Sat Sep 4 13:48:03 IST 2021 /usr/local/freesurfer/subjects/pt019 /usr/local/freesurfer/bin/recon-all -s pt019 -i Pt019.nii -all subjid pt019 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 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 31455 maxlocks unlimited maxsignal 31455 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8096868 417832 7092604 4060 586432 7345796 Swap: 8266748 468492 7798256 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $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: stable6 $ TimeStamp: 2021/09/04-08:18:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 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 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:04-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:05-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/09/04-08:18:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: research1-HP-280-G3-MT Platform: Linux PlatformVersion: 4.4.0-210-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/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 /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/subjects/pt019 mri_convert /usr/local/freesurfer/subjects/phd/Pt019.nii /usr/local/freesurfer/subjects/pt019/mri/orig/001.mgz mri_convert.bin /usr/local/freesurfer/subjects/phd/Pt019.nii /usr/local/freesurfer/subjects/pt019/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/phd/Pt019.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0204977, -0.99841, -0.052505) j_ras = (0.015217, -0.0521985, 0.998521) k_ras = (0.999674, 0.0212663, -0.0141228) writing to /usr/local/freesurfer/subjects/pt019/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Sep 4 13:48:14 IST 2021 Found 1 runs /usr/local/freesurfer/subjects/pt019/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/pt019/mri/orig/001.mgz /usr/local/freesurfer/subjects/pt019/mri/rawavg.mgz /usr/local/freesurfer/subjects/pt019 mri_convert /usr/local/freesurfer/subjects/pt019/mri/rawavg.mgz /usr/local/freesurfer/subjects/pt019/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/pt019/mri/rawavg.mgz /usr/local/freesurfer/subjects/pt019/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/pt019/mri/rawavg.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0204977, -0.99841, -0.052505) j_ras = (0.015217, -0.0521985, 0.998521) k_ras = (0.999674, 0.0212663, -0.0141228) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/pt019/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/pt019/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/pt019/mri/orig.mgz /usr/local/freesurfer/subjects/pt019/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Sep 4 13:48:22 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/pt019/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Sat Sep 4 13:48:22 IST 2021 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 tmpdir is ./tmp.mri_nu_correct.mni.27512 /usr/local/freesurfer/subjects/pt019/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27512/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27512/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 2.32831e-10, -1) k_ras = (0, 1, -1.74623e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27512/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Sep 4 13:48:23 IST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.27512/nu0.mnc ./tmp.mri_nu_correct.mni.27512/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27512/0/ -iterations 1000 -distance 50 [root@research1-HP-280-G3-MT:/usr/local/freesurfer/subjects/pt019/mri/] [2021-09-04 13:48:24] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.27512/0/ ./tmp.mri_nu_correct.mni.27512/nu0.mnc ./tmp.mri_nu_correct.mni.27512/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 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: 53 CV of field change: 0.000966237 mri_convert ./tmp.mri_nu_correct.mni.27512/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.27512/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.27512/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 2.32831e-10, -1) k_ras = (0, 1, -1.74623e-10) 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... Sat Sep 4 13:49:08 IST 2021 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 Sat Sep 4 13:49:08 IST 2021 Ended at Sat Sep 4 13:49:30 IST 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Sep 4 13:49:32 IST 2021 /usr/local/freesurfer/subjects/pt019/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7480, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/pt019/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/pt019/mri/transforms/talairach_avi.log TalAviQA: 0.96562 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Sat Sep 4 13:49:32 IST 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/pt019/mri /usr/local/freesurfer/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 research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Sat Sep 4 13:49:32 IST 2021 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 tmpdir is ./tmp.mri_nu_correct.mni.28389 /usr/local/freesurfer/subjects/pt019/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28389/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28389/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 2.32831e-10, -1) k_ras = (0, 1, -1.74623e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28389/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Sep 4 13:49:33 IST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.28389/nu0.mnc ./tmp.mri_nu_correct.mni.28389/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28389/0/ [root@research1-HP-280-G3-MT:/usr/local/freesurfer/subjects/pt019/mri/] [2021-09-04 13:49:33] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28389/0/ ./tmp.mri_nu_correct.mni.28389/nu0.mnc ./tmp.mri_nu_correct.mni.28389/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 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: 50 CV of field change: 0.000986107 -------------------------------------------------------- Iteration 2 Sat Sep 4 13:50:03 IST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.28389/nu1.mnc ./tmp.mri_nu_correct.mni.28389/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.28389/1/ [root@research1-HP-280-G3-MT:/usr/local/freesurfer/subjects/pt019/mri/] [2021-09-04 13:50:03] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28389/1/ ./tmp.mri_nu_correct.mni.28389/nu1.mnc ./tmp.mri_nu_correct.mni.28389/nu2.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 Number of iterations: 28 CV of field change: 0.000962288 mri_binarize --i ./tmp.mri_nu_correct.mni.28389/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28389/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/pt019/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.28389/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.28389/ones.mgz sysname Linux hostname research1-HP-280-G3-MT machine x86_64 user root input ./tmp.mri_nu_correct.mni.28389/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.28389/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28389/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28389/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28389/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28389/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.28389/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28389/input.mean.dat sysname Linux hostname research1-HP-280-G3-MT machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28389/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.28389/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28389/ones.mgz --i ./tmp.mri_nu_correct.mni.28389/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28389/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28389/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.28389/ones.mgz --i ./tmp.mri_nu_correct.mni.28389/nu2.mnc --sum ./tmp.mri_nu_correct.mni.28389/sum.junk --avgwf ./tmp.mri_nu_correct.mni.28389/output.mean.dat sysname Linux hostname research1-HP-280-G3-MT machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.28389/ones.mgz Loading ./tmp.mri_nu_correct.mni.28389/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.28389/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.28389/nu2.mnc ./tmp.mri_nu_correct.mni.28389/nu2.mnc mul 1.09948096782975364398 Saving result to './tmp.mri_nu_correct.mni.28389/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.28389/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.28389/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.28389/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 1.86265e-09) j_ras = (0, 2.32831e-10, -1) k_ras = (0, 1, -1.74623e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 5 seconds. mapping ( 8, 95) to ( 3, 110) Sat Sep 4 13:50:50 IST 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/pt019/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Sep 4 13:50:51 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.01664 0.01542 -0.01836 1.58964; -0.04498 1.02733 0.31574 -9.66723; 0.03496 -0.28528 1.15308 -25.17790; 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 = 6 Starting OpenSpline(): npoints = 6 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 103 gm peak at 72 (72), valley at 19 (19) csf peak at 19, setting threshold to 54 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 88 (88), valley at 46 (46) csf peak at 33, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 26 seconds. #-------------------------------------------- #@# Skull Stripping Sat Sep 4 13:52:17 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_em_register -rusage /usr/local/freesurfer/subjects/pt019/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 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 '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... 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=15.0 skull bounding box = (45, 39, 23) --> (210, 255, 230) using (100, 111, 127) as brain centroid... mean wm in atlas = 108, using box (80,84,101) --> (120, 137,152) to find MRI wm before smoothing, mri peak at 82 robust fit to distribution - 79 +- 27.1 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.556 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.556278 @ (0.000, 0.000, 0.000) max log p = -4.478639 @ (-4.545, -4.545, -4.545) max log p = -4.462544 @ (2.273, 2.273, -2.273) max log p = -4.448155 @ (-1.136, 1.136, 1.136) max log p = -4.423454 @ (-0.568, 0.568, -1.705) max log p = -4.423454 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -0.6, -7.4): log p = -4.423 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.174, old_max_log_p =-4.423 (thresh=-4.4) 1.06375 0.00000 0.00000 -12.19162; 0.00000 1.19413 0.31997 -58.63308; 0.00000 -0.27823 1.03837 27.78935; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.174, old_max_log_p =-4.174 (thresh=-4.2) 1.06375 0.00000 0.00000 -12.19162; 0.00000 1.19413 0.31997 -58.63308; 0.00000 -0.27823 1.03837 27.78935; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.138, old_max_log_p =-4.174 (thresh=-4.2) 1.04325 -0.03834 -0.01027 -3.10255; 0.03546 1.21586 0.32579 -66.85745; 0.00000 -0.27301 1.01890 27.47311; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.131, old_max_log_p =-4.138 (thresh=-4.1) 1.02200 -0.07690 -0.01946 4.10911; 0.06955 1.22224 0.29179 -68.09203; 0.00118 -0.23746 1.04831 20.86139; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.131, old_max_log_p =-4.131 (thresh=-4.1) 1.02200 -0.07690 -0.01946 4.10911; 0.06955 1.22224 0.29179 -68.09203; 0.00118 -0.23746 1.04831 20.86139; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.114, old_max_log_p =-4.131 (thresh=-4.1) 1.01967 -0.05091 0.00528 -1.10766; 0.04452 1.22459 0.30162 -66.27675; -0.01635 -0.24588 1.04224 23.59248; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.114, old_max_log_p =-4.114 (thresh=-4.1) 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 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 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.114 (old=-4.556) transform before final EM align: 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 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 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.01907 -0.03086 0.01034 -4.36136; 0.02773 1.22465 0.31037 -65.13760; -0.01672 -0.25589 1.03974 25.30077; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 627.140000 mri_em_register stimesec 1.068000 mri_em_register ru_maxrss 613688 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161747 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150296 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 181 mri_em_register ru_nivcsw 311 registration took 10 minutes and 28 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/pt019/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/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=138 z=106 r=83 first estimation of the main basin volume: 2442516 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=152, y=98, z=89, Imax=255 CSF=20, 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=377386600 voxels, voxel volume =1.000 = 377386600 mmm3 = 377386.592 cm3 done. PostAnalyze...Basin Prior 35 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=128,y=118, z=110, r=9159 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=17, CSF_MAX=61 , nb = 43965 RIGHT_CER CSF_MIN=0, CSF_intensity=25, CSF_MAX=50 , nb = -1037705731 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1048042739 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=17, CSF_MAX=61 , nb = -1088476869 LEFT_BRAIN CSF_MIN=0, CSF_intensity=17, CSF_MAX=61 , nb = 1077735990 OTHER CSF_MIN=15, CSF_intensity=28, CSF_MAX=39 , nb = 1074712056 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 61, 42, 11, 86 after analyzing : 35, 42, 42, 53 RIGHT_CER before analyzing : 50, 43, 29, 87 after analyzing : 38, 43, 43, 54 LEFT_CER before analyzing : 5, 4, 0, 17 after analyzing : 4, 18, 25, 19 RIGHT_BRAIN before analyzing : 61, 23, 22, 24 after analyzing : 23, 24, 25, 24 LEFT_BRAIN before analyzing : 61, 38, 36, 40 after analyzing : 32, 38, 38, 38 OTHER before analyzing : 39, 35, 11, 86 after analyzing : 33, 35, 35, 47 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.784, std = 7.544 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.29, sigma = 4.97 after rotation: sse = 3.29, sigma = 4.97 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.52, its var is 4.31 before Erosion-Dilatation 0.41% of inacurate vertices after Erosion-Dilatation 0.00% 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...39 iterations mri_strip_skull: done peeling brain Brain Size = 1560132 voxels, voxel volume = 1.000 mm3 = 1560132 mmm3 = 1560.132 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 13.212000 mri_watershed stimesec 0.120000 mri_watershed ru_maxrss 836040 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212514 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9688 mri_watershed ru_oublock 2896 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 45 mri_watershed ru_nivcsw 22 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Sep 4 14:03:00 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_em_register -rusage /usr/local/freesurfer/subjects/pt019/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 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 '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (58, 58, 37) --> (199, 192, 196) using (105, 103, 117) as brain centroid... mean wm in atlas = 107, using box (88,87,97) --> (122, 119,136) to find MRI wm before smoothing, mri peak at 92 robust fit to distribution - 81 +- 22.2 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.286 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.285933 @ (0.000, 0.000, 0.000) max log p = -4.166101 @ (-4.545, 4.545, -4.545) max log p = -4.081493 @ (2.273, -6.818, -6.818) max log p = -4.063732 @ (-1.136, 3.409, 1.136) max log p = -4.045231 @ (1.705, -0.568, 0.568) max log p = -4.045231 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 0.6, -9.7): log p = -4.045 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.988, old_max_log_p =-4.045 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.11081 0.25882 -42.37890; 0.00000 -0.31997 1.03837 31.41119; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.979, old_max_log_p =-3.988 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.05955 0.39214 -50.65908; 0.00000 -0.42755 0.92103 57.06892; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.974, old_max_log_p =-3.979 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.10629 0.26857 -42.89088; 0.00000 -0.30701 1.03666 30.03914; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.974, old_max_log_p =-3.974 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.70455; 0.00000 1.10629 0.26857 -42.89088; 0.00000 -0.30701 1.03666 30.03914; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.856, old_max_log_p =-3.974 (thresh=-4.0) 0.98002 -0.03615 -0.01111 6.28932; 0.03208 1.10434 0.33932 -52.50859; 0.00000 -0.36722 0.97808 43.38410; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.843, old_max_log_p =-3.856 (thresh=-3.9) 0.98002 -0.03615 -0.01111 6.28932; 0.03268 1.12505 0.34568 -55.72980; 0.00000 -0.36722 0.97808 43.38410; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.843, old_max_log_p =-3.843 (thresh=-3.8) 0.98002 -0.03615 -0.01111 6.28932; 0.03268 1.12505 0.34568 -55.72980; 0.00000 -0.36722 0.97808 43.38410; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.830, old_max_log_p =-3.843 (thresh=-3.8) 0.97916 -0.02297 0.01018 1.58503; 0.01653 1.13299 0.31227 -51.44103; -0.01502 -0.33074 0.99240 39.43923; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.828, old_max_log_p =-3.830 (thresh=-3.8) 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 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 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.828 (old=-4.286) transform before final EM align: 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 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 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.1 tol 0.000000 final transform: 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 668.232000 mri_em_register stimesec 1.256000 mri_em_register ru_maxrss 603196 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162494 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 111 mri_em_register ru_nivcsw 302 registration took 11 minutes and 10 seconds. #-------------------------------------- #@# CA Normalize Sat Sep 4 14:14:10 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (58, 58, 37) --> (199, 192, 196) using (105, 103, 117) as brain centroid... mean wm in atlas = 107, using box (88,87,97) --> (122, 119,136) to find MRI wm before smoothing, mri peak at 92 robust fit to distribution - 81 +- 22.2 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 0.97785 -0.03220 0.00761 3.13101; 0.02451 1.13144 0.31197 -52.25795; -0.01504 -0.33113 0.99356 39.36188; 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 (130, 62, 37) --> (197, 164, 194) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 137 (3.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 62, 35) --> (130, 158, 194) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 3 of 147 (2.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 142, 66) --> (182, 177, 118) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 38 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 142, 63) --> (130, 178, 118) Right_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0 6 of 9 (66.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 128, 99) --> (148, 188, 128) Brain_Stem: limiting intensities to 104.0 --> 132.0 4 of 46 (8.7%) samples deleted using 377 total control points for intensity normalization... bias field = 0.975 +- 0.142 0 of 359 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 62, 37) --> (197, 164, 194) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 138 (5.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 62, 35) --> (130, 158, 194) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 143 (5.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 142, 66) --> (182, 177, 118) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 67 of 126 (53.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 142, 63) --> (130, 178, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 69 (18.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 128, 99) --> (148, 188, 128) Brain_Stem: limiting intensities to 91.0 --> 132.0 32 of 88 (36.4%) samples deleted using 564 total control points for intensity normalization... bias field = 0.961 +- 0.095 0 of 433 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 62, 37) --> (197, 164, 194) Left_Cerebral_White_Matter: limiting intensities to 119.0 --> 132.0 188 of 200 (94.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (63, 62, 35) --> (130, 158, 194) Right_Cerebral_White_Matter: limiting intensities to 116.0 --> 132.0 210 of 234 (89.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 142, 66) --> (182, 177, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 59 of 164 (36.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 142, 63) --> (130, 178, 118) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 48 of 80 (60.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 128, 99) --> (148, 188, 128) Brain_Stem: limiting intensities to 94.0 --> 132.0 103 of 179 (57.5%) samples deleted using 857 total control points for intensity normalization... bias field = 0.896 +- 0.056 0 of 246 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 59 seconds. #-------------------------------------- #@# CA Reg Sat Sep 4 14:15:09 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/pt019/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 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 '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.20 (predicted orig area = 6.7) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.924, neg=0, invalid=762 0001: dt=226.721408, rms=0.860 (6.949%), neg=0, invalid=762 0002: dt=465.619893, rms=0.832 (3.212%), neg=0, invalid=762 0003: dt=156.176101, rms=0.824 (1.003%), neg=0, invalid=762 0004: dt=1183.744000, rms=0.812 (1.386%), neg=0, invalid=762 0005: dt=174.153846, rms=0.805 (0.846%), neg=0, invalid=762 0006: dt=517.888000, rms=0.803 (0.353%), neg=0, invalid=762 0007: dt=129.472000, rms=0.801 (0.258%), neg=0, invalid=762 0008: dt=1775.616000, rms=0.796 (0.565%), neg=0, invalid=762 0009: dt=144.000000, rms=0.793 (0.366%), neg=0, invalid=762 0010: dt=517.888000, rms=0.790 (0.387%), neg=0, invalid=762 0011: dt=73.984000, rms=0.790 (0.010%), neg=0, invalid=762 0012: dt=73.984000, rms=0.790 (0.007%), neg=0, invalid=762 0013: dt=73.984000, rms=0.790 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.790, neg=0, invalid=762 0014: dt=129.472000, rms=0.789 (0.173%), neg=0, invalid=762 0015: dt=517.888000, rms=0.788 (0.163%), neg=0, invalid=762 0016: dt=517.888000, rms=0.788 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.791, neg=0, invalid=762 0017: dt=248.832000, rms=0.764 (3.434%), neg=0, invalid=762 0018: dt=141.099114, rms=0.743 (2.818%), neg=0, invalid=762 0019: dt=90.784708, rms=0.735 (1.064%), neg=0, invalid=762 0020: dt=201.061947, rms=0.726 (1.152%), neg=0, invalid=762 0021: dt=76.472262, rms=0.718 (1.144%), neg=0, invalid=762 0022: dt=103.680000, rms=0.715 (0.417%), neg=0, invalid=762 0023: dt=9.072000, rms=0.714 (0.097%), neg=0, invalid=762 0024: dt=9.072000, rms=0.714 (0.068%), neg=0, invalid=762 0025: dt=2.268000, rms=0.714 (0.019%), neg=0, invalid=762 0026: dt=0.567000, rms=0.714 (0.004%), neg=0, invalid=762 0027: dt=0.141750, rms=0.714 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 0028: dt=145.152000, rms=0.710 (0.602%), neg=0, invalid=762 0029: dt=36.288000, rms=0.710 (0.074%), neg=0, invalid=762 0030: dt=9.072000, rms=0.709 (0.020%), neg=0, invalid=762 0031: dt=2.268000, rms=0.709 (0.006%), neg=0, invalid=762 0032: dt=1.134000, rms=0.709 (0.002%), neg=0, invalid=762 0033: dt=0.141750, rms=0.709 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=762 0034: dt=52.472622, rms=0.717 (1.950%), neg=0, invalid=762 0035: dt=32.000000, rms=0.704 (1.853%), neg=0, invalid=762 0036: dt=44.800000, rms=0.701 (0.456%), neg=0, invalid=762 0037: dt=38.400000, rms=0.696 (0.647%), neg=0, invalid=762 0038: dt=32.000000, rms=0.696 (0.047%), neg=0, invalid=762 0039: dt=32.000000, rms=0.694 (0.320%), neg=0, invalid=762 0040: dt=32.000000, rms=0.691 (0.355%), neg=0, invalid=762 0041: dt=32.000000, rms=0.689 (0.302%), neg=0, invalid=762 0042: dt=32.000000, rms=0.687 (0.330%), neg=0, invalid=762 0043: dt=32.000000, rms=0.684 (0.381%), neg=0, invalid=762 0044: dt=32.000000, rms=0.682 (0.288%), neg=0, invalid=762 0045: dt=32.000000, rms=0.681 (0.134%), neg=0, invalid=762 0046: dt=32.000000, rms=0.681 (0.074%), neg=0, invalid=762 0047: dt=32.000000, rms=0.680 (0.129%), neg=0, invalid=762 0048: dt=32.000000, rms=0.679 (0.149%), neg=0, invalid=762 0049: dt=32.000000, rms=0.678 (0.108%), neg=0, invalid=762 0050: dt=32.000000, rms=0.678 (0.075%), neg=0, invalid=762 0051: dt=32.000000, rms=0.677 (0.028%), neg=0, invalid=762 0052: dt=32.000000, rms=0.677 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0053: dt=0.000000, rms=0.677 (0.072%), neg=0, invalid=762 0054: dt=0.000000, rms=0.677 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0055: dt=0.000000, rms=0.731 (0.062%), neg=0, invalid=762 0056: dt=0.000000, rms=0.731 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0057: dt=0.000000, rms=0.731 (0.062%), neg=0, invalid=762 0058: dt=0.000000, rms=0.731 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.835, neg=0, invalid=762 0059: dt=1.455446, rms=0.814 (2.461%), neg=0, invalid=762 0060: dt=1.083942, rms=0.809 (0.669%), neg=0, invalid=762 0061: dt=0.448000, rms=0.808 (0.106%), neg=0, invalid=762 0062: dt=0.448000, rms=0.807 (0.038%), neg=0, invalid=762 0063: dt=0.448000, rms=0.807 (-0.094%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.808, neg=0, invalid=762 0064: dt=0.448000, rms=0.807 (0.119%), neg=0, invalid=762 0065: dt=0.256000, rms=0.807 (0.009%), neg=0, invalid=762 0066: dt=0.256000, rms=0.807 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=762 0067: dt=0.879731, rms=0.713 (2.701%), neg=0, invalid=762 0068: dt=0.096000, rms=0.712 (0.156%), neg=0, invalid=762 0069: dt=0.096000, rms=0.712 (-0.104%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.712, neg=0, invalid=762 0070: dt=0.028000, rms=0.712 (0.081%), neg=0, invalid=762 0071: dt=0.007000, rms=0.712 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.15524 (22) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (1915 voxels, overlap=0.651) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (1915 voxels, peak = 23), gca=23.1 gca peak = 0.15565 (16) mri peak = 0.26622 (24) Right_Lateral_Ventricle (43): linear fit = 1.41 x + 0.0 (1648 voxels, overlap=0.487) Right_Lateral_Ventricle (43): linear fit = 1.41 x + 0.0 (1648 voxels, peak = 23), gca=22.6 gca peak = 0.26829 (96) mri peak = 0.09509 (109) Right_Pallidum (52): linear fit = 1.14 x + 0.0 (651 voxels, overlap=0.025) Right_Pallidum (52): linear fit = 1.14 x + 0.0 (651 voxels, peak = 110), gca=109.9 gca peak = 0.20183 (93) mri peak = 0.09888 (107) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (654 voxels, overlap=0.029) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (654 voxels, peak = 104), gca=103.7 gca peak = 0.21683 (55) mri peak = 0.06680 (64) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (636 voxels, overlap=0.357) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (636 voxels, peak = 62), gca=61.9 gca peak = 0.30730 (58) mri peak = 0.07307 (67) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (933 voxels, overlap=0.586) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (933 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.08074 (90) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (55197 voxels, overlap=0.897) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (55197 voxels, peak = 98), gca=98.5 gca peak = 0.12076 (102) mri peak = 0.08216 (92) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (59510 voxels, overlap=0.846) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (59510 voxels, peak = 97), gca=97.4 gca peak = 0.14995 (59) mri peak = 0.03419 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25494 voxels, overlap=0.903) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25494 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03510 (64) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (24880 voxels, overlap=0.778) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (24880 voxels, peak = 64), gca=63.5 gca peak = 0.14161 (67) mri peak = 0.08099 (71) Right_Caudate (50): linear fit = 1.04 x + 0.0 (743 voxels, overlap=0.550) Right_Caudate (50): linear fit = 1.04 x + 0.0 (743 voxels, peak = 70), gca=70.0 gca peak = 0.15243 (71) mri peak = 0.10931 (76) Left_Caudate (11): linear fit = 1.03 x + 0.0 (635 voxels, overlap=0.907) Left_Caudate (11): linear fit = 1.03 x + 0.0 (635 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.02939 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26879 voxels, overlap=0.899) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (26879 voxels, peak = 60), gca=59.6 gca peak = 0.13252 (56) mri peak = 0.03330 (54) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (30211 voxels, overlap=0.941) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (30211 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.06461 (83) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9023 voxels, overlap=0.893) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9023 voxels, peak = 86), gca=86.1 gca peak = 0.20573 (83) mri peak = 0.05471 (80) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7984 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7984 voxels, peak = 83), gca=83.0 gca peak = 0.21969 (57) mri peak = 0.07717 (64) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (318 voxels, overlap=0.477) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (318 voxels, peak = 64), gca=63.6 gca peak = 0.39313 (56) mri peak = 0.07584 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (459 voxels, overlap=0.029) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (459 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.05054 (96) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4576 voxels, overlap=0.805) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4576 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.06225 (87) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3087 voxels, overlap=0.604) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3087 voxels, peak = 88), gca=88.4 gca peak = 0.13399 (79) mri peak = 0.07622 (81) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1989 voxels, overlap=1.001) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1989 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.04487 (83) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1822 voxels, overlap=0.752) Right_Putamen (51): linear fit = 1.10 x + 0.0 (1822 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.07879 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11174 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11174 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.10830 (100) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1234 voxels, overlap=0.020) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1234 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.08462 (100) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1246 voxels, overlap=0.169) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1246 voxels, peak = 101), gca=101.0 gca peak = 0.20494 (23) mri peak = 0.08827 (27) gca peak = 0.15061 (21) mri peak = 0.14895 (21) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (447 voxels, overlap=0.368) Fourth_Ventricle (15): linear fit = 1.11 x + 0.0 (447 voxels, peak = 23), gca=23.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) 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 1.13 x + 0.0 estimating mean wm scale to be 0.97 x + 0.0 estimating mean csf scale to be 1.23 x + 0.0 Left_Pallidum too bright - rescaling by 0.916 (from 1.115) to 95.0 (was 103.7) Right_Pallidum too bright - rescaling by 0.864 (from 1.145) to 95.0 (was 109.9) 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=0.678, neg=0, invalid=762 0072: dt=138.989899, rms=0.674 (0.665%), neg=0, invalid=762 0073: dt=369.920000, rms=0.669 (0.659%), neg=0, invalid=762 0074: dt=129.472000, rms=0.668 (0.208%), neg=0, invalid=762 0075: dt=129.472000, rms=0.667 (0.073%), neg=0, invalid=762 0076: dt=887.808000, rms=0.664 (0.425%), neg=0, invalid=762 0077: dt=55.488000, rms=0.664 (0.058%), neg=0, invalid=762 0078: dt=32.368000, rms=0.664 (0.012%), neg=0, invalid=762 0079: dt=32.368000, rms=0.664 (0.003%), neg=0, invalid=762 0080: dt=32.368000, rms=0.664 (0.004%), neg=0, invalid=762 0081: dt=32.368000, rms=0.664 (0.004%), neg=0, invalid=762 0082: dt=32.368000, rms=0.664 (0.019%), neg=0, invalid=762 0083: dt=32.368000, rms=0.663 (0.041%), neg=0, invalid=762 0084: dt=32.368000, rms=0.663 (0.061%), neg=0, invalid=762 0085: dt=32.368000, rms=0.663 (0.068%), neg=0, invalid=762 0086: dt=32.368000, rms=0.662 (0.065%), neg=0, invalid=762 0087: dt=32.368000, rms=0.662 (0.059%), neg=0, invalid=762 0088: dt=32.368000, rms=0.661 (0.055%), neg=0, invalid=762 0089: dt=32.368000, rms=0.661 (0.051%), neg=0, invalid=762 0090: dt=32.368000, rms=0.661 (0.041%), neg=0, invalid=762 0091: dt=32.368000, rms=0.661 (0.036%), neg=0, invalid=762 0092: dt=32.368000, rms=0.660 (0.040%), neg=0, invalid=762 0093: dt=32.368000, rms=0.660 (0.044%), neg=0, invalid=762 0094: dt=32.368000, rms=0.660 (0.048%), neg=0, invalid=762 0095: dt=32.368000, rms=0.659 (0.049%), neg=0, invalid=762 0096: dt=32.368000, rms=0.659 (0.045%), neg=0, invalid=762 0097: dt=32.368000, rms=0.659 (0.043%), neg=0, invalid=762 0098: dt=32.368000, rms=0.659 (0.038%), neg=0, invalid=762 0099: dt=32.368000, rms=0.658 (0.034%), neg=0, invalid=762 0100: dt=32.368000, rms=0.658 (0.032%), neg=0, invalid=762 0101: dt=32.368000, rms=0.658 (0.030%), neg=0, invalid=762 0102: dt=32.368000, rms=0.658 (0.034%), neg=0, invalid=762 0103: dt=32.368000, rms=0.657 (0.037%), neg=0, invalid=762 0104: dt=32.368000, rms=0.657 (0.040%), neg=0, invalid=762 0105: dt=32.368000, rms=0.657 (0.040%), neg=0, invalid=762 0106: dt=32.368000, rms=0.657 (0.039%), neg=0, invalid=762 0107: dt=32.368000, rms=0.656 (0.036%), neg=0, invalid=762 0108: dt=32.368000, rms=0.656 (0.032%), neg=0, invalid=762 0109: dt=32.368000, rms=0.656 (0.029%), neg=0, invalid=762 0110: dt=32.368000, rms=0.656 (0.028%), neg=0, invalid=762 0111: dt=32.368000, rms=0.656 (0.028%), neg=0, invalid=762 0112: dt=32.368000, rms=0.656 (0.027%), neg=0, invalid=762 0113: dt=32.368000, rms=0.655 (0.029%), neg=0, invalid=762 0114: dt=32.368000, rms=0.655 (0.033%), neg=0, invalid=762 0115: dt=32.368000, rms=0.655 (0.031%), neg=0, invalid=762 0116: dt=32.368000, rms=0.655 (0.030%), neg=0, invalid=762 0117: dt=32.368000, rms=0.655 (0.027%), neg=0, invalid=762 0118: dt=32.368000, rms=0.654 (0.025%), neg=0, invalid=762 0119: dt=32.368000, rms=0.654 (0.024%), neg=0, invalid=762 0120: dt=32.368000, rms=0.654 (0.024%), neg=0, invalid=762 0121: dt=1479.680000, rms=0.654 (0.070%), neg=0, invalid=762 0122: dt=92.480000, rms=0.653 (0.039%), neg=0, invalid=762 0123: dt=92.480000, rms=0.653 (0.022%), neg=0, invalid=762 0124: dt=92.480000, rms=0.653 (0.019%), neg=0, invalid=762 0125: dt=92.480000, rms=0.653 (0.012%), neg=0, invalid=762 0126: dt=18.496000, rms=0.653 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0127: dt=221.952000, rms=0.652 (0.268%), neg=0, invalid=762 0128: dt=369.920000, rms=0.651 (0.105%), neg=0, invalid=762 0129: dt=73.984000, rms=0.651 (0.016%), neg=0, invalid=762 0130: dt=73.984000, rms=0.651 (0.010%), neg=0, invalid=762 0131: dt=73.984000, rms=0.651 (0.017%), neg=0, invalid=762 0132: dt=73.984000, rms=0.650 (0.029%), neg=0, invalid=762 0133: dt=73.984000, rms=0.650 (0.046%), neg=0, invalid=762 0134: dt=73.984000, rms=0.650 (0.051%), neg=0, invalid=762 0135: dt=73.984000, rms=0.650 (0.032%), neg=0, invalid=762 0136: dt=73.984000, rms=0.649 (0.021%), neg=0, invalid=762 0137: dt=73.984000, rms=0.649 (0.017%), neg=0, invalid=762 0138: dt=517.888000, rms=0.649 (0.042%), neg=0, invalid=762 0139: dt=129.472000, rms=0.649 (0.016%), neg=0, invalid=762 0140: dt=129.472000, rms=0.649 (0.004%), neg=0, invalid=762 0141: dt=129.472000, rms=0.649 (0.007%), neg=0, invalid=762 0142: dt=129.472000, rms=0.649 (0.019%), neg=0, invalid=762 0143: dt=129.472000, rms=0.649 (0.026%), neg=0, invalid=762 0144: dt=129.472000, rms=0.648 (0.033%), neg=0, invalid=762 0145: dt=129.472000, rms=0.648 (0.030%), neg=0, invalid=762 0146: dt=129.472000, rms=0.648 (0.026%), neg=0, invalid=762 0147: dt=129.472000, rms=0.648 (0.026%), neg=0, invalid=762 0148: dt=129.472000, rms=0.648 (0.034%), neg=0, invalid=762 0149: dt=129.472000, rms=0.647 (0.040%), neg=0, invalid=762 0150: dt=129.472000, rms=0.647 (0.037%), neg=0, invalid=762 0151: dt=129.472000, rms=0.647 (0.035%), neg=0, invalid=762 0152: dt=129.472000, rms=0.647 (0.032%), neg=0, invalid=762 0153: dt=129.472000, rms=0.647 (0.028%), neg=0, invalid=762 0154: dt=129.472000, rms=0.646 (0.033%), neg=0, invalid=762 0155: dt=129.472000, rms=0.646 (0.028%), neg=0, invalid=762 0156: dt=129.472000, rms=0.646 (0.033%), neg=0, invalid=762 0157: dt=129.472000, rms=0.646 (0.027%), neg=0, invalid=762 0158: dt=129.472000, rms=0.646 (0.025%), neg=0, invalid=762 0159: dt=129.472000, rms=0.645 (0.023%), neg=0, invalid=762 0160: dt=129.472000, rms=0.645 (0.031%), neg=0, invalid=762 0161: dt=129.472000, rms=0.645 (0.028%), neg=0, invalid=762 0162: dt=129.472000, rms=0.645 (0.029%), neg=0, invalid=762 0163: dt=129.472000, rms=0.645 (0.031%), neg=0, invalid=762 0164: dt=129.472000, rms=0.644 (0.028%), neg=0, invalid=762 0165: dt=129.472000, rms=0.644 (0.026%), neg=0, invalid=762 0166: dt=129.472000, rms=0.644 (0.024%), neg=0, invalid=762 0167: dt=129.472000, rms=0.644 (0.030%), neg=0, invalid=762 0168: dt=129.472000, rms=0.644 (0.030%), neg=0, invalid=762 0169: dt=129.472000, rms=0.644 (0.023%), neg=0, invalid=762 0170: dt=129.472000, rms=0.643 (0.024%), neg=0, invalid=762 0171: dt=129.472000, rms=0.643 (0.005%), neg=0, invalid=762 0172: dt=0.000000, rms=0.643 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0173: dt=0.567000, rms=0.644 (0.057%), neg=0, invalid=762 0174: dt=0.567000, rms=0.644 (0.007%), neg=0, invalid=762 0175: dt=0.283500, rms=0.644 (0.003%), neg=0, invalid=762 0176: dt=0.141750, rms=0.644 (0.002%), neg=0, invalid=762 0177: dt=0.035437, rms=0.644 (0.000%), neg=0, invalid=762 0178: dt=0.001898, rms=0.644 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0179: dt=0.000000, rms=0.644 (0.051%), neg=0, invalid=762 0180: dt=0.000000, rms=0.644 (0.000%), neg=0, invalid=762 0181: dt=0.000879, rms=0.644 (0.000%), neg=0, invalid=762 0182: dt=0.000220, rms=0.644 (0.000%), neg=0, invalid=762 0183: dt=0.000027, rms=0.644 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0184: dt=0.000000, rms=0.646 (0.050%), neg=0, invalid=762 0185: dt=0.000000, rms=0.646 (0.000%), neg=0, invalid=762 0186: dt=0.000004, rms=0.646 (0.000%), neg=0, invalid=762 0187: dt=0.000001, rms=0.646 (0.000%), neg=0, invalid=762 0188: dt=0.000000, rms=0.646 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0189: dt=0.000000, rms=0.646 (0.050%), neg=0, invalid=762 0190: dt=0.000000, rms=0.646 (0.000%), neg=0, invalid=762 0191: dt=0.000122, rms=0.646 (0.000%), neg=0, invalid=762 0192: dt=0.000008, rms=0.646 (0.000%), neg=0, invalid=762 0193: dt=0.000002, rms=0.646 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.653, neg=0, invalid=762 0194: dt=0.864000, rms=0.648 (0.797%), neg=0, invalid=762 0195: dt=0.252000, rms=0.646 (0.209%), neg=0, invalid=762 0196: dt=0.063000, rms=0.646 (0.050%), neg=0, invalid=762 0197: dt=0.045000, rms=0.646 (0.039%), neg=0, invalid=762 0198: dt=0.000703, rms=0.646 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0199: dt=4.032000, rms=0.628 (2.707%), neg=0, invalid=762 0200: dt=3.456000, rms=0.617 (1.802%), neg=0, invalid=762 0201: dt=0.252000, rms=0.616 (0.109%), neg=0, invalid=762 0202: dt=0.216000, rms=0.616 (0.092%), neg=0, invalid=762 0203: dt=0.015750, rms=0.616 (0.006%), neg=0, invalid=762 0204: dt=0.001969, rms=0.616 (0.001%), neg=0, invalid=762 0205: dt=0.000984, rms=0.616 (0.000%), neg=0, invalid=762 0206: dt=0.000246, rms=0.616 (0.000%), neg=0, invalid=762 0207: dt=0.000211, rms=0.616 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0208: dt=0.448000, rms=0.629 (0.359%), neg=0, invalid=762 0209: dt=1.280000, rms=0.624 (0.764%), neg=0, invalid=762 0210: dt=0.892857, rms=0.622 (0.392%), neg=0, invalid=762 0211: dt=0.562500, rms=0.621 (0.203%), neg=0, invalid=762 0212: dt=0.500000, rms=0.620 (0.160%), neg=0, invalid=762 0213: dt=0.448000, rms=0.619 (0.129%), neg=0, invalid=762 0214: dt=0.448000, rms=0.618 (0.121%), neg=0, invalid=762 0215: dt=0.448000, rms=0.617 (0.109%), neg=0, invalid=762 0216: dt=0.448000, rms=0.617 (0.104%), neg=0, invalid=762 0217: dt=0.448000, rms=0.616 (0.094%), neg=0, invalid=762 0218: dt=0.448000, rms=0.616 (0.088%), neg=0, invalid=762 0219: dt=0.448000, rms=0.615 (0.084%), neg=0, invalid=762 0220: dt=0.448000, rms=0.615 (0.076%), neg=0, invalid=762 0221: dt=0.448000, rms=0.614 (0.071%), neg=0, invalid=762 0222: dt=0.448000, rms=0.614 (0.068%), neg=0, invalid=762 0223: dt=0.448000, rms=0.613 (0.062%), neg=0, invalid=762 0224: dt=0.448000, rms=0.613 (0.060%), neg=0, invalid=762 0225: dt=0.448000, rms=0.613 (0.057%), neg=0, invalid=762 0226: dt=0.448000, rms=0.612 (0.055%), neg=0, invalid=762 0227: dt=0.448000, rms=0.612 (0.050%), neg=0, invalid=762 0228: dt=0.448000, rms=0.612 (0.048%), neg=0, invalid=762 0229: dt=0.448000, rms=0.611 (0.088%), neg=0, invalid=762 0230: dt=0.448000, rms=0.611 (0.121%), neg=0, invalid=762 0231: dt=0.448000, rms=0.610 (0.142%), neg=0, invalid=762 0232: dt=0.448000, rms=0.609 (0.156%), neg=0, invalid=762 0233: dt=0.448000, rms=0.608 (0.157%), neg=0, invalid=762 0234: dt=0.448000, rms=0.607 (0.156%), neg=0, invalid=762 0235: dt=0.448000, rms=0.606 (0.144%), neg=0, invalid=762 0236: dt=0.448000, rms=0.605 (0.128%), neg=0, invalid=762 0237: dt=0.448000, rms=0.604 (0.111%), neg=0, invalid=762 0238: dt=0.448000, rms=0.604 (0.095%), neg=0, invalid=762 0239: dt=0.448000, rms=0.603 (0.078%), neg=0, invalid=762 0240: dt=0.448000, rms=0.603 (0.062%), neg=0, invalid=762 0241: dt=0.448000, rms=0.603 (0.048%), neg=0, invalid=762 0242: dt=0.448000, rms=0.603 (0.033%), neg=0, invalid=762 0243: dt=0.448000, rms=0.602 (0.028%), neg=0, invalid=762 0244: dt=0.448000, rms=0.602 (0.020%), neg=0, invalid=762 0245: dt=0.448000, rms=0.602 (0.011%), neg=0, invalid=762 0246: dt=0.448000, rms=0.602 (0.001%), neg=0, invalid=762 0247: dt=0.448000, rms=0.602 (0.002%), neg=0, invalid=762 0248: dt=0.448000, rms=0.602 (0.002%), neg=0, invalid=762 0249: dt=0.448000, rms=0.602 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=762 0250: dt=0.448000, rms=0.602 (0.134%), neg=0, invalid=762 0251: dt=0.448000, rms=0.601 (0.062%), neg=0, invalid=762 0252: dt=0.448000, rms=0.601 (0.049%), neg=0, invalid=762 0253: dt=0.448000, rms=0.601 (0.042%), neg=0, invalid=762 0254: dt=0.448000, rms=0.600 (0.070%), neg=0, invalid=762 0255: dt=0.448000, rms=0.600 (0.080%), neg=0, invalid=762 0256: dt=0.448000, rms=0.600 (0.073%), neg=0, invalid=762 0257: dt=0.448000, rms=0.599 (0.047%), neg=0, invalid=762 0258: dt=0.448000, rms=0.599 (0.031%), neg=0, invalid=762 0259: dt=0.448000, rms=0.599 (0.009%), neg=0, invalid=762 0260: dt=0.448000, rms=0.599 (-0.000%), neg=0, invalid=762 0261: dt=1.024000, rms=0.599 (0.004%), neg=0, invalid=762 0262: dt=1.280000, rms=0.599 (0.006%), neg=0, invalid=762 0263: dt=1.536000, rms=0.599 (0.013%), neg=0, invalid=762 0264: dt=1.536000, rms=0.599 (0.013%), 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=0.585, neg=0, invalid=762 0265: dt=0.112000, rms=0.581 (0.756%), neg=0, invalid=762 0266: dt=0.112000, rms=0.577 (0.584%), neg=0, invalid=762 0267: dt=0.112000, rms=0.574 (0.491%), neg=0, invalid=762 0268: dt=0.112000, rms=0.572 (0.422%), neg=0, invalid=762 0269: dt=0.112000, rms=0.570 (0.353%), neg=0, invalid=762 0270: dt=0.112000, rms=0.568 (0.307%), neg=0, invalid=762 0271: dt=0.112000, rms=0.567 (0.258%), neg=0, invalid=762 0272: dt=0.112000, rms=0.565 (0.230%), neg=0, invalid=762 0273: dt=0.223214, rms=0.563 (0.392%), neg=0, invalid=762 0274: dt=0.145833, rms=0.562 (0.200%), neg=0, invalid=762 0275: dt=0.125000, rms=0.561 (0.147%), neg=0, invalid=762 0276: dt=0.112000, rms=0.560 (0.119%), neg=0, invalid=762 0277: dt=0.112000, rms=0.560 (0.107%), neg=0, invalid=762 0278: dt=0.112000, rms=0.559 (0.100%), neg=0, invalid=762 0279: dt=0.112000, rms=0.559 (0.089%), neg=0, invalid=762 0280: dt=0.112000, rms=0.558 (0.085%), neg=0, invalid=762 0281: dt=0.112000, rms=0.558 (0.074%), neg=0, invalid=762 0282: dt=0.112000, rms=0.558 (0.074%), neg=0, invalid=762 0283: dt=0.112000, rms=0.557 (0.065%), neg=0, invalid=762 0284: dt=0.112000, rms=0.557 (0.063%), neg=0, invalid=762 0285: dt=0.112000, rms=0.556 (0.057%), neg=0, invalid=762 0286: dt=0.112000, rms=0.556 (0.057%), neg=0, invalid=762 0287: dt=0.112000, rms=0.556 (0.050%), neg=0, invalid=762 0288: dt=0.112000, rms=0.556 (0.051%), neg=0, invalid=762 0289: dt=0.112000, rms=0.555 (0.043%), neg=0, invalid=762 0290: dt=0.112000, rms=0.555 (0.047%), neg=0, invalid=762 0291: dt=0.112000, rms=0.555 (0.079%), neg=0, invalid=762 0292: dt=0.112000, rms=0.554 (0.109%), neg=0, invalid=762 0293: dt=0.112000, rms=0.553 (0.130%), neg=0, invalid=762 0294: dt=0.112000, rms=0.553 (0.140%), neg=0, invalid=762 0295: dt=0.112000, rms=0.552 (0.141%), neg=0, invalid=762 0296: dt=0.112000, rms=0.551 (0.137%), neg=0, invalid=762 0297: dt=0.112000, rms=0.550 (0.128%), neg=0, invalid=762 0298: dt=0.112000, rms=0.550 (0.115%), neg=0, invalid=762 0299: dt=0.112000, rms=0.549 (0.100%), neg=0, invalid=762 0300: dt=0.112000, rms=0.549 (0.081%), neg=0, invalid=762 0301: dt=0.112000, rms=0.548 (0.066%), neg=0, invalid=762 0302: dt=0.112000, rms=0.548 (0.052%), neg=0, invalid=762 0303: dt=0.112000, rms=0.548 (0.039%), neg=0, invalid=762 0304: dt=0.112000, rms=0.548 (0.026%), neg=0, invalid=762 0305: dt=0.112000, rms=0.548 (0.015%), neg=0, invalid=762 0306: dt=0.112000, rms=0.548 (0.011%), neg=0, invalid=762 0307: dt=0.000005, rms=0.548 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0308: dt=0.112000, rms=0.546 (0.290%), neg=0, invalid=762 0309: dt=0.112000, rms=0.546 (0.159%), neg=0, invalid=762 0310: dt=0.112000, rms=0.545 (0.115%), neg=0, invalid=762 0311: dt=0.112000, rms=0.544 (0.085%), neg=0, invalid=762 0312: dt=0.112000, rms=0.544 (0.063%), neg=0, invalid=762 0313: dt=0.112000, rms=0.544 (0.045%), neg=0, invalid=762 0314: dt=0.112000, rms=0.544 (0.031%), neg=0, invalid=762 0315: dt=0.112000, rms=0.543 (0.050%), neg=0, invalid=762 0316: dt=0.112000, rms=0.543 (0.044%), neg=0, invalid=762 0317: dt=0.112000, rms=0.543 (0.024%), neg=0, invalid=762 0318: dt=0.112000, rms=0.543 (-0.012%), neg=0, invalid=762 0319: dt=0.000000, rms=0.543 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=762 0320: dt=0.000000, rms=0.539 (0.085%), neg=0, invalid=762 0321: dt=0.000000, rms=0.539 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.540, neg=0, invalid=762 0322: dt=92.480000, rms=0.539 (0.105%), neg=0, invalid=762 0323: dt=369.920000, rms=0.539 (0.066%), neg=0, invalid=762 0324: dt=369.920000, rms=0.539 (-0.726%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0325: dt=36.288000, rms=0.538 (0.222%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0326: dt=36.288000, rms=0.538 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0327: dt=36.288000, rms=0.538 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=0, neg = 0 0328: dt=36.288000, rms=0.538 (0.045%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 17 iterations, nbhd size=1, neg = 0 0329: dt=36.288000, rms=0.538 (-0.057%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 0330: dt=87.885167, rms=0.535 (0.644%), neg=0, invalid=762 0331: dt=36.288000, rms=0.534 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0332: dt=36.288000, rms=0.534 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0333: dt=36.288000, rms=0.533 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0334: dt=36.288000, rms=0.532 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0335: dt=36.288000, rms=0.532 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0336: dt=36.288000, rms=0.531 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=0, neg = 0 0337: dt=36.288000, rms=0.530 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0338: dt=36.288000, rms=0.530 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0339: dt=36.288000, rms=0.529 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 31 after 16 iterations, nbhd size=1, neg = 0 0340: dt=331.776000, rms=0.529 (0.107%), neg=0, invalid=762 0341: dt=36.288000, rms=0.529 (0.049%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0342: dt=36.288000, rms=0.529 (0.017%), neg=0, invalid=762 0343: dt=36.288000, rms=0.528 (0.021%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0344: dt=36.288000, rms=0.528 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0345: dt=36.288000, rms=0.528 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=0, neg = 0 0346: dt=36.288000, rms=0.528 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0347: dt=36.288000, rms=0.527 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0348: dt=36.288000, rms=0.527 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0349: dt=36.288000, rms=0.527 (0.060%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0350: dt=36.288000, rms=0.527 (0.047%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 iter 0, gcam->neg = 317 after 27 iterations, nbhd size=1, neg = 0 0351: dt=50.408027, rms=0.523 (0.966%), neg=0, invalid=762 iter 0, gcam->neg = 322 after 26 iterations, nbhd size=1, neg = 0 0352: dt=63.213115, rms=0.520 (0.512%), neg=0, invalid=762 iter 0, gcam->neg = 260 after 27 iterations, nbhd size=1, neg = 0 0353: dt=38.400000, rms=0.517 (0.548%), neg=0, invalid=762 iter 0, gcam->neg = 73 after 18 iterations, nbhd size=1, neg = 0 0354: dt=25.600000, rms=0.516 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 47 after 20 iterations, nbhd size=1, neg = 0 0355: dt=25.600000, rms=0.516 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 132 after 26 iterations, nbhd size=1, neg = 0 0356: dt=25.600000, rms=0.515 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 288 after 29 iterations, nbhd size=1, neg = 0 0357: dt=25.600000, rms=0.513 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 449 after 33 iterations, nbhd size=1, neg = 0 0358: dt=25.600000, rms=0.512 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 618 after 33 iterations, nbhd size=1, neg = 0 0359: dt=25.600000, rms=0.512 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 751 after 37 iterations, nbhd size=1, neg = 0 0360: dt=25.600000, rms=0.511 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 1063 after 35 iterations, nbhd size=1, neg = 0 0361: dt=25.600000, rms=0.510 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 1127 after 33 iterations, nbhd size=1, neg = 0 0362: dt=25.600000, rms=0.510 (0.061%), neg=0, invalid=762 iter 0, gcam->neg = 258 after 19 iterations, nbhd size=1, neg = 0 0363: dt=44.800000, rms=0.509 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 79 after 21 iterations, nbhd size=1, neg = 0 0364: dt=25.600000, rms=0.508 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 72 after 21 iterations, nbhd size=1, neg = 0 0365: dt=25.600000, rms=0.508 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 159 after 24 iterations, nbhd size=1, neg = 0 0366: dt=25.600000, rms=0.508 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 239 after 26 iterations, nbhd size=1, neg = 0 0367: dt=25.600000, rms=0.508 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 328 after 25 iterations, nbhd size=1, neg = 0 0368: dt=25.600000, rms=0.508 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 55 after 37 iterations, nbhd size=2, neg = 0 0369: dt=32.000000, rms=0.508 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.508, neg=0, invalid=762 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0370: dt=38.400000, rms=0.506 (0.513%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 15 iterations, nbhd size=1, neg = 0 0371: dt=44.800000, rms=0.503 (0.499%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 14 iterations, nbhd size=1, neg = 0 0372: dt=25.600000, rms=0.503 (0.097%), neg=0, invalid=762 iter 0, gcam->neg = 44 after 16 iterations, nbhd size=1, neg = 0 0373: dt=25.600000, rms=0.502 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 145 after 21 iterations, nbhd size=1, neg = 0 0374: dt=25.600000, rms=0.501 (0.199%), neg=0, invalid=762 iter 0, gcam->neg = 276 after 20 iterations, nbhd size=1, neg = 0 0375: dt=25.600000, rms=0.500 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 310 after 24 iterations, nbhd size=1, neg = 0 0376: dt=25.600000, rms=0.499 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 274 after 26 iterations, nbhd size=1, neg = 0 0377: dt=25.600000, rms=0.499 (0.018%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 15 iterations, nbhd size=1, neg = 0 0378: dt=19.200000, rms=0.499 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0379: dt=25.600000, rms=0.499 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0380: dt=25.600000, rms=0.499 (0.033%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 21 iterations, nbhd size=1, neg = 0 0381: dt=25.600000, rms=0.498 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 79 after 9 iterations, nbhd size=0, neg = 0 0382: dt=25.600000, rms=0.498 (0.056%), neg=0, invalid=762 iter 0, gcam->neg = 77 after 18 iterations, nbhd size=1, neg = 0 0383: dt=25.600000, rms=0.498 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 128 after 15 iterations, nbhd size=1, neg = 0 0384: dt=25.600000, rms=0.498 (0.026%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 iter 0, gcam->neg = 10 after 4 iterations, nbhd size=0, neg = 0 0385: dt=3.456000, rms=0.508 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 0386: dt=3.200000, rms=0.508 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 11 iterations, nbhd size=1, neg = 0 0387: dt=3.200000, rms=0.508 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 iter 0, gcam->neg = 9 after 11 iterations, nbhd size=0, neg = 0 0388: dt=3.456000, rms=0.508 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=0, neg = 0 0389: dt=4.032000, rms=0.508 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 11 iterations, nbhd size=0, neg = 0 0390: dt=4.032000, rms=0.508 (-0.011%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0391: dt=0.448000, rms=0.524 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0392: dt=0.448000, rms=0.524 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0393: dt=0.448000, rms=0.524 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0394: dt=0.448000, rms=0.524 (-0.037%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0395: dt=1.536000, rms=0.523 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=0, neg = 0 0396: dt=1.280000, rms=0.523 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=1, neg = 0 0397: dt=1.280000, rms=0.523 (-0.058%), 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=0.508, neg=0, invalid=762 iter 0, gcam->neg = 1947 after 25 iterations, nbhd size=1, neg = 0 0398: dt=1.577138, rms=0.481 (5.230%), neg=0, invalid=762 0399: dt=0.000013, rms=0.481 (-0.006%), neg=0, invalid=762 0400: dt=0.000013, rms=0.481 (0.000%), neg=0, invalid=762 0401: dt=0.000013, rms=0.481 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=762 0402: dt=0.000000, rms=0.481 (0.105%), neg=0, invalid=762 0403: dt=0.000000, rms=0.481 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0404: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0405: dt=92.480000, rms=0.470 (0.029%), neg=0, invalid=762 0406: dt=92.480000, rms=0.470 (0.006%), neg=0, invalid=762 0407: dt=92.480000, rms=0.470 (0.007%), neg=0, invalid=762 0408: dt=92.480000, rms=0.470 (0.007%), neg=0, invalid=762 0409: dt=92.480000, rms=0.470 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0410: dt=92.480000, rms=0.470 (0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 iter 0, gcam->neg = 17 after 15 iterations, nbhd size=1, neg = 0 0411: dt=15.552000, rms=0.470 (-0.077%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 iter 0, gcam->neg = 42 after 21 iterations, nbhd size=2, neg = 0 0412: dt=145.152000, rms=0.470 (-0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 iter 0, gcam->neg = 527 after 26 iterations, nbhd size=1, neg = 0 0413: dt=34.055046, rms=0.467 (0.604%), neg=0, invalid=762 iter 0, gcam->neg = 484 after 31 iterations, nbhd size=1, neg = 0 0414: dt=44.800000, rms=0.466 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 363 after 30 iterations, nbhd size=1, neg = 0 0415: dt=32.000000, rms=0.466 (0.136%), neg=0, invalid=762 iter 0, gcam->neg = 218 after 29 iterations, nbhd size=1, neg = 0 0416: dt=32.000000, rms=0.466 (-0.148%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 iter 0, gcam->neg = 79 after 23 iterations, nbhd size=1, neg = 0 0417: dt=38.400000, rms=0.463 (0.551%), neg=0, invalid=762 iter 0, gcam->neg = 672 after 32 iterations, nbhd size=1, neg = 0 0418: dt=99.018868, rms=0.462 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 467 after 25 iterations, nbhd size=1, neg = 0 0419: dt=99.018868, rms=0.462 (-2.170%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 iter 0, gcam->neg = 435 after 34 iterations, nbhd size=1, neg = 0 0420: dt=12.169014, rms=0.462 (0.674%), neg=0, invalid=762 iter 0, gcam->neg = 456 after 27 iterations, nbhd size=1, neg = 0 0421: dt=12.300578, rms=0.461 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 435 after 31 iterations, nbhd size=1, neg = 0 0422: dt=12.300578, rms=0.461 (-0.110%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 iter 0, gcam->neg = 248 after 27 iterations, nbhd size=1, neg = 0 0423: dt=12.258065, rms=0.460 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 490 after 26 iterations, nbhd size=1, neg = 0 0424: dt=14.826667, rms=0.458 (0.399%), neg=0, invalid=762 iter 0, gcam->neg = 221 after 32 iterations, nbhd size=1, neg = 0 0425: dt=11.168627, rms=0.458 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 157 after 28 iterations, nbhd size=1, neg = 0 0426: dt=11.168627, rms=0.457 (0.218%), neg=0, invalid=762 iter 0, gcam->neg = 482 after 32 iterations, nbhd size=1, neg = 0 0427: dt=11.168627, rms=0.457 (-0.101%), neg=0, invalid=762 iter 0, gcam->neg = 272 after 28 iterations, nbhd size=1, neg = 0 0428: dt=15.150442, rms=0.457 (-0.138%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0429: dt=0.000060, rms=0.464 (0.000%), neg=0, invalid=762 0430: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0431: dt=0.000000, rms=0.464 (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=0.452, neg=0, invalid=762 iter 0, gcam->neg = 1194 after 22 iterations, nbhd size=1, neg = 0 0432: dt=0.788660, rms=0.444 (1.654%), neg=0, invalid=762 0433: dt=0.080000, rms=0.444 (0.026%), neg=0, invalid=762 0434: dt=0.080000, rms=0.444 (0.016%), neg=0, invalid=762 0435: dt=0.080000, rms=0.444 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 iter 0, gcam->neg = 44 after 5 iterations, nbhd size=0, neg = 0 0436: dt=0.540323, rms=0.442 (0.615%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0437: dt=0.256000, rms=0.441 (0.124%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0438: dt=0.256000, rms=0.440 (0.178%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0439: dt=0.256000, rms=0.439 (0.185%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 4 iterations, nbhd size=0, neg = 0 0440: dt=0.256000, rms=0.439 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 16 iterations, nbhd size=1, neg = 0 0441: dt=0.256000, rms=0.439 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 65 after 13 iterations, nbhd size=1, neg = 0 0442: dt=0.256000, rms=0.439 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 80 after 16 iterations, nbhd size=1, neg = 0 0443: dt=0.256000, rms=0.439 (-0.008%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0444: dt=0.112000, rms=0.439 (0.022%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0445: dt=0.256000, rms=0.438 (0.023%), neg=0, invalid=762 0446: dt=0.112000, rms=0.438 (0.011%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 39 minutes and 48 seconds. mri_ca_register utimesec 5984.752000 mri_ca_register stimesec 3.264000 mri_ca_register ru_maxrss 1336144 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4331047 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 64632 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 9 mri_ca_register ru_nivcsw 3459 FSRUNTIME@ mri_ca_register 1.6634 hours 1 threads #-------------------------------------- #@# SubCort Seg Sat Sep 4 15:54:57 IST 2021 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname research1-HP-280-G3-MT machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/pt019/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.66 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.15271 (21) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8096 voxels, overlap=0.873) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8096 voxels, peak = 20), gca=20.5 gca peak = 0.17677 (13) mri peak = 0.16285 (21) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (10316 voxels, overlap=0.568) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (10316 voxels, peak = 19), gca=18.5 gca peak = 0.28129 (95) mri peak = 0.08833 (109) Right_Pallidum (52): linear fit = 1.13 x + 0.0 (629 voxels, overlap=0.027) Right_Pallidum (52): linear fit = 1.13 x + 0.0 (629 voxels, peak = 108), gca=107.8 gca peak = 0.16930 (96) mri peak = 0.11007 (107) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (665 voxels, overlap=0.062) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (665 voxels, peak = 107), gca=107.0 gca peak = 0.24553 (55) mri peak = 0.07381 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1472 voxels, overlap=0.718) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1472 voxels, peak = 62), gca=62.4 gca peak = 0.30264 (59) mri peak = 0.07265 (66) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (1430 voxels, overlap=0.714) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (1430 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.07424 (91) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (25922 voxels, overlap=0.789) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (25922 voxels, peak = 100), gca=100.4 gca peak = 0.07714 (104) mri peak = 0.07060 (93) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (30503 voxels, overlap=0.817) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (30503 voxels, peak = 100), gca=100.4 gca peak = 0.09712 (58) mri peak = 0.04185 (64) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (29393 voxels, overlap=0.860) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (29393 voxels, peak = 61), gca=60.6 gca peak = 0.11620 (58) mri peak = 0.03936 (66) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (28031 voxels, overlap=0.869) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (28031 voxels, peak = 64), gca=63.5 gca peak = 0.30970 (66) mri peak = 0.06457 (72) Right_Caudate (50): linear fit = 0.94 x + 0.0 (650 voxels, overlap=0.569) Right_Caudate (50): linear fit = 0.94 x + 0.0 (650 voxels, peak = 62), gca=62.4 gca peak = 0.15280 (69) mri peak = 0.07584 (74) Left_Caudate (11): linear fit = 1.00 x + 0.0 (716 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.00 x + 0.0 (716 voxels, peak = 69), gca=69.0 gca peak = 0.13902 (56) mri peak = 0.04932 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (23902 voxels, overlap=0.978) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (23902 voxels, peak = 59), gca=58.5 gca peak = 0.14777 (55) mri peak = 0.05191 (57) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (22931 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (22931 voxels, peak = 57), gca=57.5 gca peak = 0.16765 (84) mri peak = 0.08091 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (8892 voxels, overlap=0.903) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (8892 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.07373 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8029 voxels, overlap=0.968) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8029 voxels, peak = 86), gca=86.1 gca peak = 0.29869 (57) mri peak = 0.09501 (64) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (604 voxels, overlap=0.212) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (604 voxels, peak = 66), gca=66.4 gca peak = 0.33601 (57) mri peak = 0.09813 (67) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (639 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (639 voxels, peak = 69), gca=68.7 gca peak = 0.11131 (90) mri peak = 0.05931 (86) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (3811 voxels, overlap=0.934) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (3811 voxels, peak = 94), gca=94.0 gca peak = 0.11793 (83) mri peak = 0.06970 (87) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (2841 voxels, overlap=0.816) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (2841 voxels, peak = 88), gca=88.4 gca peak = 0.08324 (81) mri peak = 0.08780 (81) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1241 voxels, overlap=0.955) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1241 voxels, peak = 82), gca=82.2 gca peak = 0.10360 (77) mri peak = 0.05742 (76) Right_Putamen (51): linear fit = 1.01 x + 0.0 (915 voxels, overlap=0.944) Right_Putamen (51): linear fit = 1.01 x + 0.0 (915 voxels, peak = 78), gca=78.2 gca peak = 0.08424 (78) mri peak = 0.06908 (88) Brain_Stem (16): linear fit = 1.12 x + 0.0 (11840 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (11840 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.09506 (102) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1154 voxels, overlap=0.016) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (1154 voxels, peak = 105), gca=105.5 gca peak = 0.14500 (87) mri peak = 0.09601 (99) Left_VentralDC (28): linear fit = 1.16 x + 0.0 (1215 voxels, overlap=0.010) Left_VentralDC (28): linear fit = 1.16 x + 0.0 (1215 voxels, peak = 101), gca=101.4 gca peak = 0.14975 (24) mri peak = 0.33797 (24) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (242 voxels, overlap=0.858) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (242 voxels, peak = 23), gca=23.4 gca peak = 0.19357 (14) mri peak = 0.26523 (21) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (279 voxels, overlap=0.316) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (279 voxels, peak = 17), gca=17.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 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 1.13 x + 0.0 estimating mean wm scale to be 0.97 x + 0.0 estimating mean csf scale to be 1.17 x + 0.0 Left_Pallidum too bright - rescaling by 0.910 (from 1.115) to 97.4 (was 107.0) Right_Pallidum too bright - rescaling by 0.903 (from 1.135) to 97.4 (was 107.8) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15136 (21) mri peak = 0.15271 (21) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (8096 voxels, overlap=0.864) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (8096 voxels, peak = 22), gca=22.2 gca peak = 0.13475 (18) mri peak = 0.16285 (21) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (10316 voxels, overlap=0.636) Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (10316 voxels, peak = 20), gca=19.5 gca peak = 0.28924 (98) mri peak = 0.08833 (109) Right_Pallidum (52): linear fit = 1.11 x + 0.0 (629 voxels, overlap=0.144) Right_Pallidum (52): linear fit = 1.11 x + 0.0 (629 voxels, peak = 108), gca=108.3 gca peak = 0.19503 (98) mri peak = 0.11007 (107) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (665 voxels, overlap=0.273) Left_Pallidum (13): linear fit = 1.09 x + 0.0 (665 voxels, peak = 106), gca=106.3 gca peak = 0.26833 (63) mri peak = 0.07381 (64) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1472 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1472 voxels, peak = 63), gca=63.0 gca peak = 0.27807 (64) mri peak = 0.07265 (66) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1430 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1430 voxels, peak = 63), gca=63.0 gca peak = 0.07843 (100) mri peak = 0.07424 (91) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (25922 voxels, overlap=0.869) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (25922 voxels, peak = 100), gca=100.5 gca peak = 0.08176 (101) mri peak = 0.07060 (93) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30503 voxels, overlap=0.868) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30503 voxels, peak = 102), gca=101.5 gca peak = 0.09226 (61) mri peak = 0.04185 (64) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (29393 voxels, overlap=0.950) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (29393 voxels, peak = 63), gca=62.5 gca peak = 0.10594 (64) mri peak = 0.03936 (66) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (28031 voxels, overlap=0.941) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (28031 voxels, peak = 63), gca=63.0 gca peak = 0.27985 (63) mri peak = 0.06457 (72) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, overlap=0.980) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, peak = 63), gca=63.0 gca peak = 0.16114 (69) mri peak = 0.07584 (74) Left_Caudate (11): linear fit = 1.01 x + 0.0 (716 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.01 x + 0.0 (716 voxels, peak = 70), gca=70.0 gca peak = 0.13179 (57) mri peak = 0.04932 (57) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (23902 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (23902 voxels, peak = 58), gca=58.4 gca peak = 0.14493 (57) mri peak = 0.05191 (57) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22931 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22931 voxels, peak = 56), gca=56.1 gca peak = 0.15817 (86) mri peak = 0.08091 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8892 voxels, overlap=0.961) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8892 voxels, peak = 86), gca=85.6 gca peak = 0.15606 (86) mri peak = 0.07373 (84) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8029 voxels, overlap=0.987) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8029 voxels, peak = 85), gca=84.7 gca peak = 0.26343 (66) mri peak = 0.09501 (64) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (604 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (604 voxels, peak = 64), gca=63.7 gca peak = 0.27482 (69) mri peak = 0.09813 (67) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (639 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (639 voxels, peak = 69), gca=69.0 gca peak = 0.10964 (94) mri peak = 0.05931 (86) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3811 voxels, overlap=0.965) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3811 voxels, peak = 93), gca=92.6 gca peak = 0.10500 (86) mri peak = 0.06970 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2841 voxels, overlap=0.941) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2841 voxels, peak = 86), gca=85.6 gca peak = 0.08952 (82) mri peak = 0.08780 (81) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1241 voxels, overlap=0.983) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1241 voxels, peak = 82), gca=82.0 gca peak = 0.08217 (78) mri peak = 0.05742 (76) Right_Putamen (51): linear fit = 0.99 x + 0.0 (915 voxels, overlap=0.980) Right_Putamen (51): linear fit = 0.99 x + 0.0 (915 voxels, peak = 77), gca=76.8 gca peak = 0.07750 (88) mri peak = 0.06908 (88) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11840 voxels, overlap=0.858) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11840 voxels, peak = 87), gca=86.7 gca peak = 0.13845 (104) mri peak = 0.09506 (102) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1154 voxels, overlap=0.764) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1154 voxels, peak = 105), gca=104.5 gca peak = 0.13104 (99) mri peak = 0.09601 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1215 voxels, overlap=0.858) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1215 voxels, peak = 99), gca=99.5 gca peak = 0.20075 (25) mri peak = 0.33797 (24) Third_Ventricle (14): linear fit = 0.92 x + 0.0 (242 voxels, overlap=0.795) Third_Ventricle (14): linear fit = 0.92 x + 0.0 (242 voxels, peak = 23), gca=22.9 gca peak = 0.16542 (20) mri peak = 0.26523 (21) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (279 voxels, overlap=0.762) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (279 voxels, peak = 20), gca=19.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15127 (30) gca peak Left_Thalamus = 0.36646 (98) gca peak CSF = 0.19259 (42) gca peak Left_Accumbens_area = 0.70439 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (26) gca peak Right_Accumbens_area = 0.32721 (62) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.15396 (37) gca peak Fifth_Ventricle = 0.65271 (37) gca peak WM_hypointensities = 0.08365 (74) gca peak non_WM_hypointensities = 0.09744 (42) gca peak Optic_Chiasm = 0.50521 (76) 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 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 0.921 (from 1.085) to 98.0 (was 106.3) Right_Pallidum too bright - rescaling by 0.905 (from 1.105) to 98.0 (was 108.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 85368 voxels changed in iteration 0 of unlikely voxel relabeling 283 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 56479 gm and wm labels changed (%38 to gray, %62 to white out of all changed labels) 460 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 88282 changed. image ll: -2.162, PF=0.500 pass 2: 25103 changed. image ll: -2.161, PF=0.500 pass 3: 8407 changed. pass 4: 3253 changed. 62872 voxels changed in iteration 0 of unlikely voxel relabeling 460 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9738 voxels changed in iteration 0 of unlikely voxel relabeling 220 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8726 voxels changed in iteration 0 of unlikely voxel relabeling 78 voxels changed in iteration 1 of unlikely voxel relabeling 22 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7260 voxels changed in iteration 0 of unlikely voxel relabeling 46 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 6 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2153.084000 mri_ca_label stimesec 0.752000 mri_ca_label ru_maxrss 2095032 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1016799 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 496 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 9 mri_ca_label ru_nivcsw 711 auto-labeling took 35 minutes and 54 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/pt019/mri/transforms/cc_up.lta pt019 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/pt019/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/pt019/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/pt019/mri/norm.mgz 19564 voxels in left wm, 43507 in right wm, xrange [122, 132] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 global minimum found at slice 128.0, rotations (-0.97, -0.35) final transformation (x=128.0, yr=-0.971, zr=-0.355): 0.99984 0.00619 -0.01695 0.69930; -0.00619 0.99998 0.00010 13.78573; 0.01695 0.00000 0.99986 43.84163; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 115 82 eigenvectors: 0.00214 0.00454 0.99999; -0.17304 -0.98490 0.00484; 0.98491 -0.17305 -0.00132; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/subjects/pt019/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Sat Sep 4 16:31:21 IST 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Sep 4 16:31:21 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 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... 4069 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 96 gm peak at 72 (72), valley at 37 (37) csf peak at 21, setting threshold to 55 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 90 gm peak at 70 (70), valley at 35 (35) csf peak at 21, 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 3 seconds. #-------------------------------------------- #@# Mask BFS Sat Sep 4 16:33:25 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1547353 voxels in mask (pct= 9.22) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Sep 4 16:33:26 IST 2021 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.2 +- 5.7 [79.0 --> 125.0] GM (72.0) : 69.6 +- 10.3 [30.0 --> 95.0] setting bottom of white matter range to 79.9 setting top of gray matter range to 90.2 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... 4858 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4621 filled 1361 bright non-wm voxels segmented. 3876 diagonally connected voxels added... white matter segmentation took 1.2 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 preserving editing changes in input volume... auto filling took 0.37 minutes reading wm segmentation from wm.seg.mgz... 433 voxels added to wm to prevent paths from MTL structures to cortex 19318 additional wm voxels added 0 additional wm voxels added SEG EDIT: 130205 voxels turned on, 48383 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 98 new 98 115,126,128 old 98 new 98 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 134 found - 134 modified | TOTAL: 134 pass 2 (xy+): 0 found - 134 modified | TOTAL: 134 pass 1 (xy-): 135 found - 135 modified | TOTAL: 269 pass 2 (xy-): 0 found - 135 modified | TOTAL: 269 pass 1 (yz+): 99 found - 99 modified | TOTAL: 368 pass 2 (yz+): 0 found - 99 modified | TOTAL: 368 pass 1 (yz-): 124 found - 124 modified | TOTAL: 492 pass 2 (yz-): 0 found - 124 modified | TOTAL: 492 pass 1 (xz+): 109 found - 109 modified | TOTAL: 601 pass 2 (xz+): 0 found - 109 modified | TOTAL: 601 pass 1 (xz-): 87 found - 87 modified | TOTAL: 688 pass 2 (xz-): 0 found - 87 modified | TOTAL: 688 Iteration Number : 1 pass 1 (+++): 52 found - 52 modified | TOTAL: 52 pass 2 (+++): 0 found - 52 modified | TOTAL: 52 pass 1 (+++): 55 found - 55 modified | TOTAL: 107 pass 2 (+++): 0 found - 55 modified | TOTAL: 107 pass 1 (+++): 34 found - 34 modified | TOTAL: 141 pass 2 (+++): 0 found - 34 modified | TOTAL: 141 pass 1 (+++): 35 found - 35 modified | TOTAL: 176 pass 2 (+++): 0 found - 35 modified | TOTAL: 176 Iteration Number : 1 pass 1 (++): 155 found - 155 modified | TOTAL: 155 pass 2 (++): 0 found - 155 modified | TOTAL: 155 pass 1 (+-): 186 found - 186 modified | TOTAL: 341 pass 2 (+-): 0 found - 186 modified | TOTAL: 341 pass 1 (--): 167 found - 167 modified | TOTAL: 508 pass 2 (--): 0 found - 167 modified | TOTAL: 508 pass 1 (-+): 174 found - 174 modified | TOTAL: 682 pass 2 (-+): 0 found - 174 modified | TOTAL: 682 Iteration Number : 2 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 9 found - 9 modified | TOTAL: 24 pass 2 (xy-): 0 found - 9 modified | TOTAL: 24 pass 1 (yz+): 13 found - 13 modified | TOTAL: 37 pass 2 (yz+): 0 found - 13 modified | TOTAL: 37 pass 1 (yz-): 21 found - 21 modified | TOTAL: 58 pass 2 (yz-): 0 found - 21 modified | TOTAL: 58 pass 1 (xz+): 15 found - 15 modified | TOTAL: 73 pass 2 (xz+): 0 found - 15 modified | TOTAL: 73 pass 1 (xz-): 5 found - 5 modified | TOTAL: 78 pass 2 (xz-): 0 found - 5 modified | TOTAL: 78 Iteration Number : 2 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 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 8 found - 8 modified | TOTAL: 10 pass 2 (+-): 0 found - 8 modified | TOTAL: 10 pass 1 (--): 11 found - 11 modified | TOTAL: 21 pass 2 (--): 0 found - 11 modified | TOTAL: 21 pass 1 (-+): 5 found - 5 modified | TOTAL: 26 pass 2 (-+): 0 found - 5 modified | TOTAL: 26 Iteration Number : 3 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+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 3 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 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 3 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 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 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 : 4 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 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 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 : 5 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 : 5 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 = 1670 (out of 506641: 0.329622) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Sep 4 16:35:01 IST 2021 /usr/local/freesurfer/subjects/pt019/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.97785 -0.03220 0.00761 3.13100; 0.02451 1.13144 0.31197 -52.25793; -0.01504 -0.33113 0.99356 39.36189; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.97785 -0.03220 0.00761 3.13100; 0.02451 1.13144 0.31197 -52.25793; -0.01504 -0.33113 0.99356 39.36189; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 999 (min = 350, max = 1400), aspect = 0.41 (min = 0.10, max = 0.75) no need to search using seed (127, 104, 108), TAL = (1.0, -20.0, 24.0) talairach voxel to voxel transform 1.02180 0.02453 -0.01553 -1.30586; -0.02418 0.80887 -0.25379 52.33518; 0.00740 0.26995 0.92166 -22.19479; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 104, 108) --> (1.0, -20.0, 24.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (1.00, -20.00, 24.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -20.00, 24.00) SRC: (110.94, 106.41, 106.23) search lh wm seed point around talairach space (-17.00, -20.00, 24.00), SRC: (147.73, 105.54, 106.49) 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 Sat Sep 4 16:35:26 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 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-): 3 found - 3 modified | TOTAL: 9 pass 2 (yz-): 0 found - 3 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 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 (+-): 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 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-): 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 : 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 Total Number of Modified Voxels = 10 (out of 245753: 0.004069) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 456 vertices, 529 faces slice 50: 6234 vertices, 6538 faces slice 60: 16258 vertices, 16639 faces slice 70: 28966 vertices, 29398 faces slice 80: 40825 vertices, 41302 faces slice 90: 53119 vertices, 53586 faces slice 100: 66566 vertices, 67070 faces slice 110: 79437 vertices, 79942 faces slice 120: 91895 vertices, 92453 faces slice 130: 104179 vertices, 104797 faces slice 140: 116296 vertices, 116923 faces slice 150: 126083 vertices, 126663 faces slice 160: 134990 vertices, 135577 faces slice 170: 142194 vertices, 142736 faces slice 180: 147999 vertices, 148500 faces slice 190: 151655 vertices, 152124 faces slice 200: 152314 vertices, 152678 faces slice 210: 152314 vertices, 152678 faces slice 220: 152314 vertices, 152678 faces slice 230: 152314 vertices, 152678 faces slice 240: 152314 vertices, 152678 faces slice 250: 152314 vertices, 152678 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... 152314 voxel in cpt #1: X=-364 [v=152314,e=458034,f=305356] located at (-29.380615, -19.806131, 16.930250) For the whole surface: X=-364 [v=152314,e=458034,f=305356] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Sep 4 16:35:30 IST 2021 /usr/local/freesurfer/subjects/pt019/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-): 5 found - 5 modified | TOTAL: 5 pass 2 (xy-): 0 found - 5 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 0 found - 0 modified | TOTAL: 8 pass 1 (xz-): 0 found - 0 modified | TOTAL: 8 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 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-): 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 : 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 Total Number of Modified Voxels = 10 (out of 242317: 0.004127) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 82 vertices, 106 faces slice 50: 3692 vertices, 3874 faces slice 60: 11913 vertices, 12290 faces slice 70: 23789 vertices, 24206 faces slice 80: 36382 vertices, 36799 faces slice 90: 48573 vertices, 48965 faces slice 100: 61042 vertices, 61535 faces slice 110: 73579 vertices, 74061 faces slice 120: 86380 vertices, 86920 faces slice 130: 99392 vertices, 99981 faces slice 140: 112806 vertices, 113407 faces slice 150: 123572 vertices, 124113 faces slice 160: 133226 vertices, 133762 faces slice 170: 141778 vertices, 142293 faces slice 180: 148010 vertices, 148507 faces slice 190: 152107 vertices, 152507 faces slice 200: 152766 vertices, 153092 faces slice 210: 152766 vertices, 153092 faces slice 220: 152766 vertices, 153092 faces slice 230: 152766 vertices, 153092 faces slice 240: 152766 vertices, 153092 faces slice 250: 152766 vertices, 153092 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... 152766 voxel in cpt #1: X=-326 [v=152766,e=459276,f=306184] located at (28.948366, -16.246868, 16.326729) For the whole surface: X=-326 [v=152766,e=459276,f=306184] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Sep 4 16:35:34 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Sat Sep 4 16:35:37 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Sat Sep 4 16:35:41 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.0 mm, total surface area = 78462 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.177 (target=0.015) step 005: RMS=0.138 (target=0.015) step 010: RMS=0.114 (target=0.015) step 015: RMS=0.104 (target=0.015) step 020: RMS=0.097 (target=0.015) step 025: RMS=0.091 (target=0.015) step 030: RMS=0.089 (target=0.015) step 035: RMS=0.087 (target=0.015) step 040: RMS=0.085 (target=0.015) step 045: RMS=0.084 (target=0.015) step 050: RMS=0.083 (target=0.015) step 055: RMS=0.082 (target=0.015) step 060: RMS=0.082 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 24.088000 mris_inflate stimesec 0.044000 mris_inflate ru_maxrss 200284 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 48564 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 10736 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 18 #-------------------------------------------- #@# Inflation1 rh Sat Sep 4 16:36:05 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.4 mm, total surface area = 78432 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.176 (target=0.015) step 005: RMS=0.137 (target=0.015) step 010: RMS=0.112 (target=0.015) step 015: RMS=0.104 (target=0.015) step 020: RMS=0.097 (target=0.015) step 025: RMS=0.091 (target=0.015) step 030: RMS=0.087 (target=0.015) step 035: RMS=0.086 (target=0.015) step 040: RMS=0.084 (target=0.015) step 045: RMS=0.083 (target=0.015) step 050: RMS=0.083 (target=0.015) step 055: RMS=0.083 (target=0.015) step 060: RMS=0.083 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 24.156000 mris_inflate stimesec 0.056000 mris_inflate ru_maxrss 201236 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 48766 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10760 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 42 #-------------------------------------------- #@# QSphere lh Sat Sep 4 16:36:29 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.70 (0.00-->13.51) (max @ vno 72234 --> 73557) face area 0.03 +- 0.05 (-0.62-->1.02) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.330... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.573, avgs=0 005/300: dt: 0.9000, rms radial error=176.315, avgs=0 010/300: dt: 0.9000, rms radial error=175.762, avgs=0 015/300: dt: 0.9000, rms radial error=175.036, avgs=0 020/300: dt: 0.9000, rms radial error=174.208, avgs=0 025/300: dt: 0.9000, rms radial error=173.323, avgs=0 030/300: dt: 0.9000, rms radial error=172.405, avgs=0 035/300: dt: 0.9000, rms radial error=171.474, avgs=0 040/300: dt: 0.9000, rms radial error=170.535, avgs=0 045/300: dt: 0.9000, rms radial error=169.594, avgs=0 050/300: dt: 0.9000, rms radial error=168.654, avgs=0 055/300: dt: 0.9000, rms radial error=167.717, avgs=0 060/300: dt: 0.9000, rms radial error=166.783, avgs=0 065/300: dt: 0.9000, rms radial error=165.853, avgs=0 070/300: dt: 0.9000, rms radial error=164.928, avgs=0 075/300: dt: 0.9000, rms radial error=164.007, avgs=0 080/300: dt: 0.9000, rms radial error=163.092, avgs=0 085/300: dt: 0.9000, rms radial error=162.182, avgs=0 090/300: dt: 0.9000, rms radial error=161.277, avgs=0 095/300: dt: 0.9000, rms radial error=160.377, avgs=0 100/300: dt: 0.9000, rms radial error=159.482, avgs=0 105/300: dt: 0.9000, rms radial error=158.592, avgs=0 110/300: dt: 0.9000, rms radial error=157.707, avgs=0 115/300: dt: 0.9000, rms radial error=156.827, avgs=0 120/300: dt: 0.9000, rms radial error=155.952, avgs=0 125/300: dt: 0.9000, rms radial error=155.082, avgs=0 130/300: dt: 0.9000, rms radial error=154.216, avgs=0 135/300: dt: 0.9000, rms radial error=153.356, avgs=0 140/300: dt: 0.9000, rms radial error=152.500, avgs=0 145/300: dt: 0.9000, rms radial error=151.649, avgs=0 150/300: dt: 0.9000, rms radial error=150.803, avgs=0 155/300: dt: 0.9000, rms radial error=149.963, avgs=0 160/300: dt: 0.9000, rms radial error=149.127, avgs=0 165/300: dt: 0.9000, rms radial error=148.296, avgs=0 170/300: dt: 0.9000, rms radial error=147.470, avgs=0 175/300: dt: 0.9000, rms radial error=146.648, avgs=0 180/300: dt: 0.9000, rms radial error=145.831, avgs=0 185/300: dt: 0.9000, rms radial error=145.019, avgs=0 190/300: dt: 0.9000, rms radial error=144.211, avgs=0 195/300: dt: 0.9000, rms radial error=143.408, avgs=0 200/300: dt: 0.9000, rms radial error=142.608, avgs=0 205/300: dt: 0.9000, rms radial error=141.814, avgs=0 210/300: dt: 0.9000, rms radial error=141.024, avgs=0 215/300: dt: 0.9000, rms radial error=140.238, avgs=0 220/300: dt: 0.9000, rms radial error=139.456, avgs=0 225/300: dt: 0.9000, rms radial error=138.679, avgs=0 230/300: dt: 0.9000, rms radial error=137.906, avgs=0 235/300: dt: 0.9000, rms radial error=137.137, avgs=0 240/300: dt: 0.9000, rms radial error=136.373, avgs=0 245/300: dt: 0.9000, rms radial error=135.613, avgs=0 250/300: dt: 0.9000, rms radial error=134.857, avgs=0 255/300: dt: 0.9000, rms radial error=134.105, avgs=0 260/300: dt: 0.9000, rms radial error=133.358, avgs=0 265/300: dt: 0.9000, rms radial error=132.614, avgs=0 270/300: dt: 0.9000, rms radial error=131.875, avgs=0 275/300: dt: 0.9000, rms radial error=131.140, avgs=0 280/300: dt: 0.9000, rms radial error=130.409, avgs=0 285/300: dt: 0.9000, rms radial error=129.683, avgs=0 290/300: dt: 0.9000, rms radial error=128.960, avgs=0 295/300: dt: 0.9000, rms radial error=128.242, avgs=0 300/300: dt: 0.9000, rms radial error=127.527, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17898.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00033 epoch 2 (K=40.0), pass 1, starting sse = 3335.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00190 epoch 3 (K=160.0), pass 1, starting sse = 612.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/11 = 0.01093 epoch 4 (K=640.0), pass 1, starting sse = 201.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/17 = 0.01465 final distance error %32.79 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 163.376000 mris_sphere stimesec 0.068000 mris_sphere ru_maxrss 201124 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 48577 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 10736 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 83 FSRUNTIME@ mris_sphere 0.0454 hours 1 threads #-------------------------------------------- #@# QSphere rh Sat Sep 4 16:39:13 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.04 +- 0.70 (0.00-->12.80) (max @ vno 80474 --> 80475) face area 0.03 +- 0.05 (-0.59-->0.86) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.338... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.378, avgs=0 005/300: dt: 0.9000, rms radial error=176.121, avgs=0 010/300: dt: 0.9000, rms radial error=175.568, avgs=0 015/300: dt: 0.9000, rms radial error=174.842, avgs=0 020/300: dt: 0.9000, rms radial error=174.016, avgs=0 025/300: dt: 0.9000, rms radial error=173.131, avgs=0 030/300: dt: 0.9000, rms radial error=172.220, avgs=0 035/300: dt: 0.9000, rms radial error=171.294, avgs=0 040/300: dt: 0.9000, rms radial error=170.360, avgs=0 045/300: dt: 0.9000, rms radial error=169.423, avgs=0 050/300: dt: 0.9000, rms radial error=168.486, avgs=0 055/300: dt: 0.9000, rms radial error=167.553, avgs=0 060/300: dt: 0.9000, rms radial error=166.623, avgs=0 065/300: dt: 0.9000, rms radial error=165.698, avgs=0 070/300: dt: 0.9000, rms radial error=164.777, avgs=0 075/300: dt: 0.9000, rms radial error=163.861, avgs=0 080/300: dt: 0.9000, rms radial error=162.951, avgs=0 085/300: dt: 0.9000, rms radial error=162.045, avgs=0 090/300: dt: 0.9000, rms radial error=161.144, avgs=0 095/300: dt: 0.9000, rms radial error=160.248, avgs=0 100/300: dt: 0.9000, rms radial error=159.357, avgs=0 105/300: dt: 0.9000, rms radial error=158.471, avgs=0 110/300: dt: 0.9000, rms radial error=157.590, avgs=0 115/300: dt: 0.9000, rms radial error=156.713, avgs=0 120/300: dt: 0.9000, rms radial error=155.842, avgs=0 125/300: dt: 0.9000, rms radial error=154.975, avgs=0 130/300: dt: 0.9000, rms radial error=154.113, avgs=0 135/300: dt: 0.9000, rms radial error=153.256, avgs=0 140/300: dt: 0.9000, rms radial error=152.403, avgs=0 145/300: dt: 0.9000, rms radial error=151.556, avgs=0 150/300: dt: 0.9000, rms radial error=150.713, avgs=0 155/300: dt: 0.9000, rms radial error=149.875, avgs=0 160/300: dt: 0.9000, rms radial error=149.041, avgs=0 165/300: dt: 0.9000, rms radial error=148.212, avgs=0 170/300: dt: 0.9000, rms radial error=147.388, avgs=0 175/300: dt: 0.9000, rms radial error=146.568, avgs=0 180/300: dt: 0.9000, rms radial error=145.753, avgs=0 185/300: dt: 0.9000, rms radial error=144.942, avgs=0 190/300: dt: 0.9000, rms radial error=144.135, avgs=0 195/300: dt: 0.9000, rms radial error=143.333, avgs=0 200/300: dt: 0.9000, rms radial error=142.536, avgs=0 205/300: dt: 0.9000, rms radial error=141.742, avgs=0 210/300: dt: 0.9000, rms radial error=140.954, avgs=0 215/300: dt: 0.9000, rms radial error=140.169, avgs=0 220/300: dt: 0.9000, rms radial error=139.390, avgs=0 225/300: dt: 0.9000, rms radial error=138.614, avgs=0 230/300: dt: 0.9000, rms radial error=137.842, avgs=0 235/300: dt: 0.9000, rms radial error=137.075, avgs=0 240/300: dt: 0.9000, rms radial error=136.312, avgs=0 245/300: dt: 0.9000, rms radial error=135.554, avgs=0 250/300: dt: 0.9000, rms radial error=134.799, avgs=0 255/300: dt: 0.9000, rms radial error=134.049, avgs=0 260/300: dt: 0.9000, rms radial error=133.303, avgs=0 265/300: dt: 0.9000, rms radial error=132.561, avgs=0 270/300: dt: 0.9000, rms radial error=131.824, avgs=0 275/300: dt: 0.9000, rms radial error=131.090, avgs=0 280/300: dt: 0.9000, rms radial error=130.360, avgs=0 285/300: dt: 0.9000, rms radial error=129.635, avgs=0 290/300: dt: 0.9000, rms radial error=128.914, avgs=0 295/300: dt: 0.9000, rms radial error=128.197, avgs=0 300/300: dt: 0.9000, rms radial error=127.483, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17862.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00048 epoch 2 (K=40.0), pass 1, starting sse = 3311.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00203 epoch 3 (K=160.0), pass 1, starting sse = 617.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/11 = 0.01050 epoch 4 (K=640.0), pass 1, starting sse = 209.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/18 = 0.01405 final distance error %33.29 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 166.492000 mris_sphere stimesec 0.072000 mris_sphere ru_maxrss 201604 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 48774 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10768 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 51 FSRUNTIME@ mris_sphere 0.0463 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sat Sep 4 16:41:59 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Sep 4 16:41:59 IST 2021 /usr/local/freesurfer/subjects/pt019/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Sep 4 16:41:59 IST 2021 mris_fix_topology -rusage /usr/local/freesurfer/subjects/pt019/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 pt019 lh 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-364 (nv=152314, nf=305356, ne=458034, g=183) 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 10 iterations marking ambiguous vertices... 68798 ambiguous faces found in tessellation segmenting defects... 72 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 1 -merging segment 23 into 1 -merging segment 36 into 1 -merging segment 63 into 1 -merging segment 29 into 1 -merging segment 67 into 1 -merging segment 14 into 10 -merging segment 22 into 19 -merging segment 24 into 19 -merging segment 41 into 33 -merging segment 35 into 34 -merging segment 40 into 34 -merging segment 44 into 38 -merging segment 46 into 43 -merging segment 1 into 47 57 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/pt019/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3749 (-4.6874) -vertex loglikelihood: -6.3564 (-3.1782) -normal dot loglikelihood: -3.5778 (-3.5778) -quad curv loglikelihood: -6.0004 (-3.0002) Total Loglikelihood : -25.3095 CORRECTING DEFECT 0 (vertices=17, convex hull=44, v0=3885) After retessellation of defect 0 (v0=3885), euler #=-28 (114388,335592,221176) : difference with theory (-54) = -26 CORRECTING DEFECT 1 (vertices=33, convex hull=92, v0=15291) After retessellation of defect 1 (v0=15291), euler #=-27 (114410,335694,221257) : difference with theory (-53) = -26 CORRECTING DEFECT 2 (vertices=40, convex hull=81, v0=25480) After retessellation of defect 2 (v0=25480), euler #=-26 (114424,335768,221318) : difference with theory (-52) = -26 CORRECTING DEFECT 3 (vertices=17, convex hull=54, v0=28289) After retessellation of defect 3 (v0=28289), euler #=-25 (114434,335818,221359) : difference with theory (-51) = -26 CORRECTING DEFECT 4 (vertices=41, convex hull=69, v0=31044) After retessellation of defect 4 (v0=31044), euler #=-24 (114454,335905,221427) : difference with theory (-50) = -26 CORRECTING DEFECT 5 (vertices=58, convex hull=92, v0=36737) After retessellation of defect 5 (v0=36737), euler #=-23 (114489,336049,221537) : difference with theory (-49) = -26 CORRECTING DEFECT 6 (vertices=12, convex hull=20, v0=37003) After retessellation of defect 6 (v0=37003), euler #=-22 (114489,336060,221549) : difference with theory (-48) = -26 CORRECTING DEFECT 7 (vertices=34, convex hull=22, v0=49041) After retessellation of defect 7 (v0=49041), euler #=-21 (114496,336086,221569) : difference with theory (-47) = -26 CORRECTING DEFECT 8 (vertices=3114, convex hull=1428, v0=52843) XL defect detected... After retessellation of defect 8 (v0=52843), euler #=-20 (114908,338055,223127) : difference with theory (-46) = -26 CORRECTING DEFECT 9 (vertices=14, convex hull=23, v0=57745) After retessellation of defect 9 (v0=57745), euler #=-19 (114909,338063,223135) : difference with theory (-45) = -26 CORRECTING DEFECT 10 (vertices=37, convex hull=30, v0=59069) After retessellation of defect 10 (v0=59069), euler #=-18 (114914,338087,223155) : difference with theory (-44) = -26 CORRECTING DEFECT 11 (vertices=8, convex hull=33, v0=59436) After retessellation of defect 11 (v0=59436), euler #=-17 (114919,338113,223177) : difference with theory (-43) = -26 CORRECTING DEFECT 12 (vertices=43, convex hull=53, v0=69632) After retessellation of defect 12 (v0=69632), euler #=-16 (114937,338189,223236) : difference with theory (-42) = -26 CORRECTING DEFECT 13 (vertices=7, convex hull=11, v0=73942) After retessellation of defect 13 (v0=73942), euler #=-15 (114937,338190,223238) : difference with theory (-41) = -26 CORRECTING DEFECT 14 (vertices=92, convex hull=86, v0=76825) After retessellation of defect 14 (v0=76825), euler #=-14 (114963,338307,223330) : difference with theory (-40) = -26 CORRECTING DEFECT 15 (vertices=55, convex hull=68, v0=85556) After retessellation of defect 15 (v0=85556), euler #=-13 (114999,338442,223430) : difference with theory (-39) = -26 CORRECTING DEFECT 16 (vertices=407, convex hull=263, v0=87979) After retessellation of defect 16 (v0=87979), euler #=-10 (115098,338875,223767) : difference with theory (-38) = -28 CORRECTING DEFECT 17 (vertices=20, convex hull=61, v0=88408) After retessellation of defect 17 (v0=88408), euler #=-9 (115108,338930,223813) : difference with theory (-37) = -28 CORRECTING DEFECT 18 (vertices=26, convex hull=59, v0=90255) After retessellation of defect 18 (v0=90255), euler #=-8 (115124,339000,223868) : difference with theory (-36) = -28 CORRECTING DEFECT 19 (vertices=15, convex hull=26, v0=96202) After retessellation of defect 19 (v0=96202), euler #=-7 (115125,339012,223880) : difference with theory (-35) = -28 CORRECTING DEFECT 20 (vertices=6, convex hull=19, v0=96738) After retessellation of defect 20 (v0=96738), euler #=-6 (115126,339022,223890) : difference with theory (-34) = -28 CORRECTING DEFECT 21 (vertices=63, convex hull=106, v0=96757) After retessellation of defect 21 (v0=96757), euler #=-5 (115167,339190,224018) : difference with theory (-33) = -28 CORRECTING DEFECT 22 (vertices=33, convex hull=68, v0=96900) After retessellation of defect 22 (v0=96900), euler #=-4 (115187,339275,224084) : difference with theory (-32) = -28 CORRECTING DEFECT 23 (vertices=53, convex hull=54, v0=97751) After retessellation of defect 23 (v0=97751), euler #=-3 (115202,339343,224138) : difference with theory (-31) = -28 CORRECTING DEFECT 24 (vertices=96, convex hull=118, v0=99151) After retessellation of defect 24 (v0=99151), euler #=-2 (115264,339592,224326) : difference with theory (-30) = -28 CORRECTING DEFECT 25 (vertices=96, convex hull=135, v0=99862) After retessellation of defect 25 (v0=99862), euler #=-1 (115330,339852,224521) : difference with theory (-29) = -28 CORRECTING DEFECT 26 (vertices=441, convex hull=301, v0=100171) After retessellation of defect 26 (v0=100171), euler #=1 (115541,340641,225101) : difference with theory (-28) = -29 CORRECTING DEFECT 27 (vertices=684, convex hull=292, v0=101263) After retessellation of defect 27 (v0=101263), euler #=4 (115603,340967,225368) : difference with theory (-27) = -31 CORRECTING DEFECT 28 (vertices=32, convex hull=24, v0=106448) After retessellation of defect 28 (v0=106448), euler #=5 (115606,340985,225384) : difference with theory (-26) = -31 CORRECTING DEFECT 29 (vertices=278, convex hull=182, v0=109060) After retessellation of defect 29 (v0=109060), euler #=6 (115705,341377,225678) : difference with theory (-25) = -31 CORRECTING DEFECT 30 (vertices=330, convex hull=69, v0=112524) After retessellation of defect 30 (v0=112524), euler #=7 (115720,341454,225741) : difference with theory (-24) = -31 CORRECTING DEFECT 31 (vertices=22, convex hull=21, v0=112884) After retessellation of defect 31 (v0=112884), euler #=8 (115723,341474,225759) : difference with theory (-23) = -31 CORRECTING DEFECT 32 (vertices=495, convex hull=426, v0=113934) L defect detected... After retessellation of defect 32 (v0=113934), euler #=10 (115928,342303,226385) : difference with theory (-22) = -32 CORRECTING DEFECT 33 (vertices=630, convex hull=250, v0=117205) After retessellation of defect 33 (v0=117205), euler #=11 (116092,342921,226840) : difference with theory (-21) = -32 CORRECTING DEFECT 34 (vertices=29039, convex hull=8209, v0=118726) normal vector of length zero at vertex 121849 with 0 faces vertex 121849 has 0 face XL defect detected... Numerical result out of range Linux research1-HP-280-G3-MT 4.4.0-210-generic #242-Ubuntu SMP Fri Apr 16 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s pt019 exited with ERRORS at Sun Sep 5 14:41:39 IST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting