Thu Aug 5 00:29:48 CST 2021 /media/sf_T1/recon/demo3 /home/BAW/freesurfer/bin/recon-all -s demo3 -i ./T1dcm2nii/demo3/T1.nii.gz -all -qcache subjid demo3 setenv SUBJECTS_DIR /media/sf_T1/recon FREESURFER_HOME /home/BAW/freesurfer Actual FREESURFER_HOME /home/BAW/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 4509200 971840 3537360 4284 80240 511356 -/+ buffers/cache: 380244 4128956 Swap: 8191996 0 8191996 ######################################## 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: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 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: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 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: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 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: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 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: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/08/04-16:29:48-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: bat Machine: bogon Platform: Linux PlatformVersion: 2.6.32-754.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/BAW/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 /home/BAW/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /media/sf_T1/recon/demo3 mri_convert /media/sf_T1/T1dcm2nii/demo3/T1.nii.gz /media/sf_T1/recon/demo3/mri/orig/001.mgz mri_convert.bin /media/sf_T1/T1dcm2nii/demo3/T1.nii.gz /media/sf_T1/recon/demo3/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_T1/T1dcm2nii/demo3/T1.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998549, -0.0234243, -0.0484875) j_ras = (0.016933, 0.991343, -0.1302) k_ras = (0.0511176, 0.12919, 0.990301) writing to /media/sf_T1/recon/demo3/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Aug 5 00:29:54 CST 2021 Found 1 runs /media/sf_T1/recon/demo3/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 /media/sf_T1/recon/demo3/mri/orig/001.mgz /media/sf_T1/recon/demo3/mri/rawavg.mgz /media/sf_T1/recon/demo3 mri_convert /media/sf_T1/recon/demo3/mri/rawavg.mgz /media/sf_T1/recon/demo3/mri/orig.mgz --conform mri_convert.bin /media/sf_T1/recon/demo3/mri/rawavg.mgz /media/sf_T1/recon/demo3/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_T1/recon/demo3/mri/rawavg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998549, -0.0234243, -0.0484875) j_ras = (0.016933, 0.991343, -0.1302) k_ras = (0.0511176, 0.12919, 0.990301) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_T1/recon/demo3/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_T1/recon/demo3/mri/transforms/talairach.xfm /media/sf_T1/recon/demo3/mri/orig.mgz /media/sf_T1/recon/demo3/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Aug 5 00:30:02 CST 2021 /media/sf_T1/recon/demo3/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /media/sf_T1/recon/demo3/mri /home/BAW/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 bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Aug 5 00:30:02 CST 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.4412 /media/sf_T1/recon/demo3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4412/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4412/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (-7.45058e-09, 0, -1) k_ras = (-1.39698e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4412/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 5 00:30:04 CST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.4412/nu0.mnc ./tmp.mri_nu_correct.mni.4412/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4412/0/ -iterations 1000 -distance 50 [bat@bogon:/media/sf_T1/recon/demo3/mri/] [2021-08-05 00:30:04] running: /home/BAW/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.4412/0/ ./tmp.mri_nu_correct.mni.4412/nu0.mnc ./tmp.mri_nu_correct.mni.4412/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 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00099105 mri_convert ./tmp.mri_nu_correct.mni.4412/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4412/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.4412/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (-7.45058e-09, 0, -1) k_ras = (-1.39698e-09, 1, 0) 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... Thu Aug 5 00:30:51 CST 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 Thu Aug 5 00:30:51 CST 2021 Ended at Thu Aug 5 00:31:09 CST 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Aug 5 00:31:11 CST 2021 /media/sf_T1/recon/demo3/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7296, pval=0.6675 >= threshold=0.0050) awk -f /home/BAW/freesurfer/bin/extract_talairach_avi_QA.awk /media/sf_T1/recon/demo3/mri/transforms/talairach_avi.log tal_QC_AZS /media/sf_T1/recon/demo3/mri/transforms/talairach_avi.log TalAviQA: 0.97653 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 5 00:31:11 CST 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /media/sf_T1/recon/demo3/mri /home/BAW/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 bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Aug 5 00:31:11 CST 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.5243 /media/sf_T1/recon/demo3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5243/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5243/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (-7.45058e-09, 0, -1) k_ras = (-1.39698e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5243/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Aug 5 00:31:13 CST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.5243/nu0.mnc ./tmp.mri_nu_correct.mni.5243/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5243/0/ [bat@bogon:/media/sf_T1/recon/demo3/mri/] [2021-08-05 00:31:13] running: /home/BAW/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.5243/0/ ./tmp.mri_nu_correct.mni.5243/nu0.mnc ./tmp.mri_nu_correct.mni.5243/nu1.imp Processing:.................................................................Done 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-------------------------------------------------------- Iteration 2 Thu Aug 5 00:31:50 CST 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.5243/nu1.mnc ./tmp.mri_nu_correct.mni.5243/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5243/1/ [bat@bogon:/media/sf_T1/recon/demo3/mri/] [2021-08-05 00:31:50] running: /home/BAW/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.5243/1/ ./tmp.mri_nu_correct.mni.5243/nu1.mnc ./tmp.mri_nu_correct.mni.5243/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 29 CV of field change: 0.000999636 mri_binarize --i ./tmp.mri_nu_correct.mni.5243/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5243/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sf_T1/recon/demo3/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5243/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5243/ones.mgz sysname Linux hostname bogon machine x86_64 user bat input ./tmp.mri_nu_correct.mni.5243/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5243/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.5243/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5243/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5243/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.5243/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5243/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5243/input.mean.dat sysname Linux hostname bogon machine x86_64 user bat UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5243/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.5243/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5243/ones.mgz --i ./tmp.mri_nu_correct.mni.5243/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5243/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5243/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.5243/ones.mgz --i ./tmp.mri_nu_correct.mni.5243/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5243/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5243/output.mean.dat sysname Linux hostname bogon machine x86_64 user bat UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5243/ones.mgz Loading ./tmp.mri_nu_correct.mni.5243/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.5243/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5243/nu2.mnc ./tmp.mri_nu_correct.mni.5243/nu2.mnc mul 1.01930694692039445981 Saving result to './tmp.mri_nu_correct.mni.5243/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5243/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5243/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.5243/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, 3.72529e-09) j_ras = (-7.45058e-09, 0, -1) k_ras = (-1.39698e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (10, 122) to ( 3, 110) Thu Aug 5 00:32:42 CST 2021 mri_nu_correct.mni done mri_add_xform_to_header -c /media/sf_T1/recon/demo3/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 5 00:32:42 CST 2021 /media/sf_T1/recon/demo3/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 1.06464 -0.03093 -0.08063 -1.49896; 0.00567 1.16190 0.02848 -33.51154; 0.08336 -0.03992 1.15952 -0.07388; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 77 (77), valley at 43 (43) csf peak at 26, setting threshold to 60 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 75 (75), valley at 37 (37) csf peak at 25, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 5 seconds. #-------------------------------------------- #@# Skull Stripping Thu Aug 5 00:33:47 CST 2021 /media/sf_T1/recon/demo3/mri mri_em_register -rusage /media/sf_T1/recon/demo3/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /home/BAW/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 '/home/BAW/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=18.0 skull bounding box = (50, 52, 32) --> (212, 255, 215) using (104, 120, 124) as brain centroid... mean wm in atlas = 108, using box (84,95,101) --> (123, 145,146) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 104 +- 6.4 after smoothing, mri peak at 104, scaling input intensities by 1.038 scaling channel 0 by 1.03846 initial log_p = -4.619 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.592546 @ (-9.091, -9.091, -27.273) max log p = -4.466565 @ (4.545, -4.545, 4.545) max log p = -4.416584 @ (2.273, -2.273, 6.818) max log p = -4.416160 @ (1.136, -1.136, -1.136) max log p = -4.410803 @ (0.568, -3.977, 1.705) max log p = -4.410803 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -21.0, -15.3): log p = -4.411 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.075, old_max_log_p =-4.411 (thresh=-4.4) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.15000 0.00000 -30.50226; 0.00000 0.00000 1.15000 -34.28052; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.075, old_max_log_p =-4.075 (thresh=-4.1) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.15000 0.00000 -30.50226; 0.00000 0.00000 1.15000 -34.28052; 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=-4.017, old_max_log_p =-4.075 (thresh=-4.1) 1.04920 -0.11274 0.02959 0.90162; 0.10535 1.14193 0.07608 -52.23519; -0.03444 -0.07135 1.12558 -14.16700; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.017, old_max_log_p =-4.017 (thresh=-4.0) 1.04920 -0.11274 0.02959 0.90162; 0.10535 1.14193 0.07608 -52.23519; -0.03444 -0.07135 1.12558 -14.16700; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.997, old_max_log_p =-4.017 (thresh=-4.0) 1.05100 -0.12186 0.01992 3.70788; 0.11434 1.14285 0.06716 -51.96791; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.997, old_max_log_p =-3.997 (thresh=-4.0) 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 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 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.997 (old=-4.619) transform before final EM align: 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 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 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.05100 -0.12186 0.01992 3.70788; 0.11421 1.14151 0.06708 -51.74040; -0.02486 -0.06267 1.12241 -16.79571; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 512.485090 mri_em_register stimesec 0.658899 mri_em_register ru_maxrss 609784 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157279 mri_em_register ru_majflt 8 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150264 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 316 mri_em_register ru_nivcsw 42008 registration took 8 minutes and 36 seconds. mri_watershed -rusage /media/sf_T1/recon/demo3/touch/rusage.mri_watershed.dat -T1 -brain_atlas /home/BAW/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=129 y=128 z=122 r=83 first estimation of the main basin volume: 2458653 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=109, y=105, z=95, Imax=255 CSF=16, 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=8675379698 voxels, voxel volume =1.000 = 8675379698 mmm3 = 8675379.200 cm3 done. PostAnalyze...Basin Prior 39 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=129,y=128, z=117, r=8958 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=42 , nb = 44216 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=13 , nb = -1035418394 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = 1083807741 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=43 , nb = 1068942200 LEFT_BRAIN CSF_MIN=0, CSF_intensity=7, CSF_MAX=35 , nb = 1069007578 OTHER CSF_MIN=18, CSF_intensity=29, CSF_MAX=62 , nb = 1077122366 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 : 42, 49, 53, 74 after analyzing : 42, 51, 53, 56 RIGHT_CER before analyzing : 13, 21, 49, 85 after analyzing : 13, 39, 49, 50 LEFT_CER before analyzing : 14, 27, 56, 82 after analyzing : 14, 46, 56, 55 RIGHT_BRAIN before analyzing : 43, 48, 52, 73 after analyzing : 43, 50, 52, 55 LEFT_BRAIN before analyzing : 35, 45, 53, 74 after analyzing : 35, 50, 53, 56 OTHER before analyzing : 62, 4, 0, 2 after analyzing : 4, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 64.940, std = 5.491 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.54, sigma = 6.60 after rotation: sse = 4.54, sigma = 6.60 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.92, its var is 5.99 before Erosion-Dilatation 1.00% 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...46 iterations mri_strip_skull: done peeling brain Brain Size = 1452273 voxels, voxel volume = 1.000 mm3 = 1452273 mmm3 = 1452.273 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 10.365424 mri_watershed stimesec 0.183972 mri_watershed ru_maxrss 829612 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212690 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9656 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 728 mri_watershed ru_nivcsw 953 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Aug 5 00:42:35 CST 2021 /media/sf_T1/recon/demo3/mri mri_em_register -rusage /media/sf_T1/recon/demo3/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /home/BAW/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 '/home/BAW/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=21.0 skull bounding box = (62, 73, 52) --> (197, 187, 198) using (107, 111, 125) as brain centroid... mean wm in atlas = 107, using box (90,97,107) --> (123, 124,142) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 5.2 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 initial log_p = -4.222 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.097897 @ (-9.091, -9.091, -9.091) max log p = -3.987485 @ (4.545, -4.545, -4.545) max log p = -3.923354 @ (2.273, -2.273, 2.273) max log p = -3.888858 @ (1.136, 3.409, -1.136) max log p = -3.882641 @ (-0.568, -0.568, 0.568) max log p = -3.882641 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -13.1, -11.9): log p = -3.883 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.779, old_max_log_p =-3.883 (thresh=-3.9) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.00000 0.00000 -13.06818; 0.00000 0.00000 1.06375 -19.41455; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.779, old_max_log_p =-3.779 (thresh=-3.8) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.00000 0.00000 -13.06818; 0.00000 0.00000 1.06375 -19.41455; 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=-3.644, old_max_log_p =-3.779 (thresh=-3.8) 1.04921 -0.09514 -0.03926 9.05478; 0.10985 1.05006 0.06728 -37.88244; 0.03859 -0.06691 1.12139 -24.15556; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.636, old_max_log_p =-3.644 (thresh=-3.6) 1.04921 -0.09514 -0.03926 9.05478; 0.11191 1.06975 0.06854 -40.82941; 0.03859 -0.06691 1.12139 -24.15556; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.631, old_max_log_p =-3.636 (thresh=-3.6) 1.04921 -0.09514 -0.03926 9.05478; 0.11266 1.09145 0.03241 -39.42440; 0.04223 -0.03187 1.12303 -29.32513; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.630, old_max_log_p =-3.631 (thresh=-3.6) 1.05308 -0.06159 -0.00029 -0.38871; 0.07808 1.07194 0.06789 -36.69404; 0.00425 -0.06563 1.14309 -22.49489; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.597, old_max_log_p =-3.630 (thresh=-3.6) 1.05042 -0.07898 -0.00192 2.38364; 0.09562 1.07060 0.10517 -43.67070; 0.00181 -0.10074 1.14429 -18.27612; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.594, old_max_log_p =-3.597 (thresh=-3.6) 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.594 (old=-4.222) transform before final EM align: 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05042 -0.07898 -0.00192 2.38364; 0.09551 1.06934 0.10505 -43.47973; 0.00181 -0.10085 1.14564 -18.42110; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 4.0 after pass:transform: ( 1.05, -0.08, -0.00, 2.38) ( 0.10, 1.07, 0.11, -43.48) ( 0.00, -0.10, 1.15, -18.42) dfp_em_step_func: 012: -log(p) = 4.0 after pass:transform: ( 1.05, -0.08, -0.00, 2.38) ( 0.10, 1.07, 0.11, -43.48) ( 0.00, -0.10, 1.15, -18.42) dfp_em_step_func: 013: -log(p) = 4.0 after pass:transform: ( 1.05, -0.08, -0.00, 2.38) ( 0.10, 1.07, 0.11, -43.48) ( 0.00, -0.10, 1.15, -18.42) dfp_em_step_func: 014: -log(p) = 4.0 after pass:transform: ( 1.05, -0.08, -0.00, 2.38) ( 0.10, 1.07, 0.11, -43.48) ( 0.00, -0.10, 1.15, -18.42) dfp_em_step_func: 015: -log(p) = 4.0 after pass:transform: ( 1.05, -0.08, -0.00, 2.38) ( 0.10, 1.07, 0.11, -43.48) ( 0.00, -0.10, 1.15, -18.42) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 017: -log(p) = 4.0 tol 0.000000 final transform: 1.05062 -0.07876 -0.00164 2.38364; 0.09568 1.06968 0.10521 -43.47973; 0.00209 -0.10056 1.14590 -18.42110; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 545.268106 mri_em_register stimesec 0.761884 mri_em_register ru_maxrss 599004 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159058 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 437 mri_em_register ru_nivcsw 44395 registration took 9 minutes and 8 seconds. #-------------------------------------- #@# CA Normalize Thu Aug 5 00:51:42 CST 2021 /media/sf_T1/recon/demo3/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/BAW/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 '/home/BAW/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=21.0 skull bounding box = (62, 73, 52) --> (197, 187, 198) using (107, 111, 125) as brain centroid... mean wm in atlas = 107, using box (90,97,107) --> (123, 124,142) to find MRI wm before smoothing, mri peak at 103 robust fit to distribution - 103 +- 5.2 after smoothing, mri peak at 103, scaling input intensities by 1.039 scaling channel 0 by 1.03883 using 246344 sample points... INFO: compute sample coordinates transform 1.05062 -0.07876 -0.00164 2.38364; 0.09568 1.06968 0.10521 -43.47973; 0.00209 -0.10056 1.14590 -18.42110; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 65, 51) --> (192, 173, 197) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 967 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 69, 51) --> (129, 179, 197) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 1235 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 149, 73) --> (178, 186, 120) Left_Cerebellum_White_Matter: limiting intensities to 107.0 --> 132.0 0 of 39 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 149, 71) --> (131, 189, 121) Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 0 of 22 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 139, 104) --> (148, 205, 130) Brain_Stem: limiting intensities to 99.0 --> 132.0 0 of 67 (0.0%) samples deleted using 2330 total control points for intensity normalization... bias field = 0.934 +- 0.063 19 of 2330 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 65, 51) --> (192, 173, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 1 of 1445 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 69, 51) --> (129, 179, 197) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 1790 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 149, 73) --> (178, 186, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 92 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 149, 71) --> (131, 189, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 67 (32.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 139, 104) --> (148, 205, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 155 (0.6%) samples deleted using 3549 total control points for intensity normalization... bias field = 1.015 +- 0.059 29 of 3480 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 65, 51) --> (192, 173, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 3 of 1469 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 69, 51) --> (129, 179, 197) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 7 of 1849 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 149, 73) --> (178, 186, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 163 (25.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 149, 71) --> (131, 189, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 79 (44.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 139, 104) --> (148, 205, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 24 of 161 (14.9%) samples deleted using 3721 total control points for intensity normalization... bias field = 1.014 +- 0.047 27 of 3564 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 0 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Thu Aug 5 00:52:28 CST 2021 /media/sf_T1/recon/demo3/mri mri_ca_register -rusage /media/sf_T1/recon/demo3/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/BAW/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 '/home/BAW/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.31 (predicted orig area = 6.1) 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=0.865, neg=0, invalid=762 0001: dt=221.952000, rms=0.766 (11.485%), neg=0, invalid=762 0002: dt=182.123457, rms=0.745 (2.644%), neg=0, invalid=762 0003: dt=295.936000, rms=0.734 (1.547%), neg=0, invalid=762 0004: dt=129.472000, rms=0.728 (0.829%), neg=0, invalid=762 0005: dt=517.888000, rms=0.719 (1.151%), neg=0, invalid=762 0006: dt=134.400000, rms=0.716 (0.475%), neg=0, invalid=762 0007: dt=517.888000, rms=0.712 (0.616%), neg=0, invalid=762 0008: dt=129.472000, rms=0.708 (0.443%), neg=0, invalid=762 0009: dt=443.904000, rms=0.706 (0.313%), neg=0, invalid=762 0010: dt=129.472000, rms=0.704 (0.327%), neg=0, invalid=762 0011: dt=517.888000, rms=0.702 (0.278%), neg=0, invalid=762 0012: dt=129.472000, rms=0.700 (0.281%), neg=0, invalid=762 0013: dt=369.920000, rms=0.699 (0.172%), neg=0, invalid=762 0014: dt=369.920000, rms=0.699 (-0.328%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.699, neg=0, invalid=762 0015: dt=129.472000, rms=0.697 (0.332%), neg=0, invalid=762 0016: dt=517.888000, rms=0.694 (0.367%), neg=0, invalid=762 0017: dt=129.472000, rms=0.694 (0.076%), neg=0, invalid=762 0018: dt=129.472000, rms=0.693 (0.060%), neg=0, invalid=762 0019: dt=129.472000, rms=0.693 (0.109%), neg=0, invalid=762 0020: dt=129.472000, rms=0.692 (0.160%), neg=0, invalid=762 0021: dt=129.472000, rms=0.690 (0.189%), neg=0, invalid=762 0022: dt=129.472000, rms=0.689 (0.210%), neg=0, invalid=762 0023: dt=129.472000, rms=0.687 (0.229%), neg=0, invalid=762 0024: dt=129.472000, rms=0.686 (0.240%), neg=0, invalid=762 0025: dt=129.472000, rms=0.684 (0.217%), neg=0, invalid=762 0026: dt=129.472000, rms=0.683 (0.204%), neg=0, invalid=762 0027: dt=129.472000, rms=0.681 (0.181%), neg=0, invalid=762 0028: dt=129.472000, rms=0.680 (0.188%), neg=0, invalid=762 0029: dt=129.472000, rms=0.679 (0.185%), neg=0, invalid=762 0030: dt=129.472000, rms=0.678 (0.175%), neg=0, invalid=762 0031: dt=129.472000, rms=0.677 (0.163%), neg=0, invalid=762 0032: dt=129.472000, rms=0.676 (0.153%), neg=0, invalid=762 0033: dt=129.472000, rms=0.675 (0.133%), neg=0, invalid=762 0034: dt=129.472000, rms=0.674 (0.129%), neg=0, invalid=762 0035: dt=129.472000, rms=0.673 (0.126%), neg=0, invalid=762 0036: dt=129.472000, rms=0.672 (0.123%), neg=0, invalid=762 0037: dt=129.472000, rms=0.671 (0.124%), neg=0, invalid=762 0038: dt=129.472000, rms=0.671 (0.116%), neg=0, invalid=762 0039: dt=1183.744000, rms=0.670 (0.072%), neg=0, invalid=762 0040: dt=1183.744000, rms=0.670 (-2.048%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.676, neg=0, invalid=762 0041: dt=135.830588, rms=0.668 (1.122%), neg=0, invalid=762 0042: dt=189.614907, rms=0.658 (1.628%), neg=0, invalid=762 0043: dt=89.600000, rms=0.653 (0.663%), neg=0, invalid=762 0044: dt=95.361419, rms=0.649 (0.656%), neg=0, invalid=762 0045: dt=88.113314, rms=0.646 (0.428%), neg=0, invalid=762 0046: dt=124.416000, rms=0.643 (0.439%), neg=0, invalid=762 0047: dt=74.640964, rms=0.641 (0.381%), neg=0, invalid=762 0048: dt=145.152000, rms=0.639 (0.328%), neg=0, invalid=762 0049: dt=69.696335, rms=0.637 (0.340%), neg=0, invalid=762 0050: dt=145.152000, rms=0.635 (0.249%), neg=0, invalid=762 0051: dt=145.152000, rms=0.635 (0.011%), neg=0, invalid=762 0052: dt=145.152000, rms=0.630 (0.819%), neg=0, invalid=762 0053: dt=145.152000, rms=0.624 (0.914%), neg=0, invalid=762 0054: dt=145.152000, rms=0.621 (0.441%), neg=0, invalid=762 0055: dt=145.152000, rms=0.617 (0.749%), neg=0, invalid=762 0056: dt=145.152000, rms=0.611 (0.950%), neg=0, invalid=762 0057: dt=145.152000, rms=0.608 (0.389%), neg=0, invalid=762 0058: dt=145.152000, rms=0.607 (0.166%), neg=0, invalid=762 0059: dt=145.152000, rms=0.603 (0.698%), neg=0, invalid=762 0060: dt=145.152000, rms=0.601 (0.363%), neg=0, invalid=762 0061: dt=145.152000, rms=0.600 (0.202%), neg=0, invalid=762 0062: dt=145.152000, rms=0.598 (0.293%), neg=0, invalid=762 0063: dt=145.152000, rms=0.597 (0.203%), neg=0, invalid=762 0064: dt=145.152000, rms=0.595 (0.312%), neg=0, invalid=762 0065: dt=145.152000, rms=0.594 (0.069%), neg=0, invalid=762 0066: dt=145.152000, rms=0.595 (-0.063%), neg=0, invalid=762 0067: dt=36.288000, rms=0.593 (0.181%), neg=0, invalid=762 0068: dt=36.288000, rms=0.593 (0.030%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.594, neg=0, invalid=762 0069: dt=145.152000, rms=0.591 (0.513%), neg=0, invalid=762 0070: dt=62.208000, rms=0.591 (0.046%), neg=0, invalid=762 0071: dt=62.208000, rms=0.590 (0.026%), neg=0, invalid=762 0072: dt=62.208000, rms=0.590 (0.041%), neg=0, invalid=762 0073: dt=62.208000, rms=0.590 (0.054%), neg=0, invalid=762 0074: dt=62.208000, rms=0.590 (0.054%), neg=0, invalid=762 0075: dt=62.208000, rms=0.589 (0.058%), neg=0, invalid=762 0076: dt=62.208000, rms=0.589 (0.039%), neg=0, invalid=762 0077: dt=62.208000, rms=0.589 (0.023%), neg=0, invalid=762 0078: dt=20.736000, rms=0.589 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0079: dt=0.000000, rms=0.618 (0.097%), neg=0, invalid=762 0080: dt=0.000000, rms=0.618 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0081: dt=0.000000, rms=0.618 (0.097%), neg=0, invalid=762 0082: dt=0.000000, rms=0.618 (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=0.704, neg=0, invalid=762 0083: dt=5.056604, rms=0.680 (3.407%), neg=0, invalid=762 0084: dt=2.373626, rms=0.680 (0.138%), neg=0, invalid=762 0085: dt=2.373626, rms=0.680 (-0.059%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.680, neg=0, invalid=762 0086: dt=0.375000, rms=0.680 (0.072%), neg=0, invalid=762 0087: dt=0.000000, rms=0.680 (-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=0.760, neg=0, invalid=762 0088: dt=1.536000, rms=0.753 (0.924%), neg=0, invalid=762 0089: dt=2.061111, rms=0.746 (0.903%), neg=0, invalid=762 0090: dt=0.448000, rms=0.746 (0.071%), neg=0, invalid=762 0091: dt=0.448000, rms=0.746 (0.046%), neg=0, invalid=762 0092: dt=0.448000, rms=0.745 (0.052%), neg=0, invalid=762 0093: dt=0.448000, rms=0.745 (0.047%), neg=0, invalid=762 0094: dt=0.448000, rms=0.745 (0.025%), neg=0, invalid=762 0095: dt=1.792000, rms=0.743 (0.202%), neg=0, invalid=762 0096: dt=0.112000, rms=0.743 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.744, neg=0, invalid=762 0097: dt=1.024000, rms=0.742 (0.147%), neg=0, invalid=762 0098: dt=1.024000, rms=0.742 (0.019%), neg=0, invalid=762 0099: dt=1.024000, rms=0.742 (0.012%), neg=0, invalid=762 0100: dt=1.024000, rms=0.742 (-0.006%), 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=0.696, neg=0, invalid=762 0101: dt=0.888889, rms=0.677 (2.843%), neg=0, invalid=762 0102: dt=0.080000, rms=0.676 (0.153%), neg=0, invalid=762 0103: dt=0.080000, rms=0.676 (-0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.676, neg=0, invalid=762 0104: dt=0.028000, rms=0.675 (0.092%), neg=0, invalid=762 0105: dt=0.007000, rms=0.675 (0.002%), neg=0, invalid=762 0106: dt=0.007000, rms=0.675 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.15155 (21) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1503 voxels, overlap=0.705) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (1503 voxels, peak = 20), gca=19.5 gca peak = 0.15565 (16) mri peak = 0.12926 (18) Right_Lateral_Ventricle (43): linear fit = 1.16 x + 0.0 (635 voxels, overlap=0.676) Right_Lateral_Ventricle (43): linear fit = 1.16 x + 0.0 (635 voxels, peak = 19), gca=18.6 gca peak = 0.26829 (96) mri peak = 0.09949 (102) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (791 voxels, overlap=0.262) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (791 voxels, peak = 103), gca=103.2 gca peak = 0.20183 (93) mri peak = 0.07317 (105) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (695 voxels, overlap=0.229) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (695 voxels, peak = 103), gca=102.8 gca peak = 0.21683 (55) mri peak = 0.08567 (72) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (770 voxels, overlap=0.018) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (770 voxels, peak = 67), gca=67.4 gca peak = 0.30730 (58) mri peak = 0.10297 (73) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (886 voxels, overlap=0.013) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (886 voxels, peak = 73), gca=72.8 gca peak = 0.11430 (101) mri peak = 0.10143 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54368 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (54368 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.09081 