: 0.2500, sse=867301.7, rms=2.891 (7.809%) 028: dt: 0.2500, sse=859694.1, rms=2.826 (2.244%) rms = 2.80, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=856241.7, rms=2.800 (0.945%) 030: dt: 0.1250, sse=847300.6, rms=2.712 (3.139%) rms = 2.70, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=845700.6, rms=2.698 (0.523%) positioning took 0.4 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=50.5, 763 (4) missing vertices, mean dist 0.1 [0.1 (%47.0)->0.3 (%53.0))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %52 local maxima, %27 large gradients and %15 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kt-B8, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=907970.6, rms=3.143 rms = 3.74, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=864692.8, rms=2.777 (11.640%) 033: dt: 0.2500, sse=855121.6, rms=2.692 (3.062%) rms = 2.66, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=850696.4, rms=2.660 (1.213%) 035: dt: 0.1250, sse=843938.3, rms=2.592 (2.538%) rms = 2.58, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=842230.2, rms=2.578 (0.530%) positioning took 0.3 minutes NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING mean border=49.7, 1428 (4) missing vertices, mean dist 0.1 [0.1 (%49.3)->0.3 (%50.7))] NONREPRODUCIBLE NUMBERS NOT USED FOR ANYTHING %58 local maxima, %21 large gradients and %15 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kt-B8, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=867052.1, rms=2.807 rms = 3.36, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=845836.4, rms=2.606 (7.149%) 038: dt: 0.2500, sse=839859.5, rms=2.555 (1.939%) rms = 2.53, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=835897.6, rms=2.527 (1.105%) 040: dt: 0.1250, sse=828995.9, rms=2.457 (2.794%) rms = 2.44, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=826766.3, rms=2.438 (0.743%) positioning took 0.3 minutes writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.area.pial vertex spacing 1.00 +- 0.42 (0.01-->5.28) (max @ vno 39156 --> 38001) face area 0.40 +- 0.30 (0.00-->4.74) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 108203 vertices processed 25000 of 108203 vertices processed 50000 of 108203 vertices processed 75000 of 108203 vertices processed 100000 of 108203 vertices processed 0 of 108203 vertices processed 25000 of 108203 vertices processed 50000 of 108203 vertices processed 75000 of 108203 vertices processed 100000 of 108203 vertices processed thickness calculation complete, 144:572 truncations. 34882 vertices at 0 distance 87915 vertices at 1 distance 56230 vertices at 2 distance 18581 vertices at 3 distance 5243 vertices at 4 distance 1597 vertices at 5 distance 505 vertices at 6 distance 166 vertices at 7 distance 81 vertices at 8 distance 34 vertices at 9 distance 23 vertices at 10 distance 28 vertices at 11 distance 5 vertices at 12 distance 7 vertices at 13 distance 6 vertices at 14 distance 4 vertices at 15 distance 4 vertices at 16 distance 1 vertices at 17 distance 5 vertices at 18 distance 0 vertices at 19 distance 3 vertices at 20 distance writing curvature file /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.thickness positioning took 5.7 minutes #-------------------------------------------- #@# Surf Volume lh 2018. 07. 09. (���) 17:37:05 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf vertexvol --s 161019_x3DT1_SAG --lh --th3 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Could not set locale No such file or directory Could not set locale Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Could not set locale No such file or directory Could not set locale Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 161019_x3DT1_SAG lh /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.volume Could not set locale No such file or directory Could not set locale masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label Total face volume 173863 Total vertex volume 169979 (mask=0) #@# 161019_x3DT1_SAG lh 169979 vertexvol Done #-------------------------------------------- #@# Surf Volume rh 2018. 07. 09. (���) 17:37:07 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf vertexvol --s 161019_x3DT1_SAG --rh --th3 /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Could not set locale No such file or directory Could not set locale Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Could not set locale No such file or directory Could not set locale Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume 161019_x3DT1_SAG rh /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.volume Could not set locale No such file or directory Could not set locale masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label Total face volume 172105 Total vertex volume 168066 (mask=0) #@# 161019_x3DT1_SAG rh 168066 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask 2018. 07. 09. (���) 17:37:09 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 161019_x3DT1_SAG SUBJECTS_DIR is /home/kt/Downloads/Thalamus/Outputs loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 36 writing volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz mris_volmask took 7.14 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh 2018. 07. 09. (���) 17:44:17 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 161019_x3DT1_SAG lh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1139 779 1732 2.195 0.464 0.099 0.019 7 0.8 bankssts 834 529 1133 2.496 0.692 0.143 0.029 16 1.0 caudalanteriorcingulate 2934 1917 5215 2.310 0.574 0.121 0.028 31 3.3 caudalmiddlefrontal 1810 1131 1940 1.674 0.341 0.157 0.034 32 2.6 cuneus 399 259 1341 3.298 1.020 0.122 0.029 5 0.5 entorhinal 3533 2465 7031 2.445 0.659 0.148 0.041 56 6.0 fusiform 6013 4077 9857 2.130 0.525 0.144 0.034 87 8.4 inferiorparietal 3822 2649 8100 2.619 0.614 0.140 0.033 52 5.4 inferiortemporal 1562 999 2450 2.237 0.804 0.127 0.036 23 2.0 isthmuscingulate 5906 3812 7145 1.761 0.440 0.148 0.036 90 8.5 lateraloccipital 2762 1967 5216 2.459 0.594 0.143 0.036 44 3.9 lateralorbitofrontal 3470 2339 4458 1.781 0.460 0.154 0.039 53 5.6 lingual 2030 1346 3267 2.174 0.654 0.131 0.040 30 3.2 medialorbitofrontal 3864 2592 8336 2.649 0.588 0.128 0.029 52 4.6 middletemporal 792 517 1116 1.913 0.595 0.097 0.019 5 0.6 parahippocampal 1800 1120 2610 2.182 0.573 0.118 0.030 16 2.2 paracentral 1759 1178 3087 2.303 0.481 0.124 0.027 19 1.9 parsopercularis 923 593 1899 2.436 0.559 0.155 0.041 18 1.7 parsorbitalis 1393 942 2481 2.374 0.549 0.127 0.027 16 1.5 parstriangularis 1558 1008 1392 1.521 0.307 0.138 0.035 17 2.2 pericalcarine 5804 3758 7773 1.820 0.591 0.119 0.028 59 6.6 postcentral 1279 889 2082 2.101 0.675 0.142 0.028 20 1.3 posteriorcingulate 6923 4331 10851 2.309 0.574 0.111 0.024 58 6.9 precentral 4417 3051 6883 2.084 0.589 0.139 0.037 57 6.6 precuneus 1024 679 2127 2.817 0.967 0.136 0.039 18 1.6 rostralanteriorcingulate 5728 3920 9588 2.190 0.527 0.149 0.036 88 8.9 rostralmiddlefrontal 7556 5097 14690 2.543 0.535 0.132 0.035 91 10.4 superiorfrontal 7045 4608 10271 1.955 0.506 0.131 0.028 87 7.9 superiorparietal 4470 3032 7893 2.289 0.707 0.102 0.020 38 3.5 superiortemporal 4870 3296 8426 2.341 0.500 0.136 0.032 66 6.0 supramarginal 344 220 761 2.569 0.387 0.179 0.047 7 0.7 frontalpole 568 412 2659 3.705 0.610 0.153 0.047 9 1.0 temporalpole 542 312 654 1.962 0.479 0.117 0.022 5 0.4 transversetemporal 3062 2045 5497 2.651 0.910 0.107 0.030 25 3.3 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 161019_x3DT1_SAG lh pial Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1139 783 1732 2.195 0.464 0.113 0.022 11 1.2 bankssts 834 499 1133 2.496 0.692 0.110 0.028 53 0.9 caudalanteriorcingulate 2934 2493 5215 2.310 0.574 0.134 0.024 32 3.1 caudalmiddlefrontal 1810 1275 1940 1.674 0.341 0.136 0.030 29 2.3 cuneus 399 538 1341 3.298 1.020 0.191 0.033 5 0.7 entorhinal 3533 3174 7031 2.445 0.659 0.164 0.040 50 6.2 fusiform 6013 4996 9857 2.130 0.525 0.158 0.035 89 8.9 inferiorparietal 3822 3364 8100 2.619 0.614 0.161 0.056 72 7.0 inferiortemporal 1562 1205 2450 2.237 0.804 0.147 0.037 50 2.3 isthmuscingulate 5906 4383 7145 1.761 0.440 0.141 0.032 86 7.8 lateraloccipital 2762 2267 5216 2.459 0.594 0.147 0.036 38 3.9 lateralorbitofrontal 3470 2805 4458 1.781 0.460 0.156 0.040 54 5.8 lingual 2030 1636 3267 2.174 0.654 0.146 0.038 36 3.4 medialorbitofrontal 3864 3543 8336 2.649 0.588 0.149 0.028 47 4.7 middletemporal 792 680 1116 1.913 0.595 0.120 0.023 5 0.9 parahippocampal 1800 1300 2610 2.182 0.573 0.122 0.027 26 2.0 paracentral 1759 1454 3087 2.303 0.481 0.138 0.027 18 2.0 parsopercularis 923 946 1899 2.436 0.559 0.198 0.041 18 1.9 parsorbitalis 1393 1156 2481 2.374 0.549 0.150 0.029 19 1.8 parstriangularis 1558 857 1392 1.521 0.307 0.118 0.033 22 2.0 pericalcarine 5804 4712 7773 1.820 0.591 0.130 0.026 55 6.4 postcentral 1279 1070 2082 2.101 0.675 0.169 0.041 27 2.0 posteriorcingulate 6923 4941 10851 2.309 0.574 0.109 0.019 64 5.7 precentral 4417 3414 6883 2.084 0.589 0.151 0.036 68 6.6 precuneus 1024 885 2127 2.817 0.967 0.169 0.038 45 1.6 rostralanteriorcingulate 5728 4746 9588 2.190 0.527 0.163 0.035 90 9.3 rostralmiddlefrontal 7556 6274 14690 2.543 0.535 0.143 0.032 138 9.8 superiorfrontal 7045 5705 10271 1.955 0.506 0.145 0.031 91 9.1 superiorparietal 4470 3675 7893 2.289 0.707 0.114 0.019 34 3.6 superiortemporal 4870 3834 8426 2.341 0.500 0.137 0.028 57 5.6 supramarginal 344 372 761 2.569 0.387 0.208 0.034 5 0.6 frontalpole 568 932 2659 3.705 0.610 0.250 0.043 9 1.2 temporalpole 542 371 654 1.962 0.479 0.108 0.018 4 0.4 transversetemporal 3062 1958 5497 2.651 0.910 0.107 0.027 39 3.1 insula #----------------------------------------- #@# Parcellation Stats rh 2018. 07. 09. (���) 17:44:59 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 161019_x3DT1_SAG rh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1139 779 1638 2.164 0.452 0.113 0.021 9 0.9 bankssts 883 554 1297 2.219 0.587 0.147 0.031 15 1.1 caudalanteriorcingulate 2199 1449 3902 2.493 0.556 0.132 0.037 26 3.9 caudalmiddlefrontal 2110 1368 2212 1.567 0.332 0.149 0.036 28 3.3 cuneus 364 269 1594 3.409 0.826 0.133 0.037 4 0.4 entorhinal 3100 2127 6709 2.612 0.700 0.142 0.037 50 4.5 fusiform 6423 4477 10966 2.139 0.544 0.144 0.034 92 9.6 inferiorparietal 3100 2213 6947 2.712 0.667 0.154 0.043 48 5.8 inferiortemporal 1224 771 1919 2.157 0.662 0.134 0.032 20 1.4 isthmuscingulate 5530 3648 7473 1.930 0.481 0.148 0.036 75 8.3 lateraloccipital 3004 2105 5609 2.539 0.672 0.149 0.044 42 5.5 lateralorbitofrontal 3874 2651 4885 1.784 0.485 0.153 0.040 57 6.5 lingual 2118 1447 4007 2.394 0.677 0.139 0.037 31 3.0 medialorbitofrontal 3877 2693 8907 2.699 0.589 0.134 0.031 58 5.3 middletemporal 930 594 1135 1.771 0.546 0.098 0.017 7 0.6 parahippocampal 1768 1142 2718 2.245 0.601 0.129 0.039 17 2.9 paracentral 1575 1027 2607 2.319 0.448 0.127 0.026 17 1.6 parsopercularis 973 654 1933 2.465 0.540 0.173 0.052 20 2.0 parsorbitalis 1808 1203 3097 2.309 0.478 0.128 0.027 20 1.9 parstriangularis 1865 1184 1691 1.522 0.352 0.139 0.037 23 2.7 pericalcarine 5576 3686 6970 1.750 0.557 0.117 0.025 51 6.0 postcentral 1387 973 2483 2.245 0.685 0.157 0.033 25 1.9 posteriorcingulate 5964 3728 9399 2.357 0.558 0.112 0.025 48 6.2 precentral 4555 3127 6646 2.004 0.521 0.142 0.034 63 5.9 precuneus 758 527 1709 2.758 0.528 0.161 0.043 18 1.3 rostralanteriorcingulate 6891 4746 11459 2.227 0.490 0.147 0.035 98 9.9 rostralmiddlefrontal 7084 4748 13428 2.533 0.551 0.135 0.037 85 10.7 superiorfrontal 6568 4443 9343 1.901 0.488 0.137 0.033 86 8.5 superiorparietal 4271 2856 7913 2.450 0.648 0.102 0.020 36 3.3 superiortemporal 4745 3248 7506 2.157 0.511 0.128 0.029 56 5.6 supramarginal 427 286 1092 2.754 0.479 0.192 0.061 12 1.1 frontalpole 632 469 2553 3.312 0.853 0.158 0.043 10 1.2 temporalpole 478 274 618 1.951 0.485 0.105 0.024 4 0.4 transversetemporal 3240 2188 5692 2.626 0.963 0.118 0.037 35 5.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 161019_x3DT1_SAG rh pial Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1139 712 1638 2.164 0.452 0.125 0.028 18 1.4 bankssts 883 600 1297 2.219 0.587 0.160 0.045 40 1.3 caudalanteriorcingulate 2199 1614 3902 2.493 0.556 0.129 0.036 37 3.0 caudalmiddlefrontal 2110 1590 2212 1.567 0.332 0.134 0.031 24 3.0 cuneus 364 601 1594 3.409 0.826 0.241 0.048 4 0.8 entorhinal 3100 2841 6709 2.612 0.700 0.163 0.041 63 5.2 fusiform 6423 5576 10966 2.139 0.544 0.158 0.031 88 9.2 inferiorparietal 3100 2747 6947 2.712 0.667 0.174 0.044 116 6.8 inferiortemporal 1224 963 1919 2.157 0.662 0.156 0.046 47 1.7 isthmuscingulate 5530 4162 7473 1.930 0.481 0.144 0.033 100 8.2 lateraloccipital 3004 2300 5609 2.539 0.672 0.148 0.039 52 5.2 lateralorbitofrontal 3874 2904 4885 1.784 0.485 0.144 0.035 51 6.2 lingual 2118 1907 4007 2.394 0.677 0.170 0.038 37 3.5 medialorbitofrontal 3877 3809 8907 2.699 0.589 0.153 0.030 39 5.1 middletemporal 930 720 1135 1.771 0.546 0.114 0.021 9 0.9 parahippocampal 1768 1248 2718 2.245 0.601 0.122 0.027 16 2.0 paracentral 1575 1196 2607 2.319 0.448 0.133 0.029 18 1.8 parsopercularis 973 917 1933 2.465 0.540 0.181 0.036 14 1.4 parsorbitalis 1808 1483 3097 2.309 0.478 0.158 0.034 25 2.7 parstriangularis 1865 1127 1691 1.522 0.352 0.125 0.032 26 2.4 pericalcarine 5576 4450 6970 1.750 0.557 0.125 0.025 45 6.1 postcentral 1387 1175 2483 2.245 0.685 0.159 0.035 24 2.2 posteriorcingulate 5964 4184 9399 2.357 0.558 0.106 0.021 52 5.0 precentral 4555 3466 6646 2.004 0.521 0.148 0.034 74 6.5 precuneus 758 754 1709 2.758 0.528 0.178 0.040 21 1.3 rostralanteriorcingulate 6891 5529 11459 2.227 0.490 0.151 0.032 112 9.8 rostralmiddlefrontal 7084 5656 13428 2.533 0.551 0.144 0.032 110 9.3 superiorfrontal 6568 5402 9343 1.901 0.488 0.149 0.031 99 8.6 superiorparietal 4271 3521 7913 2.450 0.648 0.118 0.021 58 3.7 superiortemporal 4745 3693 7506 2.157 0.511 0.130 0.028 46 5.4 supramarginal 427 487 1092 2.754 0.479 0.205 0.039 5 0.8 frontalpole 632 1006 2553 3.312 0.853 0.228 0.042 7 1.3 temporalpole 478 348 618 1.951 0.485 0.097 0.014 2 0.2 transversetemporal 3240 2009 5692 2.626 0.963 0.113 0.026 48 3.4 insula #----------------------------------------- #@# Cortical Parc 2 lh 2018. 07. 09. (���) 17:45:40 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG lh ../surf/lh.sphere.reg /home/kt/Downloads/freesurferDev/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 25 labels changed using aseg relabeling using gibbs priors... 000: 7407 changed, 109637 examined... 001: 1692 changed, 28714 examined... 002: 481 changed, 8997 examined... 003: 180 changed, 2793 examined... 004: 83 changed, 1046 examined... 005: 61 changed, 481 examined... 006: 30 changed, 346 examined... 007: 16 changed, 162 examined... 008: 8 changed, 90 examined... 009: 0 changed, 49 examined... 11 labels changed using aseg 000: 205 total segments, 118 labels (1354 vertices) changed 001: 91 total segments, 4 labels (17 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1166 vertices marked for relabeling... 1166 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc 2 rh 2018. 07. 09. (���) 17:45:53 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG rh ../surf/rh.sphere.reg /home/kt/Downloads/freesurferDev/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 11 labels changed using aseg relabeling using gibbs priors... 000: 7137 changed, 108203 examined... 001: 1685 changed, 28051 examined... 002: 454 changed, 8983 examined... 003: 190 changed, 2585 examined... 004: 91 changed, 1086 examined... 005: 34 changed, 518 examined... 006: 20 changed, 206 examined... 007: 9 changed, 108 examined... 008: 3 changed, 51 examined... 009: 3 changed, 16 examined... 010: 4 changed, 23 examined... 011: 1 changed, 23 examined... 012: 2 changed, 5 examined... 013: 1 changed, 10 examined... 014: 2 changed, 7 examined... 015: 2 changed, 13 examined... 016: 1 changed, 6 examined... 017: 2 changed, 7 examined... 018: 3 changed, 13 examined... 019: 0 changed, 9 examined... 16 labels changed using aseg 000: 203 total segments, 118 labels (1080 vertices) changed 001: 87 total segments, 2 labels (18 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 23 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1014 vertices marked for relabeling... 1014 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh 2018. 07. 09. (���) 17:46:05 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 161019_x3DT1_SAG lh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 888 623 1483 2.173 0.528 0.167 0.041 16 1.6 G&S_frontomargin 1293 887 1856 1.918 0.504 0.161 0.040 22 2.0 G&S_occipital_inf 1512 921 2366 2.136 0.565 0.124 0.037 16 2.2 G&S_paracentral 1393 903 2302 2.233 0.504 0.143 0.034 19 1.9 G&S_subcentral 604 418 1328 2.500 0.418 0.184 0.047 14 1.2 G&S_transv_frontopol 1727 1190 3387 2.733 0.734 0.142 0.036 27 2.5 G&S_cingul-Ant 829 562 1165 2.172 0.437 0.123 0.024 10 0.8 G&S_cingul-Mid-Ant 911 653 1648 2.360 0.612 0.124 0.024 8 0.8 G&S_cingul-Mid-Post 514 347 1276 2.865 0.492 0.161 0.049 10 0.9 G_cingul-Post-dorsal 405 249 611 2.220 0.683 0.165 0.062 10 1.0 G_cingul-Post-ventral 1636 999 1902 1.702 0.353 0.162 0.035 32 2.3 G_cuneus 1024 674 2194 2.583 0.439 0.128 0.029 13 1.2 G_front_inf-Opercular 346 235 862 2.542 0.406 0.145 0.033 7 0.5 G_front_inf-Orbital 799 534 1761 2.487 0.397 0.148 0.039 13 1.3 G_front_inf-Triangul 3145 2053 6522 2.480 0.512 0.150 0.039 55 5.3 G_front_middle 5253 3452 11334 2.653 0.530 0.139 0.040 71 8.4 G_front_sup 532 335 1043 2.924 0.762 0.108 0.030 5 0.6 G_Ins_lg&S_cent_ins 533 323 1711 3.730 0.655 0.118 0.036 6 0.8 G_insular_short 1819 1169 3156 2.146 0.509 0.154 0.043 31 3.0 G_occipital_middle 1376 813 1795 1.959 0.465 0.135 0.029 18 1.7 G_occipital_sup 1593 1086 3404 2.514 0.509 0.154 0.043 32 2.7 G_oc-temp_lat-fusifor 2666 1722 3568 1.803 0.458 0.163 0.044 46 4.8 G_oc-temp_med-Lingual 949 592 2130 2.525 0.983 0.109 0.025 9 0.9 G_oc-temp_med-Parahip 1991 1338 4317 2.574 0.557 0.157 0.044 45 3.5 G_orbital 2360 1557 4904 2.408 0.540 0.164 0.046 53 4.1 G_pariet_inf-Angular 2291 1553 4564 2.429 0.478 0.134 0.033 34 2.8 G_pariet_inf-Supramar 2288 1529 4369 2.180 0.539 0.146 0.034 36 3.1 G_parietal_sup 2260 1386 3590 1.951 0.662 0.127 0.037 29 3.3 G_postcentral 2562 1441 4735 2.582 0.465 0.113 0.029 28 2.8 G_precentral 2277 1566 4591 2.328 0.511 0.160 0.049 45 4.3 G_precuneus 887 584 1655 2.196 0.512 0.163 0.056 20 1.9 G_rectus 781 494 1031 2.312 0.917 0.104 0.042 10 1.0 G_subcallosal 430 221 643 2.273 0.478 0.113 0.025 5 0.3 G_temp_sup-G_T_transv 1621 1023 3773 2.613 0.678 0.126 0.032 24 1.9 G_temp_sup-Lateral 660 482 1517 2.780 0.822 0.070 0.012 2 0.3 G_temp_sup-Plan_polar 599 447 1170 2.304 0.511 0.100 0.020 5 0.5 G_temp_sup-Plan_tempo 2220 1526 5793 2.793 0.614 0.153 0.041 40 3.8 G_temporal_inf 2210 1400 5467 2.786 0.555 0.140 0.035 38 3.0 G_temporal_middle 247 160 284 2.066 0.608 0.103 0.015 2 0.1 Lat_Fis-ant-Horizont 211 155 323 2.292 0.305 0.116 0.023 1 0.2 Lat_Fis-ant-Vertical 898 605 1012 2.002 0.575 0.105 0.021 5 0.8 Lat_Fis-post 1574 946 1676 1.658 0.341 0.146 0.041 27 2.5 Pole_occipital 1249 922 4772 3.446 0.696 0.155 0.046 20 2.4 Pole_temporal 1989 1348 1937 1.659 0.425 0.130 0.033 20 2.8 S_calcarine 2997 1984 3069 1.699 0.523 0.104 0.019 18 2.5 S_central 814 568 1035 1.996 0.547 0.098 0.017 4 0.5 S_cingul-Marginalis 365 274 638 2.608 0.369 0.098 0.021 1 0.3 S_circular_insula_ant 1093 760 1264 1.852 0.658 0.083 0.012 4 0.5 S_circular_insula_inf 1379 961 1892 2.315 0.552 0.099 0.017 6 1.0 S_circular_insula_sup 560 389 791 2.223 0.653 0.145 0.047 7 1.2 S_collat_transv_ant 278 190 338 1.673 0.405 0.111 0.021 2 0.3 S_collat_transv_post 1638 1129 2058 1.997 0.414 0.131 0.028 16 1.7 S_front_inf 991 670 1318 1.934 0.468 0.134 0.031 11 1.3 S_front_middle 2089 1441 3168 2.236 0.469 0.115 0.025 16 2.0 S_front_sup 280 195 345 1.991 0.453 0.129 0.023 2 0.4 S_interm_prim-Jensen 2704 1783 3137 1.869 0.439 0.126 0.025 27 2.9 S_intrapariet&P_trans 834 583 781 1.543 0.320 0.150 0.034 9 1.2 S_oc_middle&Lunatus 1159 776 1158 1.659 0.332 0.132 0.027 11 1.2 S_oc_sup&transversal 447 309 450 1.706 0.479 0.117 0.020 3 0.4 S_occipital_ant 780 532 1114 2.349 0.520 0.132 0.031 7 1.0 S_oc-temp_lat 1454 1051 1761 1.844 0.480 0.124 0.023 12 1.5 S_oc-temp_med&Lingual 253 188 305 1.792 0.602 0.130 0.022 2 0.3 S_orbital_lateral 465 321 629 2.043 0.748 0.120 0.023 4 0.4 S_orbital_med-olfact 1027 736 1734 2.329 0.631 0.139 0.034 13 1.4 S_orbital-H_Shaped 1579 1070 1729 1.695 0.546 0.122 0.025 13 1.6 S_parieto_occipital 1263 768 1097 1.998 0.935 0.121 0.025 21 1.1 S_pericallosal 2999 2024 3598 1.940 0.489 0.114 0.020 23 2.5 S_postcentral 1405 947 2002 2.102 0.435 0.102 0.017 10 1.1 S_precentral-inf-part 1477 1024 2111 2.108 0.586 0.104 0.017 9 1.1 S_precentral-sup-part 558 386 740 2.139 0.582 0.128 0.037 8 0.8 S_suborbital 964 665 1268 1.947 0.557 0.130 0.029 8 1.1 S_subparietal 1280 920 1885 2.365 0.450 0.117 0.019 10 1.1 S_temporal_inf 5174 3613 7327 2.088 0.508 0.115 0.022 44 4.7 S_temporal_sup 258 189 309 1.836 0.351 0.116 0.017 2 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh 2018. 07. 09. (���) 17:46:28 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 161019_x3DT1_SAG rh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 698 481 1146 2.311 0.454 0.148 0.030 12 0.7 G&S_frontomargin 910 650 1844 2.404 0.513 0.149 0.037 12 1.5 G&S_occipital_inf 1137 705 1788 2.167 0.494 0.143 0.049 15 2.2 G&S_paracentral 1165 765 1919 2.327 0.518 0.153 0.035 17 1.6 G&S_subcentral 873 614 1836 2.403 0.558 0.174 0.049 16 2.0 G&S_transv_frontopol 2307 1589 4148 2.500 0.565 0.147 0.041 37 4.0 G&S_cingul-Ant 971 666 1617 2.336 0.516 0.130 0.029 10 1.2 G&S_cingul-Mid-Ant 1076 758 1951 2.415 0.526 0.140 0.032 14 1.4 G&S_cingul-Mid-Post 418 298 1126 2.657 0.610 0.180 0.049 9 0.8 G_cingul-Post-dorsal 297 180 524 2.315 0.683 0.139 0.031 4 0.4 G_cingul-Post-ventral 1975 1256 2192 1.597 0.344 0.153 0.038 28 3.1 G_cuneus 1043 664 2210 2.509 0.385 0.135 0.030 16 1.2 G_front_inf-Opercular 337 209 728 2.423 0.433 0.171 0.056 8 0.7 G_front_inf-Orbital 747 482 1543 2.401 0.425 0.137 0.030 11 0.9 G_front_inf-Triangul 3461 2270 7062 2.478 0.552 0.167 0.047 67 7.5 G_front_middle 4626 2988 10296 2.682 0.534 0.145 0.043 70 7.9 G_front_sup 480 320 989 2.974 1.100 0.128 0.044 7 0.8 G_Ins_lg&S_cent_ins 584 375 1668 3.499 0.961 0.130 0.045 7 1.0 G_insular_short 1559 1037 2935 2.272 0.525 0.157 0.041 27 2.4 G_occipital_middle 1373 845 1994 1.965 0.531 0.139 0.037 18 2.0 G_occipital_sup 1572 1036 3359 2.548 0.635 0.148 0.038 29 2.3 G_oc-temp_lat-fusifor 2482 1612 3347 1.807 0.501 0.152 0.040 41 4.1 G_oc-temp_med-Lingual 1152 764 2651 2.558 0.961 0.129 0.037 13 1.5 G_oc-temp_med-Parahip 2199 1506 4964 2.607 0.672 0.164 0.051 45 4.8 G_orbital 2537 1766 5594 2.379 0.515 0.168 0.047 52 5.3 G_pariet_inf-Angular 2202 1498 4236 2.357 0.484 0.139 0.030 32 2.8 G_pariet_inf-Supramar 2101 1443 3812 2.048 0.481 0.161 0.044 43 3.4 G_parietal_sup 2074 1300 2855 1.809 0.518 0.127 0.029 24 2.7 G_postcentral 2246 1228 4386 2.676 0.463 0.102 0.025 20 2.2 G_precentral 2116 1445 3573 2.045 0.531 0.155 0.041 36 3.5 G_precuneus 766 514 1608 2.302 0.632 0.146 0.050 14 1.5 G_rectus 447 288 553 2.183 0.854 0.090 0.043 7 0.7 G_subcallosal 343 193 562 2.187 0.519 0.113 0.027 3 0.3 G_temp_sup-G_T_transv 1484 941 3569 2.826 0.568 0.120 0.028 20 1.5 G_temp_sup-Lateral 675 481 1485 2.803 0.575 0.077 0.012 2 0.3 G_temp_sup-Plan_polar 759 533 1259 2.069 0.543 0.123 0.027 9 1.0 G_temp_sup-Plan_tempo 1575 1117 4151 2.804 0.688 0.170 0.057 32 3.9 G_temporal_inf 2399 1661 6122 2.748 0.569 0.150 0.039 48 4.1 G_temporal_middle 290 192 339 2.026 0.405 0.115 0.019 2 0.2 Lat_Fis-ant-Horizont 268 184 310 2.041 0.415 0.122 0.026 1 0.3 Lat_Fis-ant-Vertical 1237 838 1408 1.914 0.530 0.101 0.019 7 1.0 Lat_Fis-post 2591 1625 2857 1.666 0.379 0.153 0.041 40 4.3 Pole_occipital 1458 1074 5475 3.284 0.798 0.164 0.047 29 2.8 Pole_temporal 2003 1405 2018 1.643 0.456 0.130 0.034 18 3.0 S_calcarine 2661 1850 2649 1.643 0.521 0.100 0.020 13 2.2 S_central 1049 734 1520 1.992 0.544 0.114 0.025 10 1.0 S_cingul-Marginalis 452 307 693 2.681 0.437 0.104 0.022 2 0.4 S_circular_insula_ant 1014 685 1119 1.852 0.569 0.080 0.010 3 0.5 S_circular_insula_inf 1175 810 1652 2.399 0.554 0.106 0.019 6 1.1 S_circular_insula_sup 568 415 1470 3.181 0.596 0.130 0.029 6 0.7 S_collat_transv_ant 379 267 341 1.630 0.319 0.167 0.041 5 0.7 S_collat_transv_post 1579 1091 2022 2.078 0.429 0.127 0.024 15 1.6 S_front_inf 1818 1269 2513 2.095 0.462 0.129 0.027 17 1.8 S_front_middle 1690 1175 2652 2.359 0.511 0.118 0.026 12 1.7 S_front_sup 413 293 468 2.044 0.408 0.125 0.024 3 0.4 S_interm_prim-Jensen 2579 1808 2945 1.790 0.406 0.122 0.025 23 2.6 S_intrapariet&P_trans 683 462 789 1.903 0.432 0.145 0.029 8 0.8 S_oc_middle&Lunatus 1214 805 1297 1.848 0.345 0.127 0.027 11 1.4 S_oc_sup&transversal 621 414 673 2.030 0.432 0.140 0.036 6 0.9 S_occipital_ant 551 397 971 2.467 0.517 0.143 0.031 7 0.6 S_oc-temp_lat 1718 1204 1999 1.933 0.467 0.119 0.024 14 1.7 S_oc-temp_med&Lingual 452 322 592 2.059 0.396 0.126 0.028 3 0.6 S_orbital_lateral 620 434 802 2.154 0.689 0.121 0.024 5 0.6 S_orbital_med-olfact 1177 837 1985 2.479 0.636 0.152 0.047 14 2.4 S_orbital-H_Shaped 1637 1104 1756 1.714 0.443 0.129 0.025 17 1.7 S_parieto_occipital 1258 754 1002 1.938 0.665 0.140 0.025 24 1.1 S_pericallosal 2395 1637 2562 1.750 0.458 0.111 0.022 18 2.1 S_postcentral 1224 835 1722 2.306 0.426 0.103 0.016 7 0.8 S_precentral-inf-part 1014 714 1297 2.174 0.407 0.110 0.023 6 1.1 S_precentral-sup-part 199 145 380 2.402 0.881 0.147 0.033 2 0.2 S_suborbital 1100 767 1530 2.124 0.492 0.139 0.032 12 1.4 S_subparietal 897 630 1308 2.439 0.472 0.127 0.024 7 1.0 S_temporal_inf 5077 3562 7146 2.130 0.502 0.109 0.019 34 4.3 S_temporal_sup 196 130 201 1.879 0.315 0.116 0.015 1 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh 2018. 07. 09. (���) 17:46:51 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG lh ../surf/lh.sphere.reg /home/kt/Downloads/freesurferDev/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1132 labels changed using aseg relabeling using gibbs priors... 000: 1622 changed, 109637 examined... 001: 389 changed, 7741 examined... 002: 119 changed, 2167 examined... 003: 60 changed, 659 examined... 004: 33 changed, 342 examined... 005: 14 changed, 176 examined... 006: 10 changed, 78 examined... 007: 10 changed, 75 examined... 008: 8 changed, 52 examined... 009: 10 changed, 41 examined... 010: 9 changed, 44 examined... 011: 5 changed, 53 examined... 012: 5 changed, 29 examined... 013: 6 changed, 24 examined... 014: 3 changed, 30 examined... 015: 0 changed, 14 examined... 307 labels changed using aseg 000: 41 total segments, 8 labels (132 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 769 vertices marked for relabeling... 769 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. #----------------------------------------- #@# Cortical Parc 3 rh 2018. 07. 09. (���) 17:47:00 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 161019_x3DT1_SAG rh ../surf/rh.sphere.reg /home/kt/Downloads/freesurferDev/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Could not set locale No such file or directory Could not set locale setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id$ reading atlas from /home/kt/Downloads/freesurferDev/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1270 labels changed using aseg relabeling using gibbs priors... 000: 1690 changed, 108203 examined... 001: 414 changed, 7900 examined... 002: 127 changed, 2287 examined... 003: 73 changed, 752 examined... 004: 36 changed, 413 examined... 005: 19 changed, 167 examined... 006: 17 changed, 111 examined... 007: 12 changed, 86 examined... 008: 12 changed, 62 examined... 009: 12 changed, 60 examined... 010: 13 changed, 59 examined... 011: 6 changed, 70 examined... 012: 4 changed, 37 examined... 013: 4 changed, 26 examined... 014: 2 changed, 23 examined... 015: 0 changed, 15 examined... 340 labels changed using aseg 000: 54 total segments, 21 labels (396 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 544 vertices marked for relabeling... 544 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 8 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh 2018. 07. 09. (���) 17:47:09 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 161019_x3DT1_SAG lh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1451 925 2121 2.399 0.643 0.135 0.027 25 1.5 caudalanteriorcingulate 3164 2082 5598 2.301 0.575 0.120 0.027 32 3.3 caudalmiddlefrontal 2383 1504 2675 1.697 0.388 0.152 0.032 39 3.2 cuneus 379 240 1283 3.221 1.005 0.117 0.030 4 0.5 entorhinal 3184 2211 5725 2.317 0.569 0.145 0.038 49 5.0 fusiform 6085 4097 9964 2.134 0.537 0.145 0.035 92 8.6 inferiorparietal 3815 2674 8891 2.738 0.665 0.146 0.037 55 6.2 inferiortemporal 1511 974 2405 2.240 0.796 0.129 0.036 22 1.9 isthmuscingulate 5970 3821 7168 1.763 0.437 0.149 0.037 92 8.6 lateraloccipital 3420 2354 6357 2.453 0.654 0.149 0.041 64 5.7 lateralorbitofrontal 3604 2428 4613 1.776 0.460 0.154 0.039 54 5.9 lingual 1926 1289 3081 2.183 0.636 0.137 0.043 31 3.1 medialorbitofrontal 5053 3412 10231 2.563 0.581 0.124 0.027 60 5.5 middletemporal 813 527 1103 1.876 0.566 0.093 0.018 5 0.5 parahippocampal 2105 1317 3282 2.266 0.590 0.118 0.030 19 2.6 paracentral 1656 1108 2848 2.290 0.473 0.124 0.025 18 1.6 parsopercularis 781 543 1619 2.434 0.481 0.129 0.028 11 0.9 parsorbitalis 1738 1180 2926 2.295 0.560 0.132 0.028 20 2.0 parstriangularis 1554 1000 1387 1.534 0.320 0.136 0.034 17 2.2 pericalcarine 6584 4280 8892 1.852 0.582 0.119 0.028 67 7.6 postcentral 1405 969 2240 2.156 0.662 0.139 0.028 21 1.5 posteriorcingulate 6793 4258 10580 2.304 0.568 0.111 0.024 57 6.8 precentral 4377 3004 6994 2.114 0.586 0.142 0.039 63 6.8 precuneus 1380 917 2794 2.735 0.939 0.136 0.038 23 2.1 rostralanteriorcingulate 4117 2793 7074 2.209 0.537 0.149 0.038 63 6.5 rostralmiddlefrontal 7966 5394 15325 2.500 0.551 0.137 0.036 100 11.7 superiorfrontal 5666 3746 8356 1.956 0.512 0.127 0.027 63 6.2 superiorparietal 5866 4022 11856 2.426 0.809 0.107 0.023 54 5.2 superiortemporal 4427 3002 7602 2.338 0.500 0.136 0.031 59 5.4 supramarginal 566 327 683 1.956 0.509 0.115 0.022 5 0.5 transversetemporal 2177 1469 4307 2.742 0.894 0.099 0.023 13 2.0 insula #----------------------------------------- #@# Parcellation Stats 3 rh 2018. 07. 09. (���) 17:47:30 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab 161019_x3DT1_SAG rh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1036 650 1545 2.259 0.583 0.148 0.032 18 1.3 caudalanteriorcingulate 2327 1525 4051 2.477 0.554 0.133 0.037 27 4.1 caudalmiddlefrontal 2436 1571 2583 1.582 0.351 0.146 0.035 32 3.6 cuneus 345 254 1516 3.431 0.786 0.138 0.041 4 0.4 entorhinal 2863 1935 5608 2.534 0.625 0.135 0.033 41 3.7 fusiform 6439 4488 11026 2.149 0.541 0.145 0.034 93 9.7 inferiorparietal 3299 2379 8136 2.785 0.725 0.160 0.046 56 6.5 inferiortemporal 1203 764 1933 2.186 0.645 0.134 0.032 19 1.4 isthmuscingulate 5719 3745 7641 1.917 0.481 0.149 0.037 79 8.7 lateraloccipital 3681 2553 6758 2.499 0.681 0.157 0.050 61 7.9 lateralorbitofrontal 3881 2643 4867 1.784 0.484 0.152 0.040 57 6.4 lingual 1836 1247 3408 2.352 0.667 0.135 0.042 31 2.9 medialorbitofrontal 4739 3302 10165 2.609 0.605 0.132 0.030 65 6.2 middletemporal 958 614 1174 1.773 0.552 0.097 0.016 7 0.6 parahippocampal 1814 1170 2796 2.250 0.600 0.125 0.037 16 2.7 paracentral 1766 1145 2836 2.290 0.440 0.123 0.025 18 1.6 parsopercularis 791 541 1487 2.353 0.590 0.160 0.038 13 1.3 parsorbitalis 1830 1218 3082 2.320 0.476 0.129 0.029 20 2.1 parstriangularis 1814 1165 1664 1.523 0.354 0.141 0.038 22 2.8 pericalcarine 6082 4035 7592 1.757 0.552 0.119 0.025 57 6.5 postcentral 1411 994 2512 2.249 0.684 0.157 0.034 25 2.0 posteriorcingulate 5765 3615 9185 2.354 0.559 0.112 0.026 47 6.2 precentral 4731 3245 6961 1.997 0.523 0.143 0.035 67 6.4 precuneus 977 674 2069 2.630 0.705 0.151 0.041 21 1.7 rostralanteriorcingulate 5124 3539 8685 2.255 0.501 0.150 0.035 75 7.4 rostralmiddlefrontal 9113 6135 17059 2.488 0.556 0.139 0.037 116 14.1 superiorfrontal 5369 3682 7822 1.920 0.489 0.135 0.033 71 6.7 superiorparietal 5779 3893 11687 2.511 0.725 0.109 0.023 53 5.2 superiortemporal 4444 3041 6995 2.161 0.514 0.126 0.028 51 5.0 supramarginal 444 253 586 1.949 0.501 0.105 0.024 4 0.4 transversetemporal 2407 1640 4637 2.730 0.968 0.108 0.028 20 2.7 insula #----------------------------------------- #@# WM/GM Contrast lh 2018. 07. 09. (���) 17:47:49 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts pctsurfcon --s 161019_x3DT1_SAG --lh-only Log file is /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts/pctsurfcon.log 2018. 07. 09. (���) 17:47:50 KST setenv SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs cd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts /home/kt/Downloads/freesurferDev/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/kt/Downloads/freesurferDev mri_vol2surf --mov /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.wm.mgh --regheader 161019_x3DT1_SAG --cortex Could not set locale No such file or directory Could not set locale srcvol = /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99987 0.01512 0.00525 0.00000; -0.00425 -0.06586 0.99782 -0.00003; 0.01543 -0.99771 -0.06579 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label Reading surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 59051 Masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.wm.mgh Dim: 109637 1 1 mri_vol2surf --mov /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.gm.mgh --projfrac 0.3 --regheader 161019_x3DT1_SAG --cortex Could not set locale No such file or directory Could not set locale srcvol = /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99987 0.01512 0.00525 0.00000; -0.00425 -0.06586 0.99782 -0.00003; 0.01543 -0.99771 -0.06579 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label Reading surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Done reading source surface Reading thickness /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 71989 Masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.cortex.label Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.gm.mgh Dim: 109637 1 1 mri_concat /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.wm.mgh /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24317/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.w-g.pct.mgh Could not set locale No such file or directory Could not set locale ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.w-g.pct.mgh mri_segstats --in /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.w-g.pct.mgh --annot 161019_x3DT1_SAG lh aparc --sum /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/stats/lh.w-g.pct.stats --snr Could not set locale No such file or directory Could not set locale $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --in /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.w-g.pct.mgh --annot 161019_x3DT1_SAG lh aparc --sum /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/stats/lh.w-g.pct.stats --snr sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.w-g.pct.mgh Vertex Area is 0.664555 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh 2018. 07. 09. (���) 17:47:53 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts pctsurfcon --s 161019_x3DT1_SAG --rh-only Log file is /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts/pctsurfcon.log 2018. 07. 09. (���) 17:47:53 KST setenv SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs cd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/scripts /home/kt/Downloads/freesurferDev/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/kt/Downloads/freesurferDev mri_vol2surf --mov /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.wm.mgh --regheader 161019_x3DT1_SAG --cortex Could not set locale No such file or directory Could not set locale srcvol = /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99987 0.01512 0.00525 0.00000; -0.00425 -0.06586 0.99782 -0.00003; 0.01543 -0.99771 -0.06579 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label Reading surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 59268 Masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.wm.mgh Dim: 108203 1 1 mri_vol2surf --mov /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.gm.mgh --projfrac 0.3 --regheader 161019_x3DT1_SAG --cortex Could not set locale No such file or directory Could not set locale srcvol = /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/orig.mgz as target reference. -------- original matrix ----------- 0.99987 0.01512 0.00525 0.00000; -0.00425 -0.06586 0.99782 -0.00003; 0.01543 -0.99771 -0.06579 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label Reading surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Done reading source surface Reading thickness /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 71206 Masking with /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.cortex.label Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.gm.mgh Dim: 108203 1 1 mri_concat /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.wm.mgh /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/tmp.pctsurfcon.24380/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.w-g.pct.mgh Could not set locale No such file or directory Could not set locale ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.w-g.pct.mgh mri_segstats --in /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.w-g.pct.mgh --annot 161019_x3DT1_SAG rh aparc --sum /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/stats/rh.w-g.pct.stats --snr Could not set locale No such file or directory Could not set locale $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --in /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.w-g.pct.mgh --annot 161019_x3DT1_SAG rh aparc --sum /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/stats/rh.w-g.pct.stats --snr sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.w-g.pct.mgh Vertex Area is 0.672287 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities 2018. 07. 09. (���) 17:47:56 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz Could not set locale No such file or directory Could not set locale reading input surface ../surf/lh.white... relabeling lh hypointensities... 2389 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3061 voxels changed to hypointensity... 5392 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc 2018. 07. 09. (���) 17:48:09 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_aparc2aseg --s 161019_x3DT1_SAG --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt Could not set locale No such file or directory Could not set locale relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs subject 161019_x3DT1_SAG outvol /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading lh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial Loading lh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading rh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial Loading rh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz Loading aseg from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.34 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling from 94 --> 58 rescaling Left_Thalamus from 84 --> 90 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 33 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 58 rescaling from 22 --> 58 rescaling Right_Thalamus from 85 --> 89 rescaling Right_Caudate from 62 --> 78 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 29 rescaling from 22 --> 29 rescaling from 22 --> 29 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337287 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 161 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s 2018. 07. 09. (���) 17:51:02 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_aparc2aseg --s 161019_x3DT1_SAG --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s Could not set locale No such file or directory Could not set locale relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs subject 161019_x3DT1_SAG outvol /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading lh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial Loading lh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading rh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial Loading rh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz Loading aseg from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.34 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling from 94 --> 58 rescaling Left_Thalamus from 84 --> 90 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 33 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 58 rescaling from 22 --> 58 rescaling Right_Thalamus from 85 --> 89 rescaling Right_Caudate from 62 --> 78 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 29 rescaling from 22 --> 29 rescaling from 22 --> 29 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337273 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 161 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas 2018. 07. 09. (���) 17:53:56 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_aparc2aseg --s 161019_x3DT1_SAG --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz Could not set locale No such file or directory Could not set locale relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/kt/Downloads/freesurferDev/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs subject 161019_x3DT1_SAG outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading lh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial Loading lh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading rh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial Loading rh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz Loading aseg from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.34 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 69 rescaling Left_Lateral_Ventricle from 13 --> 14 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 58 rescaling from 94 --> 58 rescaling Left_Thalamus from 84 --> 90 rescaling Left_Caudate from 75 --> 76 rescaling Left_Putamen from 80 --> 77 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 19 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 62 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 33 rescaling Left_Accumbens_area from 62 --> 69 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 68 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 26 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 58 rescaling from 22 --> 58 rescaling Right_Thalamus from 85 --> 89 rescaling Right_Caudate from 62 --> 78 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 62 rescaling Right_Amygdala from 55 --> 64 rescaling Right_Accumbens_area from 65 --> 76 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 29 rescaling from 22 --> 29 rescaling from 22 --> 29 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337273 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 161 changed. pass 2: 6 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg 2018. 07. 09. (���) 17:56:42 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz 2018. 07. 09. (���) 17:56:42 KST setenv SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs cd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri /home/kt/Downloads/freesurferDev/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-linux-centos7_x86_64-dev-20180703-82d87f8 $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux kt-B85M-DS3H-A 4.4.0-130-generic #156~14.04.1-Ubuntu SMP Thu Jun 14 13:51:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 Could not set locale No such file or directory Could not set locale $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.000000 16777216 -0.000006 mri_binarize done Started at 2018. 07. 09. (���) 17:56:42 KST Ended at 2018. 07. 09. (���) 17:56:46 KST Apas2aseg-Run-Time-Sec 4 apas2aseg Done #-------------------------------------------- #@# ASeg Stats 2018. 07. 09. (���) 17:56:46 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/kt/Downloads/freesurferDev/ASegStatsLUT.txt --subject 161019_x3DT1_SAG Could not set locale No such file or directory Could not set locale setting seed for random number genererator to 1234 $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /home/kt/Downloads/freesurferDev/ASegStatsLUT.txt --subject 161019_x3DT1_SAG sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) Computing euler number orig.nofix lheno = -44, rheno = -34 orig.nofix lhholes = 23, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc 2018. 07. 09. (���) 17:59:14 KST /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG mri_aparc2aseg --s 161019_x3DT1_SAG --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz Could not set locale No such file or directory Could not set locale SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs subject 161019_x3DT1_SAG outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc+aseg.mgz Reading lh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading lh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial Loading lh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Ripping vertices labeled as unkown Ripped 7702 vertices from left hemi Building hash of lh white Building hash of lh pial Reading rh white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading rh pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial Loading rh annotations from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for rh white annotation Ripping vertices labeled as unkown Ripped 7763 vertices from right hemi Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz Loading filled from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/ribbon.mgz Loading aseg from /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aseg.mgz Loading Ctx Seg File /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 694051 Used brute-force search on 130 voxels Fixing Parahip LH WM Found 8 clusters 0 k 23.000000 1 k 1.000000 2 k 2.000000 3 k 2.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 856.000000 Fixing Parahip RH WM Found 10 clusters 0 k 1.000000 1 k 1.000000 2 k 1033.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 161019_x3DT1_SAG --surf-wm-vol --ctab /home/kt/Downloads/freesurferDev/WMParcStatsLUT.txt --etiv Could not set locale No such file or directory Could not set locale setting seed for random number genererator to 1234 $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 161019_x3DT1_SAG --surf-wm-vol --ctab /home/kt/Downloads/freesurferDev/WMParcStatsLUT.txt --etiv sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/kt/Downloads/Thalamus/Outputs; ln -s /home/kt/Downloads/freesurferDev/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh 2018. 07. 09. (���) 18:05:11 KST mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA1_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4350 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA2_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 336 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 236 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6219 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6031 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4232 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA6_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 610 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14199 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA44_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4292 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA45_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3622 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V1_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 631 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5272 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V2_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 1475 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9589 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.MT_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2263 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1313 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1102 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2418 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1605 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1954 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1224 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 364 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3769 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 769 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4103 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 473 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 109637 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 453 mri_label2label: Done mris_label2annot --s 161019_x3DT1_SAG --hemi lh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Could not set locale No such file or directory Could not set locale Reading ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label cmdline mris_label2annot --s 161019_x3DT1_SAG --hemi lh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt subject 161019_x3DT1_SAG hemi lh SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs ColorTable /home/kt/Downloads/freesurferDev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 75201 unhit vertices Writing annot to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.BA_exvivo.annot mris_label2annot --s 161019_x3DT1_SAG --hemi lh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Could not set locale No such file or directory Could not set locale Reading ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label cmdline mris_label2annot --s 161019_x3DT1_SAG --hemi lh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt subject 161019_x3DT1_SAG hemi lh SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs ColorTable /home/kt/Downloads/freesurferDev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89119 unhit vertices Writing annot to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab 161019_x3DT1_SAG lh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/kt/Downloads/freesurferDev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 1057 623 1968 2.137 0.746 0.143 0.049 17 2.0 BA1_exvivo 3780 2558 5031 1.938 0.490 0.113 0.022 31 3.6 BA2_exvivo 1013 696 887 1.506 0.302 0.141 0.031 10 1.2 BA3a_exvivo 2156 1390 2579 1.666 0.530 0.115 0.025 20 2.2 BA3b_exvivo 1513 862 2486 2.469 0.488 0.108 0.029 13 1.7 BA4a_exvivo 1290 782 1803 2.271 0.518 0.094 0.020 7 1.1 BA4p_exvivo 7799 5048 14437 2.472 0.574 0.123 0.032 81 9.9 BA6_exvivo 1757 1186 3042 2.281 0.465 0.124 0.026 19 1.7 BA44_exvivo 2135 1462 3774 2.249 0.509 0.137 0.031 27 2.7 BA45_exvivo 2734 1758 2759 1.573 0.347 0.136 0.033 32 3.7 V1_exvivo 6648 4230 7680 1.751 0.414 0.157 0.041 114 11.0 V2_exvivo 1667 1123 2508 2.037 0.523 0.141 0.035 22 2.1 MT_exvivo 437 261 1209 3.060 0.925 0.119 0.032 5 0.5 perirhinal_exvivo 450 324 891 2.413 1.070 0.095 0.020 2 0.3 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 161019_x3DT1_SAG lh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 173863 Total vertex volume 169979 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/kt/Downloads/freesurferDev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 736 397 1480 2.253 0.845 0.144 0.055 13 1.6 BA1_exvivo 1569 1041 1990 1.798 0.450 0.101 0.020 12 1.2 BA2_exvivo 846 579 685 1.478 0.279 0.147 0.034 8 1.2 BA3a_exvivo 1347 909 1290 1.384 0.269 0.092 0.016 7 0.9 BA3b_exvivo 1452 841 2375 2.451 0.487 0.100 0.026 10 1.5 BA4a_exvivo 1054 652 1461 2.228 0.514 0.094 0.019 6 0.8 BA4p_exvivo 4358 2745 7994 2.504 0.571 0.122 0.033 44 5.9 BA6_exvivo 1118 743 1926 2.272 0.422 0.125 0.025 13 1.2 BA44_exvivo 852 587 1907 2.474 0.403 0.147 0.036 14 1.2 BA45_exvivo 2902 1869 3020 1.578 0.342 0.134 0.032 34 4.0 V1_exvivo 3457 2156 3808 1.754 0.397 0.170 0.046 69 6.5 V2_exvivo 389 289 576 1.806 0.555 0.124 0.028 4 0.4 MT_exvivo 208 120 635 3.087 0.728 0.105 0.025 1 0.2 perirhinal_exvivo 230 161 369 2.241 0.820 0.059 0.009 1 0.0 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh 2018. 07. 09. (���) 18:08:03 KST mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA1_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA2_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6942 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4052 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4688 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5898 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA6_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 290 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA44_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 269 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7181 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA45_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 382 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5737 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V1_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 908 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5635 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V2_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 1649 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9665 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.MT_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2067 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2778 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2250 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1442 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1512 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 163 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1063 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1252 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 593 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3825 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 852 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4289 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 285 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 161019_x3DT1_SAG --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Could not set locale No such file or directory Could not set locale srclabel = /home/kt/Downloads/Thalamus/Outputs/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 161019_x3DT1_SAG trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs FREESURFER_HOME /home/kt/Downloads/freesurferDev Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/kt/Downloads/Thalamus/Outputs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white Reading target registration /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 108203 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 301 mri_label2label: Done mris_label2annot --s 161019_x3DT1_SAG --hemi rh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Could not set locale No such file or directory Could not set locale Reading ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label cmdline mris_label2annot --s 161019_x3DT1_SAG --hemi rh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt subject 161019_x3DT1_SAG hemi rh SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs ColorTable /home/kt/Downloads/freesurferDev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 75322 unhit vertices Writing annot to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.BA_exvivo.annot mris_label2annot --s 161019_x3DT1_SAG --hemi rh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Could not set locale No such file or directory Could not set locale Reading ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label cmdline mris_label2annot --s 161019_x3DT1_SAG --hemi rh --ctab /home/kt/Downloads/freesurferDev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname kt-B85M-DS3H-A machine x86_64 user kt subject 161019_x3DT1_SAG hemi rh SUBJECTS_DIR /home/kt/Downloads/Thalamus/Outputs ColorTable /home/kt/Downloads/freesurferDev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 89285 unhit vertices Writing annot to /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab 161019_x3DT1_SAG rh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/kt/Downloads/freesurferDev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 953 543 1445 2.024 0.558 0.135 0.035 13 1.4 BA1_exvivo 2916 1983 3491 1.761 0.462 0.116 0.023 24 2.8 BA2_exvivo 921 648 788 1.496 0.352 0.129 0.033 7 1.2 BA3a_exvivo 1695 1178 1847 1.472 0.410 0.111 0.024 14 1.7 BA3b_exvivo 1237 756 2120 2.478 0.528 0.110 0.037 10 1.9 BA4a_exvivo 1059 681 1445 2.220 0.463 0.102 0.021 5 1.0 BA4p_exvivo 5708 3600 10652 2.556 0.541 0.120 0.033 58 7.5 BA6_exvivo 2861 1867 4761 2.377 0.450 0.128 0.024 31 2.8 BA44_exvivo 3344 2226 5601 2.253 0.504 0.136 0.031 42 4.1 BA45_exvivo 3280 2089 3266 1.540 0.353 0.147 0.040 47 5.4 V1_exvivo 6717 4400 8060 1.756 0.443 0.151 0.039 97 10.7 V2_exvivo 1468 995 2229 2.188 0.472 0.143 0.033 19 1.9 MT_exvivo 429 303 1613 3.244 0.857 0.114 0.022 3 0.4 perirhinal_exvivo 293 191 790 2.684 1.033 0.103 0.032 3 0.4 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 161019_x3DT1_SAG rh white Could not set locale No such file or directory Could not set locale computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/mri/wm.mgz... reading input surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... reading input pial surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.pial... reading input white surface /home/kt/Downloads/Thalamus/Outputs/161019_x3DT1_SAG/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 172105 Total vertex volume 168066 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /home/kt/Downloads/freesurferDev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1328608 mm^3 (det: 1.466275 ) lhCtxGM: 170341.042 170199.000 diff= 142.0 pctdiff= 0.083 rhCtxGM: 168337.085 168229.000 diff= 108.1 pctdiff= 0.064 lhCtxWM: 178739.663 178929.000 diff= -189.3 pctdiff=-0.106 rhCtxWM: 178570.900 179108.000 diff= -537.1 pctdiff=-0.301 SubCortGMVol 40513.000 SupraTentVol 780896.690 (779579.000) diff=1317.690 pctdiff=0.169 SupraTentVolNotVent 738387.690 (737070.000) diff=1317.690 pctdiff=0.178 BrainSegVol 876647.000 (873174.000) diff=3473.000 pctdiff=0.396 BrainSegVolNotVent 828918.000 (828214.690) diff=703.310 pctdiff=0.085 BrainSegVolNotVent 828918.000 CerebellumVol 91621.000 VentChorVol 42509.000 3rd4th5thCSF 5220.000 CSFVol 1747.000, OptChiasmVol 227.000 MaskVol 1289336.000 667 374 949 1.888 0.622 0.134 0.035 9 1.0 BA1_exvivo 1717 1165 2131 1.733 0.473 0.104 0.018 12 1.4 BA2_exvivo 831 583 657 1.469 0.306 0.131 0.031 6 1.0 BA3a_exvivo 1346 960 1259 1.323 0.223 0.097 0.017 8 0.9 BA3b_exvivo 739 450 1324 2.529 0.557 0.135 0.058 8 1.8 BA4a_exvivo 869 580 1205 2.216 0.448 0.099 0.020 4 0.9 BA4p_exvivo 3748 2316 6882 2.510 0.539 0.118 0.032 38 4.8 BA6_exvivo 711 478 1354 2.370 0.426 0.129 0.026 9 0.7 BA44_exvivo 851 558 1590 2.338 0.443 0.124 0.029 9 0.9 BA45_exvivo 3101 1982 3038 1.536 0.354 0.146 0.039 43 5.0 V1_exvivo 3675 2429 4342 1.680 0.421 0.158 0.041 57 6.2 V2_exvivo 224 154 323 1.884 0.390 0.106 0.020 2 0.2 MT_exvivo 248 173 853 3.181 0.822 0.083 0.013 1 0.1 perirhinal_exvivo 191 124 448 2.764 0.741 0.107 0.026 2 0.2 entorhinal_exvivo Started at 2018. 07. 09. (���) 12:08:24 KST Ended at 2018. 07. 09. (���) 18:10:54 KST #@#%# recon-all-run-time-hours 6.042 recon-all -s 161019_x3DT1_SAG finished without error at 2018. 07. 09. (���) 18:10:54 KST