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54843 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (54843 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04274 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (21864 voxels, overlap=0.004) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (21864 voxels, peak = 73), gca=73.5 gca peak = 0.15082 (58) mri peak = 0.05066 (72) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (20072 voxels, overlap=0.002) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (20072 voxels, peak = 71), gca=71.1 gca peak = 0.14161 (67) mri peak = 0.12921 (82) Right_Caudate (50): linear fit = 1.25 x + 0.0 (481 voxels, overlap=0.010) Right_Caudate (50): linear fit = 1.25 x + 0.0 (481 voxels, peak = 83), gca=83.4 gca peak = 0.15243 (71) mri peak = 0.12245 (86) Left_Caudate (11): linear fit = 1.17 x + 0.0 (787 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (787 voxels, peak = 83), gca=83.4 gca peak = 0.13336 (57) mri peak = 0.03694 (69) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (19272 voxels, overlap=0.110) Left_Cerebellum_Cortex (8): linear fit = 1.24 x + 0.0 (19272 voxels, peak = 70), gca=70.4 gca peak = 0.13252 (56) mri peak = 0.03293 (63) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (21133 voxels, overlap=0.036) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (21133 voxels, peak = 69), gca=69.2 gca peak = 0.18181 (84) mri peak = 0.05415 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (7563 voxels, overlap=0.040) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (7563 voxels, peak = 92), gca=92.0 gca peak = 0.20573 (83) mri peak = 0.04600 (71) Right_Cerebellum_White_Matter (46): linear fit = 0.87 x + 0.0 (5631 voxels, overlap=0.044) Right_Cerebellum_White_Matter (46): linear fit = 0.87 x + 0.0 (5631 voxels, peak = 72), gca=71.8 gca peak = 0.21969 (57) mri peak = 0.12069 (73) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (406 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.26 x + 0.0 (406 voxels, peak = 72), gca=72.1 gca peak = 0.39313 (56) mri peak = 0.08850 (72) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (502 voxels, overlap=0.040) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (502 voxels, peak = 64), gca=63.6 gca peak = 0.14181 (85) mri peak = 0.06292 (91) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4745 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4745 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.06064 (91) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3845 voxels, overlap=0.627) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3845 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.08191 (93) Left_Putamen (12): linear fit = 1.17 x + 0.0 (2100 voxels, overlap=0.067) Left_Putamen (12): linear fit = 1.17 x + 0.0 (2100 voxels, peak = 93), gca=92.8 gca peak = 0.14159 (79) mri peak = 0.08236 (88) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2146 voxels, overlap=0.198) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2146 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.08372 (90) Brain_Stem (16): linear fit = 1.15 x + 0.0 (8396 voxels, overlap=0.108) Brain_Stem (16): linear fit = 1.15 x + 0.0 (8396 voxels, peak = 92), gca=92.4 gca peak = 0.13281 (86) mri peak = 0.09335 (100) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (857 voxels, overlap=0.020) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (857 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.09562 (101) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1011 voxels, overlap=0.061) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1011 voxels, peak = 102), gca=101.9 gca peak = 0.20494 (23) mri peak = 0.20006 (21) gca peak = 0.15061 (21) uniform distribution in MR - rejecting arbitrary fit 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 Fourth_Ventricle = 0.15061 (21) 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 1.23 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.07 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.105) to 102.4 (was 102.8) Right_Pallidum too bright - rescaling by 0.992 (from 1.075) to 102.4 (was 103.2) 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=0.700, neg=0, invalid=762 0107: dt=104.965670, rms=0.679 (3.010%), neg=0, invalid=762 0108: dt=148.779221, rms=0.675 (0.554%), neg=0, invalid=762 0109: dt=517.888000, rms=0.666 (1.342%), neg=0, invalid=762 0110: dt=129.472000, rms=0.664 (0.324%), neg=0, invalid=762 0111: dt=517.888000, rms=0.660 (0.667%), neg=0, invalid=762 0112: dt=92.480000, rms=0.658 (0.184%), neg=0, invalid=762 0113: dt=1183.744000, rms=0.656 (0.394%), neg=0, invalid=762 0114: dt=221.952000, rms=0.653 (0.432%), neg=0, invalid=762 0115: dt=110.976000, rms=0.652 (0.100%), neg=0, invalid=762 0116: dt=887.808000, rms=0.650 (0.302%), neg=0, invalid=762 0117: dt=92.480000, rms=0.649 (0.153%), neg=0, invalid=762 0118: dt=2071.552000, rms=0.646 (0.510%), neg=0, invalid=762 0119: dt=129.472000, rms=0.644 (0.272%), neg=0, invalid=762 0120: dt=129.472000, rms=0.644 (0.052%), neg=0, invalid=762 0121: dt=517.888000, rms=0.643 (0.150%), neg=0, invalid=762 0122: dt=73.984000, rms=0.643 (0.041%), neg=0, invalid=762 0123: dt=73.984000, rms=0.643 (0.019%), neg=0, invalid=762 0124: dt=73.984000, rms=0.642 (0.029%), neg=0, invalid=762 0125: dt=73.984000, rms=0.642 (0.048%), neg=0, invalid=762 0126: dt=73.984000, rms=0.642 (0.071%), neg=0, invalid=762 0127: dt=73.984000, rms=0.641 (0.081%), neg=0, invalid=762 0128: dt=73.984000, rms=0.641 (0.083%), neg=0, invalid=762 0129: dt=73.984000, rms=0.640 (0.089%), neg=0, invalid=762 0130: dt=73.984000, rms=0.639 (0.094%), neg=0, invalid=762 0131: dt=73.984000, rms=0.639 (0.093%), neg=0, invalid=762 0132: dt=73.984000, rms=0.638 (0.105%), neg=0, invalid=762 0133: dt=73.984000, rms=0.637 (0.107%), neg=0, invalid=762 0134: dt=73.984000, rms=0.637 (0.107%), neg=0, invalid=762 0135: dt=73.984000, rms=0.636 (0.106%), neg=0, invalid=762 0136: dt=73.984000, rms=0.635 (0.105%), neg=0, invalid=762 0137: dt=73.984000, rms=0.635 (0.100%), neg=0, invalid=762 0138: dt=73.984000, rms=0.634 (0.098%), neg=0, invalid=762 0139: dt=73.984000, rms=0.634 (0.102%), neg=0, invalid=762 0140: dt=73.984000, rms=0.633 (0.097%), neg=0, invalid=762 0141: dt=73.984000, rms=0.632 (0.093%), neg=0, invalid=762 0142: dt=73.984000, rms=0.632 (0.088%), neg=0, invalid=762 0143: dt=73.984000, rms=0.631 (0.083%), neg=0, invalid=762 0144: dt=73.984000, rms=0.631 (0.078%), neg=0, invalid=762 0145: dt=73.984000, rms=0.630 (0.075%), neg=0, invalid=762 0146: dt=73.984000, rms=0.630 (0.078%), neg=0, invalid=762 0147: dt=73.984000, rms=0.629 (0.074%), neg=0, invalid=762 0148: dt=73.984000, rms=0.629 (0.072%), neg=0, invalid=762 0149: dt=73.984000, rms=0.628 (0.068%), neg=0, invalid=762 0150: dt=73.984000, rms=0.628 (0.064%), neg=0, invalid=762 0151: dt=73.984000, rms=0.628 (0.062%), neg=0, invalid=762 0152: dt=73.984000, rms=0.627 (0.063%), neg=0, invalid=762 0153: dt=73.984000, rms=0.627 (0.059%), neg=0, invalid=762 0154: dt=73.984000, rms=0.627 (0.058%), neg=0, invalid=762 0155: dt=73.984000, rms=0.626 (0.055%), neg=0, invalid=762 0156: dt=73.984000, rms=0.626 (0.053%), neg=0, invalid=762 0157: dt=73.984000, rms=0.626 (0.049%), neg=0, invalid=762 0158: dt=73.984000, rms=0.625 (0.047%), neg=0, invalid=762 0159: dt=73.984000, rms=0.625 (0.046%), neg=0, invalid=762 0160: dt=73.984000, rms=0.625 (0.045%), neg=0, invalid=762 0161: dt=73.984000, rms=0.624 (0.044%), neg=0, invalid=762 0162: dt=73.984000, rms=0.624 (0.043%), neg=0, invalid=762 0163: dt=73.984000, rms=0.624 (0.042%), neg=0, invalid=762 0164: dt=73.984000, rms=0.624 (0.044%), neg=0, invalid=762 0165: dt=73.984000, rms=0.623 (0.042%), neg=0, invalid=762 0166: dt=73.984000, rms=0.623 (0.043%), neg=0, invalid=762 0167: dt=73.984000, rms=0.623 (0.039%), neg=0, invalid=762 0168: dt=73.984000, rms=0.623 (0.039%), neg=0, invalid=762 0169: dt=73.984000, rms=0.622 (0.036%), neg=0, invalid=762 0170: dt=73.984000, rms=0.622 (0.033%), neg=0, invalid=762 0171: dt=73.984000, rms=0.622 (0.031%), neg=0, invalid=762 0172: dt=73.984000, rms=0.622 (0.032%), neg=0, invalid=762 0173: dt=73.984000, rms=0.622 (0.032%), neg=0, invalid=762 0174: dt=73.984000, rms=0.621 (0.031%), neg=0, invalid=762 0175: dt=73.984000, rms=0.621 (0.031%), neg=0, invalid=762 0176: dt=73.984000, rms=0.621 (0.030%), neg=0, invalid=762 0177: dt=73.984000, rms=0.621 (0.030%), neg=0, invalid=762 0178: dt=73.984000, rms=0.621 (0.030%), neg=0, invalid=762 0179: dt=73.984000, rms=0.620 (0.030%), neg=0, invalid=762 0180: dt=73.984000, rms=0.620 (0.028%), neg=0, invalid=762 0181: dt=73.984000, rms=0.620 (0.028%), neg=0, invalid=762 0182: dt=73.984000, rms=0.620 (0.030%), neg=0, invalid=762 0183: dt=73.984000, rms=0.620 (0.028%), neg=0, invalid=762 0184: dt=73.984000, rms=0.620 (0.024%), neg=0, invalid=762 0185: dt=73.984000, rms=0.619 (0.024%), neg=0, invalid=762 0186: dt=2071.552000, rms=0.619 (0.053%), neg=0, invalid=762 0187: dt=73.984000, rms=0.619 (0.018%), neg=0, invalid=762 0188: dt=73.984000, rms=0.619 (0.003%), neg=0, invalid=762 0189: dt=73.984000, rms=0.619 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=762 0190: dt=295.936000, rms=0.617 (0.280%), neg=0, invalid=762 0191: dt=129.472000, rms=0.617 (0.086%), neg=0, invalid=762 0192: dt=73.984000, rms=0.617 (0.003%), neg=0, invalid=762 0193: dt=73.984000, rms=0.617 (0.007%), neg=0, invalid=762 0194: dt=73.984000, rms=0.617 (0.014%), neg=0, invalid=762 0195: dt=73.984000, rms=0.617 (0.022%), neg=0, invalid=762 0196: dt=73.984000, rms=0.616 (0.029%), neg=0, invalid=762 0197: dt=73.984000, rms=0.616 (0.035%), neg=0, invalid=762 0198: dt=73.984000, rms=0.616 (0.033%), neg=0, invalid=762 0199: dt=73.984000, rms=0.616 (0.034%), neg=0, invalid=762 0200: dt=73.984000, rms=0.616 (0.030%), neg=0, invalid=762 0201: dt=73.984000, rms=0.615 (0.031%), neg=0, invalid=762 0202: dt=73.984000, rms=0.615 (0.028%), neg=0, invalid=762 0203: dt=73.984000, rms=0.615 (0.027%), neg=0, invalid=762 0204: dt=73.984000, rms=0.615 (0.025%), neg=0, invalid=762 0205: dt=73.984000, rms=0.615 (0.025%), neg=0, invalid=762 0206: dt=73.984000, rms=0.615 (0.027%), neg=0, invalid=762 0207: dt=73.984000, rms=0.614 (0.030%), neg=0, invalid=762 0208: dt=73.984000, rms=0.614 (0.027%), neg=0, invalid=762 0209: dt=73.984000, rms=0.614 (0.027%), neg=0, invalid=762 0210: dt=73.984000, rms=0.614 (0.024%), neg=0, invalid=762 0211: dt=73.984000, rms=0.614 (0.019%), neg=0, invalid=762 0212: dt=2071.552000, rms=0.614 (0.046%), neg=0, invalid=762 0213: dt=129.472000, rms=0.613 (0.016%), neg=0, invalid=762 0214: dt=129.472000, rms=0.613 (0.013%), neg=0, invalid=762 0215: dt=129.472000, rms=0.613 (0.008%), neg=0, invalid=762 0216: dt=129.472000, rms=0.613 (0.009%), neg=0, invalid=762 0217: dt=129.472000, rms=0.613 (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=0.615, neg=0, invalid=762 0218: dt=133.877551, rms=0.611 (0.614%), neg=0, invalid=762 0219: dt=248.832000, rms=0.601 (1.771%), neg=0, invalid=762 0220: dt=57.391304, rms=0.596 (0.691%), neg=0, invalid=762 0221: dt=414.720000, rms=0.590 (1.014%), neg=0, invalid=762 0222: dt=79.402831, rms=0.585 (0.960%), neg=0, invalid=762 0223: dt=79.841584, rms=0.583 (0.328%), neg=0, invalid=762 0224: dt=103.680000, rms=0.581 (0.284%), neg=0, invalid=762 0225: dt=78.683983, rms=0.580 (0.253%), neg=0, invalid=762 0226: dt=103.680000, rms=0.578 (0.246%), neg=0, invalid=762 0227: dt=79.269036, rms=0.577 (0.217%), neg=0, invalid=762 0228: dt=103.680000, rms=0.576 (0.222%), neg=0, invalid=762 0229: dt=74.434783, rms=0.575 (0.187%), neg=0, invalid=762 0230: dt=124.416000, rms=0.573 (0.226%), neg=0, invalid=762 0231: dt=62.661088, rms=0.572 (0.176%), neg=0, invalid=762 0232: dt=145.152000, rms=0.571 (0.251%), neg=0, invalid=762 0233: dt=63.634286, rms=0.570 (0.137%), neg=0, invalid=762 0234: dt=145.152000, rms=0.569 (0.221%), neg=0, invalid=762 0235: dt=36.288000, rms=0.568 (0.103%), neg=0, invalid=762 0236: dt=331.776000, rms=0.567 (0.256%), neg=0, invalid=762 0237: dt=36.288000, rms=0.565 (0.251%), neg=0, invalid=762 0238: dt=145.152000, rms=0.564 (0.176%), neg=0, invalid=762 0239: dt=36.288000, rms=0.564 (0.083%), neg=0, invalid=762 0240: dt=414.720000, rms=0.563 (0.250%), neg=0, invalid=762 0241: dt=36.288000, rms=0.561 (0.222%), neg=0, invalid=762 0242: dt=145.152000, rms=0.560 (0.139%), neg=0, invalid=762 0243: dt=36.288000, rms=0.560 (0.071%), neg=0, invalid=762 0244: dt=331.776000, rms=0.559 (0.162%), neg=0, invalid=762 0245: dt=36.288000, rms=0.558 (0.149%), neg=0, invalid=762 0246: dt=145.152000, rms=0.558 (0.122%), neg=0, invalid=762 0247: dt=82.944000, rms=0.557 (0.063%), neg=0, invalid=762 0248: dt=82.944000, rms=0.557 (0.067%), neg=0, invalid=762 0249: dt=62.208000, rms=0.557 (0.059%), neg=0, invalid=762 0250: dt=145.152000, rms=0.556 (0.076%), neg=0, invalid=762 0251: dt=36.288000, rms=0.556 (0.061%), neg=0, invalid=762 0252: dt=331.776000, rms=0.555 (0.137%), neg=0, invalid=762 0253: dt=36.288000, rms=0.554 (0.116%), neg=0, invalid=762 0254: dt=145.152000, rms=0.554 (0.073%), neg=0, invalid=762 0255: dt=36.288000, rms=0.554 (0.046%), neg=0, invalid=762 0256: dt=36.288000, rms=0.554 (0.025%), neg=0, invalid=762 0257: dt=36.288000, rms=0.553 (0.039%), neg=0, invalid=762 0258: dt=36.288000, rms=0.553 (0.057%), neg=0, invalid=762 0259: dt=36.288000, rms=0.553 (0.072%), neg=0, invalid=762 0260: dt=36.288000, rms=0.552 (0.083%), neg=0, invalid=762 0261: dt=36.288000, rms=0.552 (0.093%), neg=0, invalid=762 0262: dt=36.288000, rms=0.551 (0.100%), neg=0, invalid=762 0263: dt=18.144000, rms=0.551 (0.009%), neg=0, invalid=762 0264: dt=9.072000, rms=0.551 (0.006%), neg=0, invalid=762 0265: dt=6.480000, rms=0.551 (0.004%), neg=0, invalid=762 0266: dt=0.405000, rms=0.551 (0.001%), neg=0, invalid=762 0267: dt=0.202500, rms=0.551 (0.000%), neg=0, invalid=762 0268: dt=0.050625, rms=0.551 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0269: dt=145.152000, rms=0.548 (0.581%), neg=0, invalid=762 0270: dt=103.680000, rms=0.548 (0.092%), neg=0, invalid=762 0271: dt=145.152000, rms=0.547 (0.137%), neg=0, invalid=762 0272: dt=82.944000, rms=0.547 (0.076%), neg=0, invalid=762 0273: dt=82.944000, rms=0.546 (0.076%), neg=0, invalid=762 0274: dt=82.944000, rms=0.546 (0.059%), neg=0, invalid=762 0275: dt=103.680000, rms=0.545 (0.074%), neg=0, invalid=762 0276: dt=82.944000, rms=0.545 (0.052%), neg=0, invalid=762 0277: dt=103.680000, rms=0.545 (0.064%), neg=0, invalid=762 0278: dt=62.208000, rms=0.545 (0.055%), neg=0, invalid=762 0279: dt=145.152000, rms=0.544 (0.060%), neg=0, invalid=762 0280: dt=62.208000, rms=0.544 (0.069%), neg=0, invalid=762 0281: dt=124.416000, rms=0.544 (0.038%), neg=0, invalid=762 0282: dt=124.416000, rms=0.544 (0.006%), neg=0, invalid=762 0283: dt=124.416000, rms=0.543 (0.202%), neg=0, invalid=762 0284: dt=124.416000, rms=0.542 (0.181%), neg=0, invalid=762 0285: dt=124.416000, rms=0.541 (0.140%), neg=0, invalid=762 0286: dt=124.416000, rms=0.539 (0.244%), neg=0, invalid=762 0287: dt=124.416000, rms=0.538 (0.263%), neg=0, invalid=762 0288: dt=124.416000, rms=0.537 (0.180%), neg=0, invalid=762 0289: dt=124.416000, rms=0.537 (-0.121%), neg=0, invalid=762 0290: dt=36.288000, rms=0.537 (0.068%), neg=0, invalid=762 0291: dt=145.152000, rms=0.537 (0.039%), neg=0, invalid=762 0292: dt=145.152000, rms=0.537 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=762 0293: dt=11.200000, rms=0.543 (0.413%), neg=0, invalid=762 0294: dt=11.200000, rms=0.542 (0.290%), neg=0, invalid=762 0295: dt=44.800000, rms=0.537 (0.849%), neg=0, invalid=762 0296: dt=44.800000, rms=0.532 (0.852%), neg=0, invalid=762 0297: dt=128.000000, rms=0.524 (1.647%), neg=0, invalid=762 0298: dt=44.800000, rms=0.522 (0.378%), neg=0, invalid=762 0299: dt=2.800000, rms=0.521 (0.060%), neg=0, invalid=762 0300: dt=2.000000, rms=0.521 (0.031%), neg=0, invalid=762 0301: dt=0.062500, rms=0.521 (0.004%), neg=0, invalid=762 0302: dt=0.031250, rms=0.521 (0.000%), neg=0, invalid=762 0303: dt=0.003906, rms=0.521 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0304: dt=53.747573, rms=0.517 (0.860%), neg=0, invalid=762 0305: dt=32.000000, rms=0.515 (0.387%), neg=0, invalid=762 0306: dt=32.000000, rms=0.514 (0.244%), neg=0, invalid=762 0307: dt=32.000000, rms=0.513 (0.208%), neg=0, invalid=762 0308: dt=25.600000, rms=0.512 (0.151%), neg=0, invalid=762 0309: dt=44.800000, rms=0.511 (0.194%), neg=0, invalid=762 0310: dt=25.600000, rms=0.510 (0.134%), neg=0, invalid=762 0311: dt=44.800000, rms=0.509 (0.188%), neg=0, invalid=762 0312: dt=25.600000, rms=0.509 (0.105%), neg=0, invalid=762 0313: dt=44.800000, rms=0.508 (0.161%), neg=0, invalid=762 0314: dt=19.200000, rms=0.508 (0.103%), neg=0, invalid=762 0315: dt=179.200000, rms=0.505 (0.462%), neg=0, invalid=762 0316: dt=11.200000, rms=0.505 (0.118%), neg=0, invalid=762 0317: dt=32.000000, rms=0.504 (0.122%), neg=0, invalid=762 0318: dt=11.200000, rms=0.504 (0.038%), neg=0, invalid=762 0319: dt=11.200000, rms=0.504 (0.058%), neg=0, invalid=762 0320: dt=5.600000, rms=0.504 (0.010%), neg=0, invalid=762 0321: dt=0.700000, rms=0.504 (0.005%), neg=0, invalid=762 0322: dt=0.150000, rms=0.504 (0.000%), neg=0, invalid=762 0323: dt=0.009375, rms=0.504 (0.000%), neg=0, invalid=762 0324: dt=0.002344, rms=0.503 (0.000%), neg=0, invalid=762 0325: dt=0.001172, rms=0.503 (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=0.525, neg=0, invalid=762 0326: dt=0.000000, rms=0.524 (0.076%), neg=0, invalid=762 0327: dt=0.000000, rms=0.524 (0.000%), neg=0, invalid=762 0328: dt=0.150000, rms=0.524 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0329: dt=0.000000, rms=0.524 (0.076%), neg=0, invalid=762 0330: dt=0.000000, rms=0.524 (0.000%), neg=0, invalid=762 0331: dt=0.150000, rms=0.524 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.567, neg=0, invalid=762 0332: dt=1.536000, rms=0.564 (0.559%), neg=0, invalid=762 0333: dt=0.256000, rms=0.564 (0.007%), neg=0, invalid=762 0334: dt=0.256000, rms=0.564 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 0335: dt=1.280000, rms=0.563 (0.197%), neg=0, invalid=762 0336: dt=0.112000, rms=0.563 (0.000%), neg=0, invalid=762 0337: dt=0.112000, rms=0.563 (-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=0.510, neg=0, invalid=762 0338: dt=0.448000, rms=0.496 (2.797%), neg=0, invalid=762 0339: dt=0.448000, rms=0.493 (0.702%), neg=0, invalid=762 0340: dt=0.448000, rms=0.491 (0.403%), neg=0, invalid=762 0341: dt=0.448000, rms=0.489 (0.255%), neg=0, invalid=762 0342: dt=0.448000, rms=0.489 (0.189%), neg=0, invalid=762 0343: dt=0.448000, rms=0.488 (0.141%), neg=0, invalid=762 0344: dt=0.448000, rms=0.487 (0.114%), neg=0, invalid=762 0345: dt=0.448000, rms=0.487 (0.092%), neg=0, invalid=762 0346: dt=0.448000, rms=0.486 (0.075%), neg=0, invalid=762 0347: dt=0.448000, rms=0.486 (0.065%), neg=0, invalid=762 0348: dt=0.448000, rms=0.486 (0.053%), neg=0, invalid=762 0349: dt=0.448000, rms=0.486 (0.049%), neg=0, invalid=762 0350: dt=0.448000, rms=0.485 (0.039%), neg=0, invalid=762 0351: dt=0.448000, rms=0.485 (0.076%), neg=0, invalid=762 0352: dt=0.448000, rms=0.485 (0.087%), neg=0, invalid=762 0353: dt=0.448000, rms=0.484 (0.095%), neg=0, invalid=762 0354: dt=0.448000, rms=0.484 (0.010%), neg=0, invalid=762 0355: dt=0.448000, rms=0.484 (0.005%), neg=0, invalid=762 0356: dt=0.448000, rms=0.484 (0.009%), neg=0, invalid=762 0357: dt=0.384000, rms=0.484 (0.005%), neg=0, invalid=762 0358: dt=0.384000, rms=0.484 (0.009%), neg=0, invalid=762 0359: dt=0.384000, rms=0.484 (0.012%), neg=0, invalid=762 0360: dt=0.384000, rms=0.484 (0.015%), neg=0, invalid=762 0361: dt=0.384000, rms=0.484 (0.018%), neg=0, invalid=762 0362: dt=0.384000, rms=0.484 (0.020%), neg=0, invalid=762 0363: dt=0.384000, rms=0.484 (0.005%), neg=0, invalid=762 0364: dt=0.384000, rms=0.484 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.484, neg=0, invalid=762 0365: dt=0.448000, rms=0.479 (1.001%), neg=0, invalid=762 0366: dt=0.448000, rms=0.479 (0.124%), neg=0, invalid=762 0367: dt=0.448000, rms=0.478 (0.038%), neg=0, invalid=762 0368: dt=0.448000, rms=0.478 (0.015%), neg=0, invalid=762 0369: dt=0.448000, rms=0.478 (0.016%), neg=0, invalid=762 0370: dt=0.224000, rms=0.478 (0.001%), neg=0, invalid=762 0371: dt=0.224000, rms=0.478 (0.000%), neg=0, invalid=762 0372: dt=0.320000, rms=0.478 (0.005%), neg=0, invalid=762 0373: dt=0.256000, rms=0.478 (0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0374: dt=0.000000, rms=0.476 (0.098%), neg=0, invalid=762 0375: dt=0.000000, rms=0.476 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0376: dt=295.936000, rms=0.475 (0.244%), neg=0, invalid=762 0377: dt=73.984000, rms=0.475 (0.026%), neg=0, invalid=762 0378: dt=73.984000, rms=0.475 (0.007%), neg=0, invalid=762 0379: dt=73.984000, rms=0.475 (0.008%), neg=0, invalid=762 0380: dt=73.984000, rms=0.475 (0.014%), neg=0, invalid=762 0381: dt=73.984000, rms=0.475 (0.026%), neg=0, invalid=762 0382: dt=73.984000, rms=0.475 (0.031%), neg=0, invalid=762 0383: dt=73.984000, rms=0.475 (0.031%), neg=0, invalid=762 0384: dt=73.984000, rms=0.475 (0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0385: dt=25.920000, rms=0.474 (0.127%), neg=0, invalid=762 0386: dt=25.920000, rms=0.474 (0.013%), neg=0, invalid=762 0387: dt=25.920000, rms=0.474 (0.016%), neg=0, invalid=762 0388: dt=25.920000, rms=0.474 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0389: dt=145.152000, rms=0.472 (0.624%), neg=0, invalid=762 0390: dt=36.288000, rms=0.471 (0.146%), neg=0, invalid=762 0391: dt=36.288000, rms=0.471 (0.047%), neg=0, invalid=762 0392: dt=36.288000, rms=0.471 (0.065%), neg=0, invalid=762 0393: dt=36.288000, rms=0.470 (0.098%), neg=0, invalid=762 0394: dt=36.288000, rms=0.470 (0.128%), neg=0, invalid=762 0395: dt=36.288000, rms=0.469 (0.160%), neg=0, invalid=762 0396: dt=36.288000, rms=0.468 (0.154%), neg=0, invalid=762 0397: dt=36.288000, rms=0.467 (0.140%), neg=0, invalid=762 0398: dt=36.288000, rms=0.467 (0.117%), neg=0, invalid=762 0399: dt=36.288000, rms=0.466 (0.098%), neg=0, invalid=762 0400: dt=82.944000, rms=0.466 (0.011%), neg=0, invalid=762 0401: dt=82.944000, rms=0.466 (0.032%), neg=0, invalid=762 0402: dt=82.944000, rms=0.466 (0.027%), neg=0, invalid=762 0403: dt=82.944000, rms=0.466 (0.092%), neg=0, invalid=762 0404: dt=82.944000, rms=0.465 (0.083%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0405: dt=32.000000, rms=0.464 (0.427%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0406: dt=82.117647, rms=0.462 (0.495%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0407: dt=44.800000, rms=0.460 (0.347%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0408: dt=32.000000, rms=0.459 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0409: dt=32.000000, rms=0.458 (0.201%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 12 iterations, nbhd size=1, neg = 0 0410: dt=32.000000, rms=0.457 (0.217%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0411: dt=32.000000, rms=0.456 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 12 iterations, nbhd size=1, neg = 0 0412: dt=32.000000, rms=0.455 (0.339%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 14 iterations, nbhd size=1, neg = 0 0413: dt=32.000000, rms=0.454 (0.269%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=1, neg = 0 0414: dt=32.000000, rms=0.453 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 10 iterations, nbhd size=1, neg = 0 0415: dt=32.000000, rms=0.452 (0.177%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 12 iterations, nbhd size=1, neg = 0 0416: dt=32.000000, rms=0.451 (0.259%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 10 iterations, nbhd size=1, neg = 0 0417: dt=32.000000, rms=0.450 (0.236%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 13 iterations, nbhd size=1, neg = 0 0418: dt=32.000000, rms=0.449 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 15 iterations, nbhd size=1, neg = 0 0419: dt=32.000000, rms=0.449 (0.085%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 13 iterations, nbhd size=1, neg = 0 0420: dt=32.000000, rms=0.448 (0.203%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 13 iterations, nbhd size=1, neg = 0 0421: dt=32.000000, rms=0.447 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 13 iterations, nbhd size=1, neg = 0 0422: dt=32.000000, rms=0.447 (0.058%), neg=0, invalid=762 0423: dt=11.200000, rms=0.447 (0.053%), neg=0, invalid=762 0424: dt=11.200000, rms=0.447 (0.056%), neg=0, invalid=762 0425: dt=11.200000, rms=0.447 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=11.200000, rms=0.446 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0427: dt=11.200000, rms=0.446 (0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0428: dt=75.962617, rms=0.442 (0.985%), neg=0, invalid=762 0429: dt=25.600000, rms=0.441 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0430: dt=44.800000, rms=0.441 (0.098%), neg=0, invalid=762 0431: dt=44.800000, rms=0.441 (-0.061%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0432: dt=3.456000, rms=0.451 (0.141%), neg=0, invalid=762 0433: dt=1.008000, rms=0.450 (0.052%), neg=0, invalid=762 0434: dt=1.008000, rms=0.450 (0.004%), neg=0, invalid=762 0435: dt=1.008000, rms=0.450 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 0436: dt=8.533333, rms=0.449 (0.374%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0437: dt=10.533333, rms=0.448 (0.154%), neg=0, invalid=762 0438: dt=10.533333, rms=0.448 (0.101%), neg=0, invalid=762 0439: dt=10.533333, rms=0.448 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0440: dt=10.533333, rms=0.447 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 13 iterations, nbhd size=1, neg = 0 0441: dt=10.533333, rms=0.446 (0.276%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 12 iterations, nbhd size=1, neg = 0 0442: dt=10.533333, rms=0.443 (0.621%), neg=0, invalid=762 iter 0, gcam->neg = 62 after 12 iterations, nbhd size=1, neg = 0 0443: dt=10.533333, rms=0.440 (0.698%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 19 iterations, nbhd size=1, neg = 0 0444: dt=10.533333, rms=0.438 (0.453%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 19 iterations, nbhd size=1, neg = 0 0445: dt=10.533333, rms=0.438 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 63 after 14 iterations, nbhd size=1, neg = 0 0446: dt=10.533333, rms=0.438 (-0.019%), neg=0, invalid=762 0447: dt=0.252000, rms=0.438 (0.000%), neg=0, invalid=762 0448: dt=0.011250, rms=0.438 (0.000%), neg=0, invalid=762 0449: dt=0.000000, rms=0.438 (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=0.445, neg=0, invalid=762 0450: dt=0.000000, rms=0.444 (0.095%), neg=0, invalid=762 0451: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=762 0452: dt=0.000000, rms=0.444 (0.095%), neg=0, invalid=762 0453: dt=0.000000, rms=0.444 (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=0.433, neg=0, invalid=762 iter 0, gcam->neg = 866 after 17 iterations, nbhd size=1, neg = 0 0454: dt=1.873068, rms=0.410 (5.512%), neg=0, invalid=762 0455: dt=0.000013, rms=0.409 (0.027%), neg=0, invalid=762 0456: dt=0.000013, rms=0.409 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0457: dt=0.064000, rms=0.409 (0.167%), neg=0, invalid=762 0458: dt=0.000000, rms=0.409 (0.001%), neg=0, invalid=762 0459: dt=0.050000, rms=0.409 (-0.017%), 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=0.398, neg=0, invalid=762 0460: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0461: dt=27.744000, rms=0.398 (0.003%), neg=0, invalid=762 0462: dt=0.006773, rms=0.398 (0.000%), neg=0, invalid=762 0463: dt=0.006773, rms=0.398 (-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=0.398, neg=0, invalid=762 0464: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0465: dt=36.288000, rms=0.398 (0.031%), neg=0, invalid=762 0466: dt=62.208000, rms=0.398 (0.023%), neg=0, invalid=762 0467: dt=62.208000, rms=0.398 (0.024%), neg=0, invalid=762 0468: dt=62.208000, rms=0.398 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0469: dt=62.208000, rms=0.398 (0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=762 0470: dt=9.600000, rms=0.398 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0471: dt=2.800000, rms=0.398 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0472: dt=2.800000, rms=0.398 (0.002%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0473: dt=2.800000, rms=0.398 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 iter 0, gcam->neg = 15 after 11 iterations, nbhd size=1, neg = 0 0474: dt=97.417450, rms=0.395 (0.825%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0475: dt=24.808989, rms=0.394 (0.180%), neg=0, invalid=762 0476: dt=24.808989, rms=0.394 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0477: dt=24.808989, rms=0.394 (0.068%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0478: dt=24.808989, rms=0.393 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0479: dt=24.808989, rms=0.393 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 1 iterations, nbhd size=0, neg = 0 0480: dt=24.808989, rms=0.392 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0481: dt=24.808989, rms=0.391 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 8 iterations, nbhd size=1, neg = 0 0482: dt=24.808989, rms=0.391 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 2 iterations, nbhd size=0, neg = 0 0483: dt=24.808989, rms=0.390 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0484: dt=24.808989, rms=0.390 (0.052%), neg=0, invalid=762 0485: dt=44.800000, rms=0.390 (0.038%), neg=0, invalid=762 0486: dt=44.800000, rms=0.390 (-0.032%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0487: dt=1.008000, rms=0.394 (0.005%), neg=0, invalid=762 0488: dt=0.252000, rms=0.394 (0.000%), neg=0, invalid=762 0489: dt=0.252000, rms=0.394 (0.000%), neg=0, invalid=762 0490: dt=0.252000, rms=0.394 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=0, neg = 0 0491: dt=8.936170, rms=0.393 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0492: dt=14.750000, rms=0.393 (0.042%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0493: dt=14.750000, rms=0.393 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0494: dt=14.750000, rms=0.392 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 17 iterations, nbhd size=1, neg = 0 0495: dt=14.750000, rms=0.391 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 60 after 14 iterations, nbhd size=1, neg = 0 0496: dt=14.750000, rms=0.391 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 117 after 15 iterations, nbhd size=1, neg = 0 0497: dt=14.750000, rms=0.390 (0.184%), neg=0, invalid=762 iter 0, gcam->neg = 134 after 19 iterations, nbhd size=1, neg = 0 0498: dt=14.750000, rms=0.390 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 126 after 20 iterations, nbhd size=1, neg = 0 0499: dt=14.750000, rms=0.390 (-0.011%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 15 iterations, nbhd size=1, neg = 0 0500: dt=9.216000, rms=0.390 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 5 iterations, nbhd size=0, neg = 0 0501: dt=11.294118, rms=0.390 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 0502: dt=0.000050, rms=0.395 (0.000%), neg=0, invalid=762 0503: dt=0.000000, rms=0.395 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 0504: dt=0.000000, rms=0.395 (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=0.386, neg=0, invalid=762 iter 0, gcam->neg = 611 after 17 iterations, nbhd size=1, neg = 0 0505: dt=1.130806, rms=0.378 (2.016%), neg=0, invalid=762 0506: dt=0.000023, rms=0.378 (0.000%), neg=0, invalid=762 0507: dt=0.000023, rms=0.378 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.378, neg=0, invalid=762 0508: dt=0.096000, rms=0.378 (0.044%), neg=0, invalid=762 0509: dt=0.080000, rms=0.378 (0.014%), neg=0, invalid=762 0510: dt=0.080000, rms=0.378 (0.008%), neg=0, invalid=762 0511: dt=0.080000, rms=0.378 (-0.018%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 17 minutes and 10 seconds. mri_ca_register utimesec 4606.916642 mri_ca_register stimesec 4.746278 mri_ca_register ru_maxrss 1338984 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5132775 mri_ca_register ru_majflt 9 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1664 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 3901 mri_ca_register ru_nivcsw 371609 FSRUNTIME@ mri_ca_register 1.2860 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu Aug 5 02:09:38 CST 2021 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/BAW/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname bogon machine x86_64 setenv SUBJECTS_DIR /media/sf_T1/recon cd /media/sf_T1/recon/demo3/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /home/BAW/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 /home/BAW/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 6.12 Atlas used for the 3D morph was /home/BAW/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 = 0.16154 (19) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2073 voxels, overlap=0.850) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2073 voxels, peak = 20), gca=20.3 gca peak = 0.17677 (13) mri peak = 0.15187 (19) Right_Lateral_Ventricle (43): linear fit = 1.36 x + 0.0 (1712 voxels, overlap=0.449) Right_Lateral_Ventricle (43): linear fit = 1.36 x + 0.0 (1712 voxels, peak = 18), gca=17.6 gca peak = 0.28129 (95) mri peak = 0.12094 (104) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (659 voxels, overlap=0.105) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (659 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.11470 (105) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (619 voxels, overlap=0.060) Left_Pallidum (13): linear fit = 1.11 x + 0.0 (619 voxels, peak = 106), gca=106.1 gca peak = 0.24553 (55) mri peak = 0.11660 (72) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (835 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (835 voxels, peak = 70), gca=69.6 gca peak = 0.30264 (59) mri peak = 0.10913 (73) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (898 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (898 voxels, peak = 75), gca=75.2 gca peak = 0.07580 (103) mri peak = 0.11215 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (25561 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (25561 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.10092 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (24657 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (24657 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.05297 (73) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (24864 voxels, overlap=0.052) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (24864 voxels, peak = 72), gca=71.6 gca peak = 0.11620 (58) mri peak = 0.05629 (72) Right_Cerebral_Cortex (42): linear fit = 1.22 x + 0.0 (22153 voxels, overlap=0.142) Right_Cerebral_Cortex (42): linear fit = 1.22 x + 0.0 (22153 voxels, peak = 70), gca=70.5 gca peak = 0.30970 (66) mri peak = 0.11723 (83) Right_Caudate (50): linear fit = 1.24 x + 0.0 (853 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.24 x + 0.0 (853 voxels, peak = 82), gca=81.5 gca peak = 0.15280 (69) mri peak = 0.14268 (86) Left_Caudate (11): linear fit = 1.16 x + 0.0 (721 voxels, overlap=0.017) Left_Caudate (11): linear fit = 1.16 x + 0.0 (721 voxels, peak = 80), gca=80.4 gca peak = 0.13902 (56) mri peak = 0.06059 (69) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (23884 voxels, overlap=0.220) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (23884 voxels, peak = 67), gca=67.5 gca peak = 0.14777 (55) mri peak = 0.06091 (67) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19544 voxels, overlap=0.321) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (19544 voxels, peak = 66), gca=65.7 gca peak = 0.16765 (84) mri peak = 0.14537 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5114 voxels, overlap=0.087) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5114 voxels, peak = 91), gca=91.1 gca peak = 0.18739 (84) mri peak = 0.08868 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (9871 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (9871 voxels, peak = 91), gca=91.1 gca peak = 0.29869 (57) mri peak = 0.11275 (76) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (408 voxels, overlap=0.044) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (408 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.12474 (72) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (469 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.26 x + 0.0 (469 voxels, peak = 72), gca=72.1 gca peak = 0.11131 (90) mri peak = 0.07677 (91) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3618 voxels, overlap=0.788) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3618 voxels, peak = 93), gca=93.1 gca peak = 0.11793 (83) mri peak = 0.07723 (91) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3739 voxels, overlap=0.607) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3739 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.11024 (93) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1340 voxels, overlap=0.024) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1340 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.09482 (88) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1566 voxels, overlap=0.238) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1566 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.07231 (88) Brain_Stem (16): linear fit = 1.13 x + 0.0 (11673 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.13 x + 0.0 (11673 voxels, peak = 89), gca=88.5 gca peak = 0.12631 (89) mri peak = 0.08000 (101) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1235 voxels, overlap=0.214) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1235 voxels, peak = 102), gca=101.9 gca peak = 0.14500 (87) mri peak = 0.09238 (101) Left_VentralDC (28): linear fit = 1.15 x + 0.0 (1200 voxels, overlap=0.011) Left_VentralDC (28): linear fit = 1.15 x + 0.0 (1200 voxels, peak = 100), gca=100.5 gca peak = 0.14975 (24) mri peak = 0.18848 (23) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (93 voxels, overlap=0.785) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (93 voxels, peak = 22), gca=22.4 gca peak = 0.19357 (14) mri peak = 0.11529 (21) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (130 voxels, overlap=0.490) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (130 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 1.26 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.14 x + 0.0 Left_Pallidum too bright - rescaling by 0.965 (from 1.105) to 102.4 (was 106.1) Right_Pallidum too bright - rescaling by 1.003 (from 1.075) to 102.4 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15157 (21) mri peak = 0.16154 (19) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2073 voxels, overlap=0.832) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (2073 voxels, peak = 20), gca=19.6 gca peak = 0.15984 (17) mri peak = 0.15187 (19) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1712 voxels, overlap=0.617) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1712 voxels, peak = 17), gca=16.6 gca peak = 0.28251 (103) mri peak = 0.12094 (104) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.001) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (659 voxels, peak = 104), gca=103.5 gca peak = 0.16016 (103) mri peak = 0.11470 (105) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (619 voxels, overlap=0.860) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (619 voxels, peak = 106), gca=105.6 gca peak = 0.21932 (70) mri peak = 0.11660 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (835 voxels, overlap=0.858) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (835 voxels, peak = 70), gca=70.0 gca peak = 0.24466 (72) mri peak = 0.10913 (73) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (898 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (898 voxels, peak = 71), gca=70.9 gca peak = 0.07811 (104) mri peak = 0.11215 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (25561 voxels, overlap=0.707) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (25561 voxels, peak = 104), gca=104.0 gca peak = 0.07687 (107) mri peak = 0.10092 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (24657 voxels, overlap=0.722) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (24657 voxels, peak = 107), gca=107.0 gca peak = 0.07923 (70) mri peak = 0.05297 (73) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (24864 voxels, overlap=0.899) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (24864 voxels, peak = 70), gca=70.0 gca peak = 0.09497 (70) mri peak = 0.05629 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22153 voxels, overlap=0.955) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22153 voxels, peak = 70), gca=70.0 gca peak = 0.22967 (81) mri peak = 0.11723 (83) Right_Caudate (50): linear fit = 1.01 x + 0.0 (853 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (853 voxels, peak = 82), gca=82.2 gca peak = 0.14762 (90) mri peak = 0.14268 (86) Left_Caudate (11): linear fit = 1.00 x + 0.0 (721 voxels, overlap=0.935) Left_Caudate (11): linear fit = 1.00 x + 0.0 (721 voxels, peak = 90), gca=90.0 gca peak = 0.12011 (67) mri peak = 0.06059 (69) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23884 voxels, overlap=0.986) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23884 voxels, peak = 67), gca=67.0 gca peak = 0.12226 (66) mri peak = 0.06091 (67) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (19544 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (19544 voxels, peak = 65), gca=65.0 gca peak = 0.15554 (91) mri peak = 0.14537 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5114 voxels, overlap=0.848) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5114 voxels, peak = 91), gca=90.5 gca peak = 0.14595 (91) mri peak = 0.08868 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9871 voxels, overlap=0.971) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9871 voxels, peak = 91), gca=90.5 gca peak = 0.29104 (75) mri peak = 0.11275 (76) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (408 voxels, overlap=0.978) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (408 voxels, peak = 75), gca=75.0 gca peak = 0.29800 (72) mri peak = 0.12474 (72) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (469 voxels, overlap=0.994) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (469 voxels, peak = 71), gca=70.9 gca peak = 0.10722 (91) mri peak = 0.07677 (91) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3618 voxels, overlap=0.891) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3618 voxels, peak = 91), gca=91.0 gca peak = 0.09511 (89) mri peak = 0.07723 (91) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3739 voxels, overlap=0.963) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3739 voxels, peak = 88), gca=87.7 gca peak = 0.07366 (87) mri peak = 0.11024 (93) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1340 voxels, overlap=0.749) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1340 voxels, peak = 87), gca=86.6 gca peak = 0.08246 (88) mri peak = 0.09482 (88) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1566 voxels, overlap=0.823) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1566 voxels, peak = 89), gca=89.3 gca peak = 0.07615 (89) mri peak = 0.07231 (88) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11673 voxels, overlap=0.820) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11673 voxels, peak = 88), gca=87.7 gca peak = 0.11683 (102) mri peak = 0.08000 (101) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1235 voxels, overlap=0.839) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1235 voxels, peak = 102), gca=102.0 gca peak = 0.14850 (99) mri peak = 0.09238 (101) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1200 voxels, overlap=0.857) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1200 voxels, peak = 100), gca=100.5 gca peak = 0.21284 (24) mri peak = 0.18848 (23) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (93 voxels, overlap=0.857) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (93 voxels, peak = 22), gca=22.4 gca peak = 0.16542 (20) mri peak = 0.11529 (21) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (130 voxels, overlap=0.775) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (130 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16048 (41) gca peak Left_Thalamus = 0.36646 (105) gca peak CSF = 0.22895 (41) gca peak Left_Accumbens_area = 0.54207 (72) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.19572 (29) gca peak Right_Accumbens_area = 0.29890 (80) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14511 (37) gca peak Fifth_Ventricle = 0.53990 (36) gca peak WM_hypointensities = 0.08694 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.42743 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.98 x + 0.0 Left_Pallidum too bright - rescaling by 0.969 (from 1.025) to 102.3 (was 105.6) Right_Pallidum too bright - rescaling by 0.989 (from 1.005) to 102.3 (was 103.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 47605 voxels changed in iteration 0 of unlikely voxel relabeling 170 voxels changed in iteration 1 of unlikely voxel relabeling 14 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 38353 gm and wm labels changed (%33 to gray, %67 to white out of all changed labels) 311 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 55277 changed. image ll: -2.089, PF=0.500 pass 2: 13550 changed. image ll: -2.088, PF=0.500 pass 3: 3831 changed. 34944 voxels changed in iteration 0 of unlikely voxel relabeling 261 voxels changed in iteration 1 of unlikely voxel relabeling 29 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5605 voxels changed in iteration 0 of unlikely voxel relabeling 121 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 4558 voxels changed in iteration 0 of unlikely voxel relabeling 40 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 3990 voxels changed in iteration 0 of unlikely voxel relabeling 33 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 1561.970544 mri_ca_label stimesec 1.153824 mri_ca_label ru_maxrss 2125700 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 628177 mri_ca_label ru_majflt 9 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1584 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 1714 mri_ca_label ru_nivcsw 124317 auto-labeling took 26 minutes and 9 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/sf_T1/recon/demo3/mri/transforms/cc_up.lta demo3 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /media/sf_T1/recon/demo3/mri/transforms/cc_up.lta reading aseg from /media/sf_T1/recon/demo3/mri/aseg.auto_noCCseg.mgz reading norm from /media/sf_T1/recon/demo3/mri/norm.mgz 30285 voxels in left wm, 43793 in right wm, xrange [121, 132] searching rotation angles z=[-3 11], y=[-6 8] searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.8 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.3 searching scale 1 Z rot 10.5 searching scale 1 Z rot 10.8 searching scale 1 Z rot 11.0 global minimum found at slice 127.3, rotations (1.27, 4.26) final transformation (x=127.3, yr=1.272, zr=4.256): 0.99700 -0.07421 0.02215 6.78560; 0.07419 0.99724 0.00165 5.66755; -0.02221 0.00000 0.99975 9.85683; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 113 121 eigenvectors: -0.00006 0.00181 1.00000; 0.06814 -0.99767 0.00181; 0.99768 0.06814 -0.00006; error in mid anterior detected - correcting... writing aseg with callosum to /media/sf_T1/recon/demo3/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Thu Aug 5 02:36:11 CST 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 5 02:36:11 CST 2021 /media/sf_T1/recon/demo3/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... 383 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 78 (78), valley at 50 (50) csf peak at 33, setting threshold to 63 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 77 (77), valley at 51 (51) csf peak at 33, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 30 seconds. #-------------------------------------------- #@# Mask BFS Thu Aug 5 02:37:43 CST 2021 /media/sf_T1/recon/demo3/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1425171 voxels in mask (pct= 8.49) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Aug 5 02:37:43 CST 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 (102.0): 102.2 +- 7.0 [79.0 --> 125.0] GM (74.0) : 72.2 +- 11.6 [30.0 --> 95.0] setting bottom of white matter range to 83.8 setting top of gray matter range to 95.4 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... 5180 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4665 filled 155 bright non-wm voxels segmented. 2954 diagonally connected voxels added... white matter segmentation took 0.8 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 0.23 minutes reading wm segmentation from wm.seg.mgz... 282 voxels added to wm to prevent paths from MTL structures to cortex 3633 additional wm voxels added 0 additional wm voxels added SEG EDIT: 47362 voxels turned on, 42502 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 103 new 103 115,126,128 old 103 new 103 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 11 found - 11 modified | TOTAL: 23 pass 2 (xy-): 0 found - 11 modified | TOTAL: 23 pass 1 (yz+): 17 found - 17 modified | TOTAL: 40 pass 2 (yz+): 0 found - 17 modified | TOTAL: 40 pass 1 (yz-): 17 found - 17 modified | TOTAL: 57 pass 2 (yz-): 0 found - 17 modified | TOTAL: 57 pass 1 (xz+): 18 found - 18 modified | TOTAL: 75 pass 2 (xz+): 0 found - 18 modified | TOTAL: 75 pass 1 (xz-): 22 found - 22 modified | TOTAL: 97 pass 2 (xz-): 0 found - 22 modified | TOTAL: 97 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 15 found - 15 modified | TOTAL: 33 pass 2 (+++): 0 found - 15 modified | TOTAL: 33 pass 1 (+++): 14 found - 14 modified | TOTAL: 47 pass 2 (+++): 0 found - 14 modified | TOTAL: 47 pass 1 (+++): 24 found - 24 modified | TOTAL: 71 pass 2 (+++): 0 found - 24 modified | TOTAL: 71 Iteration Number : 1 pass 1 (++): 79 found - 79 modified | TOTAL: 79 pass 2 (++): 0 found - 79 modified | TOTAL: 79 pass 1 (+-): 101 found - 101 modified | TOTAL: 180 pass 2 (+-): 0 found - 101 modified | TOTAL: 180 pass 1 (--): 47 found - 47 modified | TOTAL: 227 pass 2 (--): 0 found - 47 modified | TOTAL: 227 pass 1 (-+): 86 found - 86 modified | TOTAL: 313 pass 2 (-+): 0 found - 86 modified | TOTAL: 313 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 5 found - 5 modified | TOTAL: 12 pass 2 (xy-): 0 found - 5 modified | TOTAL: 12 pass 1 (yz+): 0 found - 0 modified | TOTAL: 12 pass 1 (yz-): 8 found - 8 modified | TOTAL: 20 pass 2 (yz-): 0 found - 8 modified | TOTAL: 20 pass 1 (xz+): 4 found - 4 modified | TOTAL: 24 pass 2 (xz+): 0 found - 4 modified | TOTAL: 24 pass 1 (xz-): 7 found - 7 modified | TOTAL: 31 pass 2 (xz-): 0 found - 7 modified | TOTAL: 31 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 4 found - 4 modified | TOTAL: 6 pass 2 (--): 0 found - 4 modified | TOTAL: 6 pass 1 (-+): 3 found - 3 modified | TOTAL: 9 pass 2 (-+): 0 found - 3 modified | TOTAL: 9 Iteration Number : 3 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+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 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 : 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 (++): 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 = 524 (out of 442083: 0.118530) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Aug 5 02:38:47 CST 2021 /media/sf_T1/recon/demo3/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 1.05062 -0.07876 -0.00164 2.38364; 0.09568 1.06968 0.10521 -43.47974; 0.00209 -0.10056 1.14590 -18.42108; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05062 -0.07876 -0.00164 2.38364; 0.09568 1.06968 0.10521 -43.47974; 0.00209 -0.10056 1.14590 -18.42108; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 966 (min = 350, max = 1400), aspect = 0.39 (min = 0.10, max = 0.75) no need to search using seed (127, 112, 93), TAL = (1.0, -35.0, 16.0) talairach voxel to voxel transform 0.94554 0.06915 -0.00500 0.66057; -0.08368 0.92074 -0.08466 38.67352; -0.00907 0.08067 0.86526 19.46832; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 112, 93) --> (1.0, -35.0, 16.0) done. writing output to filled.mgz... filling took 0.3 minutes talairach cc position changed to (1.00, -35.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -35.00, 16.00) SRC: (111.00, 124.80, 107.98) search lh wm seed point around talairach space (-17.00, -35.00, 16.00), SRC: (145.04, 121.79, 107.66) 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 Thu Aug 5 02:39:05 CST 2021 /media/sf_T1/recon/demo3/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (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-): 5 found - 5 modified | TOTAL: 7 pass 2 (xz-): 0 found - 5 modified | TOTAL: 7 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 (+-): 0 found - 0 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 = 8 (out of 212799: 0.003759) 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 60: 2702 vertices, 2879 faces slice 70: 8848 vertices, 9108 faces slice 80: 17345 vertices, 17646 faces slice 90: 26845 vertices, 27179 faces slice 100: 36575 vertices, 36895 faces slice 110: 47487 vertices, 47865 faces slice 120: 59194 vertices, 59584 faces slice 130: 70997 vertices, 71412 faces slice 140: 81584 vertices, 81935 faces slice 150: 90575 vertices, 90900 faces slice 160: 97939 vertices, 98204 faces slice 170: 104208 vertices, 104428 faces slice 180: 109731 vertices, 109931 faces slice 190: 113814 vertices, 113960 faces slice 200: 114938 vertices, 114972 faces slice 210: 114938 vertices, 114972 faces slice 220: 114938 vertices, 114972 faces slice 230: 114938 vertices, 114972 faces slice 240: 114938 vertices, 114972 faces slice 250: 114938 vertices, 114972 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... 114938 voxel in cpt #1: X=-34 [v=114938,e=344916,f=229944] located at (-26.817833, -9.545094, 7.697898) For the whole surface: X=-34 [v=114938,e=344916,f=229944] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Aug 5 02:39:08 CST 2021 /media/sf_T1/recon/demo3/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 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 = 6 (out of 210931: 0.002845) 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 60: 1361 vertices, 1461 faces slice 70: 6630 vertices, 6831 faces slice 80: 14795 vertices, 15118 faces slice 90: 25020 vertices, 25416 faces slice 100: 35735 vertices, 36055 faces slice 110: 46030 vertices, 46406 faces slice 120: 58988 vertices, 59375 faces slice 130: 70757 vertices, 71166 faces slice 140: 81095 vertices, 81446 faces slice 150: 89987 vertices, 90288 faces slice 160: 97469 vertices, 97745 faces slice 170: 104296 vertices, 104555 faces slice 180: 109893 vertices, 110114 faces slice 190: 114536 vertices, 114718 faces slice 200: 115848 vertices, 115896 faces slice 210: 115848 vertices, 115896 faces slice 220: 115848 vertices, 115896 faces slice 230: 115848 vertices, 115896 faces slice 240: 115848 vertices, 115896 faces slice 250: 115848 vertices, 115896 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... 115848 voxel in cpt #1: X=-48 [v=115848,e=347688,f=231792] located at (27.565689, -7.934768, 5.032482) For the whole surface: X=-48 [v=115848,e=347688,f=231792] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Aug 5 02:39:10 CST 2021 /media/sf_T1/recon/demo3/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 Thu Aug 5 02:39:12 CST 2021 /media/sf_T1/recon/demo3/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 Thu Aug 5 02:39:14 CST 2021 /media/sf_T1/recon/demo3/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 42.5 mm, total surface area = 60478 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.046 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 14.069861 mris_inflate stimesec 0.066989 mris_inflate ru_maxrss 148152 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19272 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1016 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1942 mris_inflate ru_nivcsw 1151 #-------------------------------------------- #@# Inflation1 rh Thu Aug 5 02:39:28 CST 2021 /media/sf_T1/recon/demo3/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 42.1 mm, total surface area = 60833 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.154 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 13.976875 mris_inflate stimesec 0.079987 mris_inflate ru_maxrss 149372 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19584 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1962 mris_inflate ru_nivcsw 1134 #-------------------------------------------- #@# QSphere lh Thu Aug 5 02:39:42 CST 2021 /media/sf_T1/recon/demo3/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 1.08 +- 0.57 (0.00-->7.38) (max @ vno 39537 --> 40577) face area 0.03 +- 0.04 (-0.07-->0.74) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.349... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.301, avgs=0 005/300: dt: 0.9000, rms radial error=176.043, avgs=0 010/300: dt: 0.9000, rms radial error=175.488, avgs=0 015/300: dt: 0.9000, rms radial error=174.759, avgs=0 020/300: dt: 0.9000, rms radial error=173.929, avgs=0 025/300: dt: 0.9000, rms radial error=173.042, avgs=0 030/300: dt: 0.9000, rms radial error=172.123, avgs=0 035/300: dt: 0.9000, rms radial error=171.187, avgs=0 040/300: dt: 0.9000, rms radial error=170.243, avgs=0 045/300: dt: 0.9000, rms radial error=169.297, avgs=0 050/300: dt: 0.9000, rms radial error=168.351, avgs=0 055/300: dt: 0.9000, rms radial error=167.407, avgs=0 060/300: dt: 0.9000, rms radial error=166.467, avgs=0 065/300: dt: 0.9000, rms radial error=165.532, avgs=0 070/300: dt: 0.9000, rms radial error=164.601, avgs=0 075/300: dt: 0.9000, rms radial error=163.675, avgs=0 080/300: dt: 0.9000, rms radial error=162.755, avgs=0 085/300: dt: 0.9000, rms radial error=161.839, avgs=0 090/300: dt: 0.9000, rms radial error=160.929, avgs=0 095/300: dt: 0.9000, rms radial error=160.024, avgs=0 100/300: dt: 0.9000, rms radial error=159.124, avgs=0 105/300: dt: 0.9000, rms radial error=158.228, avgs=0 110/300: dt: 0.9000, rms radial error=157.338, avgs=0 115/300: dt: 0.9000, rms radial error=156.453, avgs=0 120/300: dt: 0.9000, rms radial error=155.572, avgs=0 125/300: dt: 0.9000, rms radial error=154.696, avgs=0 130/300: dt: 0.9000, rms radial error=153.825, avgs=0 135/300: dt: 0.9000, rms radial error=152.959, avgs=0 140/300: dt: 0.9000, rms radial error=152.098, avgs=0 145/300: dt: 0.9000, rms radial error=151.241, avgs=0 150/300: dt: 0.9000, rms radial error=150.390, avgs=0 155/300: dt: 0.9000, rms radial error=149.543, avgs=0 160/300: dt: 0.9000, rms radial error=148.701, avgs=0 165/300: dt: 0.9000, rms radial error=147.863, avgs=0 170/300: dt: 0.9000, rms radial error=147.030, avgs=0 175/300: dt: 0.9000, rms radial error=146.201, avgs=0 180/300: dt: 0.9000, rms radial error=145.377, avgs=0 185/300: dt: 0.9000, rms radial error=144.558, avgs=0 190/300: dt: 0.9000, rms radial error=143.743, avgs=0 195/300: dt: 0.9000, rms radial error=142.933, avgs=0 200/300: dt: 0.9000, rms radial error=142.127, avgs=0 205/300: dt: 0.9000, rms radial error=141.325, avgs=0 210/300: dt: 0.9000, rms radial error=140.528, avgs=0 215/300: dt: 0.9000, rms radial error=139.735, avgs=0 220/300: dt: 0.9000, rms radial error=138.947, avgs=0 225/300: dt: 0.9000, rms radial error=138.164, avgs=0 230/300: dt: 0.9000, rms radial error=137.384, avgs=0 235/300: dt: 0.9000, rms radial error=136.609, avgs=0 240/300: dt: 0.9000, rms radial error=135.838, avgs=0 245/300: dt: 0.9000, rms radial error=135.071, avgs=0 250/300: dt: 0.9000, rms radial error=134.309, avgs=0 255/300: dt: 0.9000, rms radial error=133.551, avgs=0 260/300: dt: 0.9000, rms radial error=132.797, avgs=0 265/300: dt: 0.9000, rms radial error=132.048, avgs=0 270/300: dt: 0.9000, rms radial error=131.303, avgs=0 275/300: dt: 0.9000, rms radial error=130.562, avgs=0 280/300: dt: 0.9000, rms radial error=129.825, avgs=0 285/300: dt: 0.9000, rms radial error=129.092, avgs=0 290/300: dt: 0.9000, rms radial error=128.363, avgs=0 295/300: dt: 0.9000, rms radial error=127.639, avgs=0 300/300: dt: 0.9000, rms radial error=126.918, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12865.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 1934.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00034 epoch 3 (K=160.0), pass 1, starting sse = 157.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01025 epoch 4 (K=640.0), pass 1, starting sse = 7.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/14 = 0.00695 final distance error %22.85 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 90.882183 mris_sphere stimesec 0.097985 mris_sphere ru_maxrss 148332 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19312 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1216 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1953 mris_sphere ru_nivcsw 7220 FSRUNTIME@ mris_sphere 0.0253 hours 1 threads #-------------------------------------------- #@# QSphere rh Thu Aug 5 02:41:14 CST 2021 /media/sf_T1/recon/demo3/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 1.08 +- 0.58 (0.00-->7.53) (max @ vno 40535 --> 41492) face area 0.03 +- 0.04 (-0.19-->0.89) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.352... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.951, avgs=0 005/300: dt: 0.9000, rms radial error=175.693, avgs=0 010/300: dt: 0.9000, rms radial error=175.139, avgs=0 015/300: dt: 0.9000, rms radial error=174.410, avgs=0 020/300: dt: 0.9000, rms radial error=173.580, avgs=0 025/300: dt: 0.9000, rms radial error=172.694, avgs=0 030/300: dt: 0.9000, rms radial error=171.777, avgs=0 035/300: dt: 0.9000, rms radial error=170.843, avgs=0 040/300: dt: 0.9000, rms radial error=169.901, avgs=0 045/300: dt: 0.9000, rms radial error=168.957, avgs=0 050/300: dt: 0.9000, rms radial error=168.014, avgs=0 055/300: dt: 0.9000, rms radial error=167.073, avgs=0 060/300: dt: 0.9000, rms radial error=166.136, avgs=0 065/300: dt: 0.9000, rms radial error=165.203, avgs=0 070/300: dt: 0.9000, rms radial error=164.275, avgs=0 075/300: dt: 0.9000, rms radial error=163.352, avgs=0 080/300: dt: 0.9000, rms radial error=162.434, avgs=0 085/300: dt: 0.9000, rms radial error=161.521, avgs=0 090/300: dt: 0.9000, rms radial error=160.613, avgs=0 095/300: dt: 0.9000, rms radial error=159.710, avgs=0 100/300: dt: 0.9000, rms radial error=158.811, avgs=0 105/300: dt: 0.9000, rms radial error=157.918, avgs=0 110/300: dt: 0.9000, rms radial error=157.029, avgs=0 115/300: dt: 0.9000, rms radial error=156.145, avgs=0 120/300: dt: 0.9000, rms radial error=155.267, avgs=0 125/300: dt: 0.9000, rms radial error=154.393, avgs=0 130/300: dt: 0.9000, rms radial error=153.524, avgs=0 135/300: dt: 0.9000, rms radial error=152.660, avgs=0 140/300: dt: 0.9000, rms radial error=151.801, avgs=0 145/300: dt: 0.9000, rms radial error=150.946, avgs=0 150/300: dt: 0.9000, rms radial error=150.096, avgs=0 155/300: dt: 0.9000, rms radial error=149.251, avgs=0 160/300: dt: 0.9000, rms radial error=148.410, avgs=0 165/300: dt: 0.9000, rms radial error=147.574, avgs=0 170/300: dt: 0.9000, rms radial error=146.742, avgs=0 175/300: dt: 0.9000, rms radial error=145.916, avgs=0 180/300: dt: 0.9000, rms radial error=145.093, avgs=0 185/300: dt: 0.9000, rms radial error=144.275, avgs=0 190/300: dt: 0.9000, rms radial error=143.462, avgs=0 195/300: dt: 0.9000, rms radial error=142.653, avgs=0 200/300: dt: 0.9000, rms radial error=141.849, avgs=0 205/300: dt: 0.9000, rms radial error=141.049, avgs=0 210/300: dt: 0.9000, rms radial error=140.254, avgs=0 215/300: dt: 0.9000, rms radial error=139.462, avgs=0 220/300: dt: 0.9000, rms radial error=138.676, avgs=0 225/300: dt: 0.9000, rms radial error=137.893, avgs=0 230/300: dt: 0.9000, rms radial error=137.115, avgs=0 235/300: dt: 0.9000, rms radial error=136.342, avgs=0 240/300: dt: 0.9000, rms radial error=135.573, avgs=0 245/300: dt: 0.9000, rms radial error=134.808, avgs=0 250/300: dt: 0.9000, rms radial error=134.047, avgs=0 255/300: dt: 0.9000, rms radial error=133.290, avgs=0 260/300: dt: 0.9000, rms radial error=132.538, avgs=0 265/300: dt: 0.9000, rms radial error=131.790, avgs=0 270/300: dt: 0.9000, rms radial error=131.046, avgs=0 275/300: dt: 0.9000, rms radial error=130.307, avgs=0 280/300: dt: 0.9000, rms radial error=129.571, avgs=0 285/300: dt: 0.9000, rms radial error=128.840, avgs=0 290/300: dt: 0.9000, rms radial error=128.113, avgs=0 295/300: dt: 0.9000, rms radial error=127.389, avgs=0 300/300: dt: 0.9000, rms radial error=126.670, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12930.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 1933.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00036 epoch 3 (K=160.0), pass 1, starting sse = 157.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/13 = 0.01151 epoch 4 (K=640.0), pass 1, starting sse = 6.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/15 = 0.00988 final distance error %22.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 95.797436 mris_sphere stimesec 0.080987 mris_sphere ru_maxrss 149564 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19628 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1983 mris_sphere ru_nivcsw 7631 FSRUNTIME@ mris_sphere 0.0267 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Thu Aug 5 02:42:50 CST 2021 /media/sf_T1/recon/demo3/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu Aug 5 02:42:50 CST 2021 /media/sf_T1/recon/demo3/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu Aug 5 02:42:50 CST 2021 mris_fix_topology -rusage /media/sf_T1/recon/demo3/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 demo3 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=-34 (nv=114938, nf=229944, ne=344916, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 2600 ambiguous faces found in tessellation segmenting defects... 27 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 21 into 20 25 defects to be corrected 0 vertices coincident reading input surface /media/sf_T1/recon/demo3/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9720 (-4.4860) -vertex loglikelihood: -6.0687 (-3.0343) -normal dot loglikelihood: -3.6588 (-3.6588) -quad curv loglikelihood: -6.1502 (-3.0751) Total Loglikelihood : -24.8496 CORRECTING DEFECT 0 (vertices=18, convex hull=61, v0=7479) After retessellation of defect 0 (v0=7479), euler #=-23 (113300,339179,225856) : difference with theory (-22) = 1 CORRECTING DEFECT 1 (vertices=121, convex hull=78, v0=9384) After retessellation of defect 1 (v0=9384), euler #=-22 (113311,339248,225915) : difference with theory (-21) = 1 CORRECTING DEFECT 2 (vertices=33, convex hull=57, v0=18948) After retessellation of defect 2 (v0=18948), euler #=-20 (113317,339290,225953) : difference with theory (-20) = 0 CORRECTING DEFECT 3 (vertices=31, convex hull=72, v0=35526) After retessellation of defect 3 (v0=35526), euler #=-19 (113335,339370,226016) : difference with theory (-19) = 0 CORRECTING DEFECT 4 (vertices=58, convex hull=59, v0=48191) After retessellation of defect 4 (v0=48191), euler #=-18 (113356,339456,226082) : difference with theory (-18) = 0 CORRECTING DEFECT 5 (vertices=29, convex hull=66, v0=48587) After retessellation of defect 5 (v0=48587), euler #=-17 (113365,339507,226125) : difference with theory (-17) = 0 CORRECTING DEFECT 6 (vertices=141, convex hull=61, v0=54518) After retessellation of defect 6 (v0=54518), euler #=-16 (113385,339590,226189) : difference with theory (-16) = 0 CORRECTING DEFECT 7 (vertices=16, convex hull=25, v0=66946) After retessellation of defect 7 (v0=66946), euler #=-15 (113391,339615,226209) : difference with theory (-15) = 0 CORRECTING DEFECT 8 (vertices=196, convex hull=77, v0=68420) After retessellation of defect 8 (v0=68420), euler #=-15 (113406,339697,226276) : difference with theory (-14) = 1 CORRECTING DEFECT 9 (vertices=75, convex hull=100, v0=68442) After retessellation of defect 9 (v0=68442), euler #=-14 (113442,339849,226393) : difference with theory (-13) = 1 CORRECTING DEFECT 10 (vertices=14, convex hull=25, v0=74892) After retessellation of defect 10 (v0=74892), euler #=-13 (113445,339867,226409) : difference with theory (-12) = 1 CORRECTING DEFECT 11 (vertices=45, convex hull=38, v0=75819) After retessellation of defect 11 (v0=75819), euler #=-12 (113451,339901,226438) : difference with theory (-11) = 1 CORRECTING DEFECT 12 (vertices=22, convex hull=44, v0=77112) After retessellation of defect 12 (v0=77112), euler #=-11 (113460,339944,226473) : difference with theory (-10) = 1 CORRECTING DEFECT 13 (vertices=151, convex hull=127, v0=77335) After retessellation of defect 13 (v0=77335), euler #=-10 (113512,340155,226633) : difference with theory (-9) = 1 CORRECTING DEFECT 14 (vertices=12, convex hull=26, v0=78393) After retessellation of defect 14 (v0=78393), euler #=-9 (113515,340173,226649) : difference with theory (-8) = 1 CORRECTING DEFECT 15 (vertices=66, convex hull=102, v0=81576) After retessellation of defect 15 (v0=81576), euler #=-8 (113540,340289,226741) : difference with theory (-7) = 1 CORRECTING DEFECT 16 (vertices=144, convex hull=52, v0=82413) After retessellation of defect 16 (v0=82413), euler #=-7 (113550,340341,226784) : difference with theory (-6) = 1 CORRECTING DEFECT 17 (vertices=80, convex hull=108, v0=85097) After retessellation of defect 17 (v0=85097), euler #=-6 (113589,340504,226909) : difference with theory (-5) = 1 CORRECTING DEFECT 18 (vertices=62, convex hull=104, v0=88757) After retessellation of defect 18 (v0=88757), euler #=-5 (113598,340576,226973) : difference with theory (-4) = 1 CORRECTING DEFECT 19 (vertices=218, convex hull=264, v0=91214) After retessellation of defect 19 (v0=91214), euler #=-3 (113716,341064,227345) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=30, convex hull=33, v0=95239) After retessellation of defect 20 (v0=95239), euler #=-2 (113723,341095,227370) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=25, convex hull=57, v0=100606) After retessellation of defect 21 (v0=100606), euler #=-1 (113733,341147,227413) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=6, convex hull=16, v0=111567) After retessellation of defect 22 (v0=111567), euler #=0 (113734,341154,227420) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=29, convex hull=32, v0=112700) After retessellation of defect 23 (v0=112700), euler #=1 (113739,341181,227443) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=28, convex hull=65, v0=114597) After retessellation of defect 24 (v0=114597), euler #=2 (113754,341256,227504) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->6.61) (max @ vno 80640 --> 86019) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->6.61) (max @ vno 80640 --> 86019) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 93 mutations (33.5%), 185 crossovers (66.5%), 76 vertices were eliminated building final representation... 1184 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113754, nf=227504, ne=341256, g=0) writing corrected surface to /media/sf_T1/recon/demo3/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 6.4 minutes 0 defective edges removing intersecting faces 000: 162 intersecting 001: 12 intersecting mris_fix_topology utimesec 383.039769 mris_fix_topology stimesec 0.174973 mris_fix_topology ru_maxrss 374268 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 48786 mris_fix_topology ru_majflt 9 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1432 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3228 mris_fix_topology ru_nivcsw 30502 FSRUNTIME@ mris_fix_topology lh 0.1068 hours 1 threads #@# Fix Topology rh Thu Aug 5 02:49:14 CST 2021 mris_fix_topology -rusage /media/sf_T1/recon/demo3/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 demo3 rh 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=-48 (nv=115848, nf=231792, ne=347688, g=25) 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 7 iterations marking ambiguous vertices... 2191 ambiguous faces found in tessellation segmenting defects... 36 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 18 into 15 -merging segment 34 into 33 34 defects to be corrected 0 vertices coincident reading input surface /media/sf_T1/recon/demo3/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9162 (-4.4581) -vertex loglikelihood: -6.0425 (-3.0213) -normal dot loglikelihood: -3.5983 (-3.5983) -quad curv loglikelihood: -6.5319 (-3.2659) Total Loglikelihood : -25.0889 CORRECTING DEFECT 0 (vertices=33, convex hull=32, v0=37198) After retessellation of defect 0 (v0=37198), euler #=-33 (114416,342484,228035) : difference with theory (-31) = 2 CORRECTING DEFECT 1 (vertices=91, convex hull=83, v0=38270) After retessellation of defect 1 (v0=38270), euler #=-32 (114449,342617,228136) : difference with theory (-30) = 2 CORRECTING DEFECT 2 (vertices=10, convex hull=23, v0=42472) After retessellation of defect 2 (v0=42472), euler #=-31 (114451,342633,228151) : difference with theory (-29) = 2 CORRECTING DEFECT 3 (vertices=90, convex hull=62, v0=44397) After retessellation of defect 3 (v0=44397), euler #=-30 (114470,342717,228217) : difference with theory (-28) = 2 CORRECTING DEFECT 4 (vertices=38, convex hull=73, v0=47171) After retessellation of defect 4 (v0=47171), euler #=-29 (114481,342778,228268) : difference with theory (-27) = 2 CORRECTING DEFECT 5 (vertices=28, convex hull=49, v0=60096) After retessellation of defect 5 (v0=60096), euler #=-28 (114490,342824,228306) : difference with theory (-26) = 2 CORRECTING DEFECT 6 (vertices=24, convex hull=44, v0=63639) After retessellation of defect 6 (v0=63639), euler #=-27 (114499,342870,228344) : difference with theory (-25) = 2 CORRECTING DEFECT 7 (vertices=65, convex hull=103, v0=64628) After retessellation of defect 7 (v0=64628), euler #=-26 (114542,343043,228475) : difference with theory (-24) = 2 CORRECTING DEFECT 8 (vertices=30, convex hull=42, v0=64755) After retessellation of defect 8 (v0=64755), euler #=-25 (114552,343089,228512) : difference with theory (-23) = 2 CORRECTING DEFECT 9 (vertices=24, convex hull=37, v0=69186) After retessellation of defect 9 (v0=69186), euler #=-24 (114558,343124,228542) : difference with theory (-22) = 2 CORRECTING DEFECT 10 (vertices=20, convex hull=47, v0=70310) After retessellation of defect 10 (v0=70310), euler #=-23 (114572,343182,228587) : difference with theory (-21) = 2 CORRECTING DEFECT 11 (vertices=23, convex hull=51, v0=70809) After retessellation of defect 11 (v0=70809), euler #=-22 (114580,343225,228623) : difference with theory (-20) = 2 CORRECTING DEFECT 12 (vertices=18, convex hull=29, v0=72441) After retessellation of defect 12 (v0=72441), euler #=-21 (114583,343245,228641) : difference with theory (-19) = 2 CORRECTING DEFECT 13 (vertices=57, convex hull=38, v0=72703) After retessellation of defect 13 (v0=72703), euler #=-20 (114591,343284,228673) : difference with theory (-18) = 2 CORRECTING DEFECT 14 (vertices=67, convex hull=33, v0=78436) After retessellation of defect 14 (v0=78436), euler #=-19 (114598,343316,228699) : difference with theory (-17) = 2 CORRECTING DEFECT 15 (vertices=50, convex hull=109, v0=78845) After retessellation of defect 15 (v0=78845), euler #=-17 (114623,343437,228797) : difference with theory (-16) = 1 CORRECTING DEFECT 16 (vertices=8, convex hull=25, v0=78924) After retessellation of defect 16 (v0=78924), euler #=-16 (114625,343450,228809) : difference with theory (-15) = 1 CORRECTING DEFECT 17 (vertices=6, convex hull=20, v0=79709) After retessellation of defect 17 (v0=79709), euler #=-15 (114627,343464,228822) : difference with theory (-14) = 1 CORRECTING DEFECT 18 (vertices=13, convex hull=16, v0=82735) After retessellation of defect 18 (v0=82735), euler #=-14 (114628,343469,228827) : difference with theory (-13) = 1 CORRECTING DEFECT 19 (vertices=68, convex hull=98, v0=84588) After retessellation of defect 19 (v0=84588), euler #=-13 (114649,343573,228911) : difference with theory (-12) = 1 CORRECTING DEFECT 20 (vertices=8, convex hull=28, v0=84675) After retessellation of defect 20 (v0=84675), euler #=-12 (114650,343586,228924) : difference with theory (-11) = 1 CORRECTING DEFECT 21 (vertices=31, convex hull=76, v0=86524) After retessellation of defect 21 (v0=86524), euler #=-11 (114660,343648,228977) : difference with theory (-10) = 1 CORRECTING DEFECT 22 (vertices=11, convex hull=16, v0=89041) After retessellation of defect 22 (v0=89041), euler #=-10 (114662,343659,228987) : difference with theory (-9) = 1 CORRECTING DEFECT 23 (vertices=80, convex hull=108, v0=89770) After retessellation of defect 23 (v0=89770), euler #=-9 (114711,343851,229131) : difference with theory (-8) = 1 CORRECTING DEFECT 24 (vertices=17, convex hull=24, v0=93245) After retessellation of defect 24 (v0=93245), euler #=-8 (114714,343869,229147) : difference with theory (-7) = 1 CORRECTING DEFECT 25 (vertices=42, convex hull=80, v0=95224) After retessellation of defect 25 (v0=95224), euler #=-7 (114726,343937,229204) : difference with theory (-6) = 1 CORRECTING DEFECT 26 (vertices=26, convex hull=60, v0=101367) After retessellation of defect 26 (v0=101367), euler #=-6 (114741,344010,229263) : difference with theory (-5) = 1 CORRECTING DEFECT 27 (vertices=51, convex hull=31, v0=104658) After retessellation of defect 27 (v0=104658), euler #=-5 (114744,344026,229277) : difference with theory (-4) = 1 CORRECTING DEFECT 28 (vertices=67, convex hull=96, v0=108309) After retessellation of defect 28 (v0=108309), euler #=-4 (114765,344133,229364) : difference with theory (-3) = 1 CORRECTING DEFECT 29 (vertices=63, convex hull=94, v0=108644) After retessellation of defect 29 (v0=108644), euler #=-3 (114789,344245,229453) : difference with theory (-2) = 1 CORRECTING DEFECT 30 (vertices=80, convex hull=25, v0=108855) After retessellation of defect 30 (v0=108855), euler #=-2 (114794,344269,229473) : difference with theory (-1) = 1 CORRECTING DEFECT 31 (vertices=25, convex hull=65, v0=111934) After retessellation of defect 31 (v0=111934), euler #=-1 (114808,344337,229528) : difference with theory (0) = 1 CORRECTING DEFECT 32 (vertices=150, convex hull=121, v0=111958) After retessellation of defect 32 (v0=111958), euler #=1 (114852,344526,229675) : difference with theory (1) = 0 CORRECTING DEFECT 33 (vertices=22, convex hull=64, v0=114845) After retessellation of defect 33 (v0=114845), euler #=2 (114866,344592,229728) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->7.19) (max @ vno 38266 --> 42397) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->7.19) (max @ vno 38266 --> 42397) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 143 mutations (37.0%), 243 crossovers (63.0%), 84 vertices were eliminated building final representation... 982 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=114866, nf=229728, ne=344592, g=0) writing corrected surface to /media/sf_T1/recon/demo3/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 6.7 minutes 0 defective edges removing intersecting faces 000: 148 intersecting 001: 7 intersecting 002: 2 intersecting mris_fix_topology utimesec 401.504961 mris_fix_topology stimesec 0.213967 mris_fix_topology ru_maxrss 376168 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 48207 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3242 mris_fix_topology ru_nivcsw 33149 FSRUNTIME@ mris_fix_topology rh 0.1120 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 113754 - 341256 + 227504 = 2 --> 0 holes F =2V-4: 227504 = 227508-4 (0) 2E=3F: 682512 = 682512 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 114866 - 344592 + 229728 = 2 --> 0 holes F =2V-4: 229728 = 229732-4 (0) 2E=3F: 689184 = 689184 (0) total defect index = 0 /media/sf_T1/recon/demo3/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 22 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /media/sf_T1/recon/demo3/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 5 02:56:02 CST 2021 /media/sf_T1/recon/demo3/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs demo3 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /media/sf_T1/recon/demo3/mri/filled.mgz... reading volume /media/sf_T1/recon/demo3/mri/brain.finalsurfs.mgz... reading volume /media/sf_T1/recon/demo3/mri/../mri/aseg.presurf.mgz... reading volume /media/sf_T1/recon/demo3/mri/wm.mgz... 21837 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /media/sf_T1/recon/demo3/surf/lh.orig... computing class statistics... border white: 219664 voxels (1.31%) border gray 238810 voxels (1.42%) WM (100.0): 99.8 +- 7.2 [70.0 --> 110.0] GM (79.0) : 77.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.9 (was 70) setting MAX_BORDER_WHITE to 111.2 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 53.9 (was 40) setting MAX_GRAY to 96.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.30) (max @ vno 80640 --> 86019) face area 0.28 +- 0.12 (0.00-->2.64) mean absolute distance = 0.91 +- 1.12 3166 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-6.1, GM=76+-7.0 mean inside = 95.8, mean outside = 80.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.1, 141 (141) missing vertices, mean dist 0.3 [1.0 (%30.8)->0.9 (%69.2))] %44 local maxima, %51 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=bogon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.06-->3.24) (max @ vno 91344 --> 113635) face area 0.28 +- 0.13 (0.00-->2.32) mean absolute distance = 0.47 +- 0.71 2783 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2321370.8, rms=9.251 001: dt: 0.5000, sse=1388096.2, rms=6.580 (28.878%) 002: dt: 0.5000, sse=939348.4, rms=4.768 (27.528%) 003: dt: 0.5000, sse=724880.2, rms=3.591 (24.690%) 004: dt: 0.5000, sse=635958.4, rms=2.895 (19.381%) 005: dt: 0.5000, sse=589002.2, rms=2.546 (12.074%) 006: dt: 0.5000, sse=571664.3, rms=2.379 (6.534%) 007: dt: 0.5000, sse=573139.9, rms=2.318 (2.577%) rms = 2.28, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=564435.6, rms=2.277 (1.766%) 009: dt: 0.2500, sse=512684.7, rms=1.539 (32.392%) 010: dt: 0.2500, sse=504663.6, rms=1.418 (7.917%) rms = 1.40, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=510322.6, rms=1.396 (1.505%) rms = 1.38, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=499602.4, rms=1.378 (1.270%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.4, 125 (62) missing vertices, mean dist -0.3 [0.5 (%72.9)->0.3 (%27.1))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=bogon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.08-->4.00) (max @ vno 84962 --> 84078) face area 0.35 +- 0.16 (0.00-->2.97) mean absolute distance = 0.32 +- 0.43 2774 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1065109.5, rms=4.770 013: dt: 0.5000, sse=772579.9, rms=3.033 (36.420%) 014: dt: 0.5000, sse=693743.8, rms=2.405 (20.693%) 015: dt: 0.5000, sse=680449.0, rms=2.126 (11.600%) rms = 2.13, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=630039.4, rms=1.668 (21.539%) 017: dt: 0.2500, sse=622717.3, rms=1.367 (18.056%) 018: dt: 0.2500, sse=608040.2, rms=1.261 (7.741%) rms = 1.22, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=607070.2, rms=1.220 (3.234%) rms = 1.20, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=607307.6, rms=1.198 (1.855%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.1, 113 (52) missing vertices, mean dist -0.2 [0.4 (%75.2)->0.2 (%24.8))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=bogon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->4.11) (max @ vno 84962 --> 84078) face area 0.34 +- 0.16 (0.00-->2.81) mean absolute distance = 0.23 +- 0.33 2439 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=833266.8, rms=3.574 021: dt: 0.5000, sse=650317.2, rms=2.017 (43.562%) 022: dt: 0.5000, sse=631209.7, rms=1.858 (7.879%) rms = 1.86, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=594980.6, rms=1.378 (25.846%) 024: dt: 0.2500, sse=601173.7, rms=1.116 (18.998%) rms = 1.08, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=580973.7, rms=1.078 (3.424%) rms = 1.06, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=590089.4, rms=1.058 (1.872%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.9, 123 (48) missing vertices, mean dist -0.1 [0.2 (%59.0)->0.2 (%41.0))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=bogon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /media/sf_T1/recon/demo3/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=607607.2, rms=1.544 027: dt: 0.5000, sse=582594.1, rms=1.144 (25.925%) rms = 1.49, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=565882.4, rms=0.904 (20.940%) rms = 0.87, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=560585.4, rms=0.869 (3.971%) rms = 0.85, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=559851.7, rms=0.849 (2.301%) positioning took 0.2 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6808 vertices erasing segment 1 (vno[0] = 45837) erasing segment 2 (vno[0] = 58770) erasing segment 3 (vno[0] = 64001) erasing segment 4 (vno[0] = 79602) erasing segment 5 (vno[0] = 82290) erasing segment 6 (vno[0] = 82321) erasing segment 7 (vno[0] = 84095) erasing segment 8 (vno[0] = 85780) writing cortex label to /media/sf_T1/recon/demo3/label/lh.cortex.label... writing curvature file /media/sf_T1/recon/demo3/surf/lh.curv writing smoothed area to lh.area writing curvature file /media/sf_T1/recon/demo3/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->4.01) (max @ vno 84078 --> 84962) face area 0.33 +- 0.16 (0.00-->2.73) refinement took 1.9 minutes #-------------------------------------------- #@# Make White Surf rh Thu Aug 5 02:57:57 CST 2021 /media/sf_T1/recon/demo3/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs demo3 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /media/sf_T1/recon/demo3/mri/filled.mgz... reading volume /media/sf_T1/recon/demo3/mri/brain.finalsurfs.mgz... reading volume /media/sf_T1/recon/demo3/mri/../mri/aseg.presurf.mgz... reading volume /media/sf_T1/recon/demo3/mri/wm.mgz... 21837 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /media/sf_T1/recon/demo3/surf/rh.orig... computing class statistics... border white: 219664 voxels (1.31%) border gray 238810 voxels (1.42%) WM (100.0): 99.8 +- 7.2 [70.0 --> 110.0] GM (79.0) : 77.3 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.9 (was 70) setting MAX_BORDER_WHITE to 111.2 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 53.9 (was 40) setting MAX_GRAY to 96.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.10) (max @ vno 38266 --> 38267) face area 0.28 +- 0.12 (0.00-->1.83) mean absolute distance = 0.88 +- 1.09 3112 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-6.1, GM=76+-7.0 mean inside = 95.9, mean outside = 80.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=84.4, 23 (23) missing vertices, mean dist 0.3 [0.9 (%31.4)->0.9 (%68.6))] %47 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=bogon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->3.55) (max @ vno 73054 --> 73062) face area 0.28 +- 0.13 (0.00-->1.85) mean absolute distance = 0.45 +- 0.69 2981 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2308856.8, rms=9.156 001: dt: 0.5000, sse=1372438.6, rms=6.475 (29.284%) 002: dt: 0.5000, sse=934396.0, rms=4.700 (27.408%) 003: dt: 0.5000, sse=738749.4, rms=3.568 (24.087%) 004: dt: 0.5000, sse=631421.9, rms=2.879 (19.306%) 005: dt: 0.5000, sse=591410.7, rms=2.525 (12.297%) 006: dt: 0.5000, sse=576343.1, rms=2.356 (6.687%) 007: dt: 0.5000, sse=567280.5, rms=2.294 (2.636%) rms = 2.25, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=563817.8, rms=2.250 (1.911%) 009: dt: 0.2500, sse=511901.8, rms=1.497 (33.454%) 010: dt: 0.2500, sse=505346.8, rms=1.368 (8.612%) rms = 1.34, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=501542.1, rms=1.343 (1.867%) rms = 1.32, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=501133.2, rms=1.319 (1.793%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.4, 24 (1) missing vertices, mean dist -0.3 [0.5 (%71.7)->0.3 (%28.3))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=bogon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.07-->3.45) (max @ vno 78177 --> 77249) face area 0.35 +- 0.16 (0.00-->2.51) mean absolute distance = 0.33 +- 0.42 3033 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1022219.8, rms=4.499 013: dt: 0.5000, sse=750396.9, rms=2.805 (37.653%) 014: dt: 0.5000, sse=681595.6, rms=2.230 (20.499%) 015: dt: 0.5000, sse=663613.7, rms=2.025 (9.211%) rms = 2.08, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=628843.6, rms=1.568 (22.543%) 017: dt: 0.2500, sse=614223.1, rms=1.307 (16.684%) 018: dt: 0.2500, sse=623750.0, rms=1.222 (6.487%) rms = 1.19, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=610613.8, rms=1.190 (2.585%) rms = 1.16, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=606151.8, rms=1.163 (2.288%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.2, 33 (0) missing vertices, mean dist -0.2 [0.4 (%75.3)->0.2 (%24.7))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=bogon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.10-->3.78) (max @ vno 78177 --> 77249) face area 0.34 +- 0.16 (0.00-->2.58) mean absolute distance = 0.23 +- 0.33 2922 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=854540.3, rms=3.683 021: dt: 0.5000, sse=669239.8, rms=2.076 (43.625%) 022: dt: 0.5000, sse=663008.9, rms=1.874 (9.735%) rms = 1.87, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=650413.6, rms=1.872 (0.105%) 024: dt: 0.2500, sse=592822.9, rms=1.181 (36.935%) 025: dt: 0.2500, sse=586636.5, rms=1.073 (9.133%) rms = 1.07, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=583767.9, rms=1.072 (0.085%) rms = 1.05, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=583467.4, rms=1.045 (2.493%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=91.1, 31 (0) missing vertices, mean dist -0.1 [0.2 (%59.4)->0.2 (%40.6))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=bogon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /media/sf_T1/recon/demo3/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=601406.7, rms=1.558 028: dt: 0.5000, sse=578566.4, rms=1.155 (25.875%) rms = 1.50, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=570065.2, rms=0.895 (22.491%) rms = 0.85, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=563576.6, rms=0.855 (4.523%) rms = 0.83, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=561756.6, rms=0.828 (3.099%) positioning took 0.2 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6428 vertices erasing segment 0 (vno[0] = 28219) erasing segment 2 (vno[0] = 76929) erasing segment 3 (vno[0] = 77201) erasing segment 4 (vno[0] = 80999) erasing segment 5 (vno[0] = 82082) erasing segment 6 (vno[0] = 82931) erasing segment 7 (vno[0] = 84801) erasing segment 8 (vno[0] = 85770) writing cortex label to /media/sf_T1/recon/demo3/label/rh.cortex.label... writing curvature file /media/sf_T1/recon/demo3/surf/rh.curv writing smoothed area to rh.area writing curvature file /media/sf_T1/recon/demo3/surf/rh.area vertex spacing 0.89 +- 0.25 (0.03-->3.90) (max @ vno 77249 --> 78177) face area 0.33 +- 0.16 (0.00-->2.58) refinement took 2.0 minutes #-------------------------------------------- #@# Smooth2 lh Thu Aug 5 02:59:55 CST 2021 /media/sf_T1/recon/demo3/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Thu Aug 5 02:59:57 CST 2021 /media/sf_T1/recon/demo3/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Aug 5 02:59:59 CST 2021 /media/sf_T1/recon/demo3/scripts mris_inflate -rusage /media/sf_T1/recon/demo3/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 42.7 mm, total surface area = 68520 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 13.951878 mris_inflate stimesec 0.087986 mris_inflate ru_maxrss 146752 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 18926 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 152 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2093 mris_inflate ru_nivcsw 1141 #-------------------------------------------- #@# Inflation2 rh Thu Aug 5 03:00:13 CST 2021 /media/sf_T1/recon/demo3/scripts mris_inflate -rusage /media/sf_T1/recon/demo3/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 42.3 mm, total surface area = 68991 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.2 minutes mris_inflate utimesec 14.118853 mris_inflate stimesec 0.075988 mris_inflate ru_maxrss 148136 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19275 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2103 mris_inflate ru_nivcsw 1131 #-------------------------------------------- #@# Curv .H and .K lh Thu Aug 5 03:00:28 CST 2021 /media/sf_T1/recon/demo3/surf mris_curvature -w lh.white.preaparc total integrated curvature = -1.569*4pi (-19.722) --> 3 handles ICI = 126.3, FI = 1394.1, variation=21760.241 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s demo3 exited with ERRORS at Thu Aug 5 03:00:29 CST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting