Wed Feb 9 02:08:39 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w /fefs1/fcit/Rbahathiq0001/freesurfer/bin/recon-all -s /fefs1/fcit/Rbahathiq0001/ABIDEII/All_ABIDEII/FS/sub-28962_ses-1_run-1_T1w -i /fefs1/fcit/Rbahathiq0001/ABIDEII/All_ABIDEII/FS/sub-28962_ses-1_run-1_T1w.nii -all -qcache subjid sub-28962_ses-1_run-1_T1w setenv SUBJECTS_DIR /fefs1/fcit/Rbahathiq0001/freesurfer/subjects FREESURFER_HOME /fefs1/fcit/Rbahathiq0001/freesurfer Actual FREESURFER_HOME /fefs1/fcit/Rbahathiq0001/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux kcn109 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 65535 memorylocked unlimited maxproc 773435 total Mem: 99019748 -/+ buffers/cache: Swap: 8393952 used 41041860 15495980 22488 free 57977888 83523768 8371464 shared 0 buffers 205336 cached 25340544 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32- 358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32-358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2022/02/08-23:08:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: Rbahathiq0001 Machine: kcn109 Platform: Linux PlatformVersion: 2.6.32358.23.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /fefs1/fcit/Rbahathiq0001/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /fefs1/fcit/Rbahathiq0001/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w mri_convert /fefs1/fcit/Rbahathiq0001/ABIDEII/All_ABIDEII/FS/sub-28962_ses-1_run1_T1w.nii /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/ mri/orig/001.mgz mri_convert /fefs1/fcit/Rbahathiq0001/ABIDEII/All_ABIDEII/FS/sub-28962_ses-1_run1_T1w.nii /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/ mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fefs1/fcit/Rbahathiq0001/ABIDEII/All_ABIDEII/FS/sub-28962_ses-1_run1_T1w.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99656, 0.0801814, -0.0209424) j_ras = (0.0801989, 0.996779, 1.63604e-08) k_ras = (-0.0208749, 0.00167954, 0.999781) writing to /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/ mri/orig/001.mgz... #-------------------------------------------#@# MotionCor Wed Feb 9 02:08:48 AST 2022 Found 1 runs /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/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 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri/ orig/001.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/rawavg.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w mri_convert /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/rawavg.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/orig.mgz --conform mri_convert /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/rawavg.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99656, 0.0801814, -0.0209424) j_ras = (0.0801989, 0.996779, 1.63604e-08) k_ras = (-0.0208749, 0.00167954, 0.999781) Original Data has (1.1, 1, 1) mm size and (160, 240, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/ mri/orig.mgz... mri_add_xform_to_header -c /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/mri/transforms/talairach.xfm /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri/ orig.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/ mri/orig.mgz INFO: extension is mgz #-------------------------------------------#@# Talairach Wed Feb 9 02:09:05 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------#@# Talairach Failure Detection Wed Feb 9 02:11:09 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7541, pval=0.6675 >= threshold=0.0050) awk -f /fefs1/fcit/Rbahathiq0001/freesurfer/bin/extract_talairach_avi_QA.awk /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri/ transforms/talairach_avi.log tal_QC_AZS /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/transforms/talairach_avi.log TalAviQA: 0.97662 z-score: 0 #-------------------------------------------#@# Nu Intensity Correction Wed Feb 9 02:11:09 AST 2022 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri /fefs1/fcit/Rbahathiq0001/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux kcn109 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Feb 9 02:11:10 AST 2022 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.1621 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1621/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1621/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -9.61518e-09, -3.72529e-09) j_ras = (-5.58794e-09, 2.32831e-10, -1) k_ras = (-1.27366e-08, 1, -3.49246e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1621/nu0.mnc... -------------------------------------------------------Iteration 1 Wed Feb 9 02:11:13 AST 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.1621/nu0.mnc ./tmp.mri_nu_correct.mni.1621/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1621/0/ [Rbahathiq0001@kcn109:/fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/] [2022-02-09 02:11:13] running: /fefs1/fcit/Rbahathiq0001/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1621/0/ ./tmp.mri_nu_correct.mni.1621/nu0.mnc ./tmp.mri_nu_correct.mni.1621/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000970391 [Rbahathiq0001@kcn109:/fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/] [2022-02-09 02:11:43] running: /fefs1/fcit/Rbahathiq0001/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.1621/nu0.mnc ./tmp.mri_nu_correct.mni.1621/0//template.mnc Transforming slices:............................................................................ ..........Done Transforming slices:............................................................................ ................................................................................... ................................................................................... ..............Done -------------------------------------------------------Iteration 2 Wed Feb 9 02:12:16 AST 2022 nu_correct -clobber ./tmp.mri_nu_correct.mni.1621/nu1.mnc ./tmp.mri_nu_correct.mni.1621/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1621/1/ [Rbahathiq0001@kcn109:/fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/] [2022-02-09 02:12:16] running: /fefs1/fcit/Rbahathiq0001/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1621/1/ ./tmp.mri_nu_correct.mni.1621/nu1.mnc ./tmp.mri_nu_correct.mni.1621/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000956615 [Rbahathiq0001@kcn109:/fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/] [2022-02-09 02:12:30] running: /fefs1/fcit/Rbahathiq0001/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.1621/nu1.mnc ./tmp.mri_nu_correct.mni.1621/1//template.mnc Transforming slices:............................................................................ ..........Done Transforming slices:............................................................................ ................................................................................... ................................................................................... ..............Done mri_binarize --i ./tmp.mri_nu_correct.mni.1621/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1621/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.1621/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1621/ones.mgz sysname Linux hostname kcn109 machine x86_64 user Rbahathiq0001 input ./tmp.mri_nu_correct.mni.1621/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1621/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1621/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1621/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1621/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1621/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1621/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1621/input.mean.dat sysname Linux hostname kcn109 machine x86_64 user Rbahathiq0001 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1621/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1621/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1621/ones.mgz --i ./tmp.mri_nu_correct.mni.1621/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1621/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1621/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1621/ones.mgz --i ./tmp.mri_nu_correct.mni.1621/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1621/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1621/output.mean.dat sysname Linux hostname kcn109 machine x86_64 user Rbahathiq0001 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1621/ones.mgz Loading ./tmp.mri_nu_correct.mni.1621/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1621/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1621/nu2.mnc ./tmp.mri_nu_correct.mni.1621/nu2.mnc mul .92580221121167612998 Saving result to './tmp.mri_nu_correct.mni.1621/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.1621/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.1621/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.1621/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -9.61518e-09, -3.72529e-09) j_ras = (-5.58794e-09, 2.32831e-10, -1) k_ras = (-1.27366e-08, 1, -3.49246e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 10 seconds. mapping (17, 156) to ( 3, 110) Wed Feb 9 02:13:34 AST 2022 mri_nu_correct.mni done mri_add_xform_to_header -c /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------#@# Intensity Normalization Wed Feb 9 02:13:36 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.040 -0.063 0.050 7.884; 0.022 1.028 0.264 -28.794; -0.060 -0.151 1.136 -26.753; 0.000 0.000 0.000 1.000; 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 111 white matter peak found at 109 gm peak at 69 (69), valley at 42 (42) csf peak at 10, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 42 (42) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------writing output to T1.mgz 3D bias adjustment took 2 minutes and 34 seconds. #-------------------------------------------#@# Skull Stripping Wed Feb 9 02:16:10 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_em_register -skull nu.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_withskull_2008-0326.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (50, 10, 25) --> (210, 150, 219) using (103, 57, 122) as brain centroid... mean wm in atlas = 126, using box (83,40,98) --> (122, 74,145) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 initial log_p = -5.0 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.520181 @ (-9.091, 27.273, -9.091) max log p = -4.393628 @ (4.545, 4.545, -4.545) max log p = -4.362215 @ (2.273, 2.273, 2.273) max log p = -4.343118 @ (-3.409, -1.136, 3.409) max log p = -4.321857 @ (1.705, 1.705, -1.705) max log p = -4.320222 @ (-0.284, -1.989, 1.420) Found translation: (-4.3, 32.7, -8.2): log p = -4.320 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.3 (thresh=-4.3) 1.064 0.000 0.000 -12.550; 0.000 1.226 0.161 2.759; 0.000 -0.139 1.055 -7.893; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.064 0.000 0.000 -12.550; 0.000 1.226 0.161 2.759; 0.000 -0.139 1.055 -7.893; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.078 0.072 0.085 -30.300; -0.077 1.258 0.231 0.258; -0.069 -0.221 1.039 11.519; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.080 0.030 0.079 -26.366; -0.039 1.266 0.199 -1.628; -0.072 -0.180 1.046 7.615; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.081 0.042 0.072 -26.293; -0.048 1.263 0.207 -1.025; -0.063 -0.189 1.041 7.266; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.083 0.042 0.072 -26.471; -0.048 1.263 0.207 -1.025; -0.063 -0.189 1.041 7.266; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08259 0.04219 0.07221 -26.47144; -0.04830 1.26273 0.20687 -1.02525; -0.06264 -0.18939 1.04148 7.26562; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08259 0.04219 0.07221 -26.47144; -0.04830 1.26273 0.20687 -1.02525; -0.06264 -0.18939 1.04148 7.26562; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.083 0.042 0.072 -26.471; -0.048 1.263 0.207 -1.025; -0.063 -0.189 1.041 7.266; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-5.0) transform before final EM align: 1.083 0.042 0.072 -26.471; -0.048 1.263 0.207 -1.025; -0.063 -0.189 1.041 7.266; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08259 0.04219 0.07221 -26.47144; -0.04830 1.26273 0.20687 -1.02525; -0.06264 -0.18939 1.04148 7.26562; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08259 0.04219 0.07221 -26.47144; -0.04830 1.26273 0.20687 -1.02525; -0.06264 -0.18939 1.04148 7.26562; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.3 tol 0.000000 final transform: 1.083 0.042 0.072 -26.471; -0.048 1.263 0.207 -1.025; -0.063 -0.189 1.041 7.266; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 33 minutes and 3 seconds. mri_watershed -T1 -brain_atlas /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: Mode: T1 normalized volume 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=130 y=76 z=122 r=65 first estimation of the main basin volume: 1185342 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=113, y=59, z=91, 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=12567158712 voxels, voxel volume =1.000 = 12567158712 mmm3 = 12567158.784 cm3 done. PostAnalyze...Basin Prior 8 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=79, z=115, r=9454 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 44882 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = -1039127359 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 1012688246 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=46 , nb = -1054779477 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=42 , nb = 1080211082 OTHER CSF_MIN=0, CSF_intensity=8, CSF_MAX=38 , nb = 1060669478 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 : 44, 45, 47, 65 after analyzing : 44, 46, 47, 50 RIGHT_CER before analyzing : 6, 4, 0, 9 after analyzing : 4, 18, 25, 19 LEFT_CER before analyzing : 36, 27, 25, 31 after analyzing : 22, 27, 27, 28 RIGHT_BRAIN before analyzing : 46, 23, 16, 28 after analyzing : 23, 24, 25, 25 LEFT_BRAIN before analyzing : 42, 38, 37, 46 after analyzing : 30, 38, 38, 40 OTHER before analyzing : 38, 25, 8, 48 after analyzing : 18, 25, 25, 30 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 71.817, std = 6.962 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.09, sigma = 5.06 after rotation: sse = 3.09, sigma = 5.06 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.22, its var is 4.60 before Erosion-Dilatation 1.06% of inacurate vertices after Erosion-Dilatation 1.93% 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...30 iterations mri_strip_skull: done peeling brain Brain Size = 1690250 voxels, voxel volume = 1.000 mm3 = 1690250 mmm3 = 1690.250 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------#@# EM Registration Wed Feb 9 02:49:42 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=23.0 skull bounding box = (60, 22, 35) --> (201, 144, 206) using (107, 63, 121) as brain centroid... mean wm in atlas = 107, using box (90,48,100) --> (124, 77,142) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.051305 @ (-9.091, 27.273, -9.091) max log p = -3.725296 @ (4.545, 13.636, -4.545) max log p = -3.724564 @ (-2.273, -2.273, -2.273) max log p = -3.698211 @ (3.409, 1.136, 3.409) max log p = -3.690405 @ (-0.568, 0.568, -0.568) max log p = -3.690405 @ (0.000, 0.000, 0.000) Found translation: (-4.0, 40.3, -13.1): log p = -3.690 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p 1.075 0.000 0.000 -13.786; 0.000 1.140 0.131 13.881; 0.000 -0.150 0.991 -0.269; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p 1.075 0.000 0.000 -13.786; 0.000 1.140 0.131 13.881; 0.000 -0.150 0.991 -0.269; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p 1.030 0.062 0.070 -23.052; -0.076 1.198 0.166 13.414; -0.067 -0.185 0.966 17.853; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p 1.030 0.062 0.070 -23.052; -0.076 1.198 0.166 13.414; -0.067 -0.185 0.966 17.853; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p 1.028 0.062 0.070 -21.763; -0.076 1.202 0.159 14.825; -0.067 -0.176 0.971 16.675; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached =-3.7 (thresh=-3.7) =-3.5 (thresh=-3.5) =-3.5 (thresh=-3.5) =-3.3 (thresh=-3.3) =-3.3 (thresh=-3.3) =-3.2 (thresh=-3.2) *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02544 0.06205 0.07016 -21.41480; -0.07609 1.20184 0.15855 14.82495; -0.06756 -0.17583 0.97192 16.57094; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.02544 0.06205 0.07016 -21.41480; -0.07609 1.20184 0.15855 14.82495; -0.06756 -0.17583 0.97192 16.57094; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.7) transform before final EM align: 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02544 0.06205 0.07016 -21.41480; -0.07609 1.20184 0.15855 14.82495; -0.06756 -0.17583 0.97192 16.57094; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.02544 0.06205 0.07016 -21.41480; -0.07609 1.20184 0.15855 14.82495; -0.06756 -0.17583 0.97192 16.57094; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000 final transform: 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 24 minutes and 36 seconds. #-------------------------------------#@# CA Normalize Wed Feb 9 03:14:19 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.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 '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-0326.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (60, 22, 35) --> (201, 143, 206) using (107, 62, 121) as brain centroid... mean wm in atlas = 107, using box (90,47,100) --> (124, 76,142) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 25, 37) --> (195, 120, 206) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 155.0 1 of 1212 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 25, 35) --> (133, 117, 205) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 155.0 0 of 1244 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 96, 65) --> (178, 135, 119) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 155.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 96, 59) --> (132, 131, 117) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 155.0 0 of 21 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 89, 98) --> (146, 147, 129) Brain_Stem: limiting intensities to 90.0 --> 155.0 0 of 9 (0.0%) samples deleted using 2495 total control points for intensity normalization... bias field = 1.010 +- 0.037 16 of 2494 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 25, 37) --> (195, 120, 206) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 151.0 1 of 1204 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 25, 35) --> (133, 117, 205) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 151.0 0 of 1243 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 96, 65) --> (178, 135, 119) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 151.0 0 of 45 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 96, 59) --> (132, 131, 117) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 151.0 0 of 45 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 89, 98) --> (146, 147, 129) Brain_Stem: limiting intensities to 82.0 --> 151.0 0 of 67 (0.0%) samples deleted using 2604 total control points for intensity normalization... bias field = 1.006 +- 0.035 22 of 2603 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (129, 25, 37) --> (195, 120, 206) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 149.0 6 of 1249 (0.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (68, 25, 35) --> (133, 117, 205) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 149.0 0 of 1275 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (132, 96, 65) --> (178, 135, 119) Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 149.0 0 of 74 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (85, 96, 59) --> (132, 131, 117) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 149.0 0 of 65 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 89, 98) --> (146, 147, 129) Brain_Stem: limiting intensities to 78.0 --> 149.0 0 of 158 (0.0%) samples deleted using 2821 total control points for intensity normalization... bias field = 1.005 +- 0.033 27 of 2815 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 56 seconds. #-------------------------------------#@# CA Reg Wed Feb 9 03:16:15 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-0326.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... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.24 (predicted orig area = 6.5) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.761, neg=0, invalid=96777 0001: dt=129.472000, rms=0.692 (9.136%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.658 (4.894%), neg=0, invalid=96777 0003: dt=295.936000, rms=0.651 (1.116%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.648 (0.402%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.643 (0.819%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.642 (0.098%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.642 (0.046%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.642 (0.019%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.642 (0.016%), neg=0, invalid=96777 0010: dt=295.936000, rms=0.638 (0.594%), neg=0, invalid=96777 0011: dt=23.120000, rms=0.638 (0.017%), neg=0, invalid=96777 0012: dt=23.120000, rms=0.638 (0.003%), neg=0, invalid=96777 0013: dt=23.120000, rms=0.638 (-0.043%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=96777 0014: dt=32.368000, rms=0.638 (0.009%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.637 (0.038%), neg=0, invalid=96777 0016: dt=517.888000, rms=0.633 (0.613%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.633 (0.013%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.633 (0.014%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.633 (-0.012%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0020: dt=124.416000, rms=0.624 (1.769%), neg=0, invalid=96777 0021: dt=62.208000, rms=0.613 (1.687%), neg=0, invalid=96777 0022: dt=20.736000, rms=0.612 (0.225%), neg=0, invalid=96777 0023: dt=20.736000, rms=0.610 (0.295%), neg=0, invalid=96777 0024: dt=20.736000, rms=0.607 (0.430%), neg=0, invalid=96777 0025: dt=20.736000, rms=0.604 (0.545%), neg=0, invalid=96777 0026: dt=20.736000, rms=0.600 (0.629%), neg=0, invalid=96777 0027: dt=20.736000, rms=0.596 (0.673%), neg=0, invalid=96777 0028: dt=20.736000, rms=0.592 (0.668%), neg=0, invalid=96777 0029: dt=20.736000, rms=0.589 (0.627%), neg=0, invalid=96777 0030: dt=20.736000, rms=0.585 (0.563%), neg=0, invalid=96777 0031: dt=20.736000, rms=0.582 (0.502%), neg=0, invalid=96777 0032: dt=20.736000, rms=0.580 (0.429%), neg=0, invalid=96777 0033: dt=20.736000, rms=0.578 (0.392%), neg=0, invalid=96777 0034: dt=20.736000, rms=0.575 (0.373%), neg=0, invalid=96777 0035: dt=20.736000, rms=0.573 (0.355%), neg=0, invalid=96777 0036: dt=20.736000, rms=0.571 (0.332%), neg=0, invalid=96777 0037: dt=20.736000, rms=0.570 (0.288%), neg=0, invalid=96777 0038: dt=20.736000, rms=0.568 (0.249%), neg=0, invalid=96777 0039: dt=20.736000, rms=0.567 (0.217%), neg=0, invalid=96777 0040: dt=20.736000, rms=0.566 (0.182%), neg=0, invalid=96777 0041: dt=20.736000, rms=0.565 (0.144%), neg=0, invalid=96777 0042: dt=20.736000, rms=0.565 (0.125%), neg=0, invalid=96777 0043: dt=20.736000, rms=0.564 (0.104%), neg=0, invalid=96777 0044: dt=20.736000, rms=0.564 (0.087%), neg=0, invalid=96777 0045: dt=103.680000, rms=0.563 (0.130%), neg=0, invalid=96777 0046: dt=9.072000, rms=0.563 (0.022%), neg=0, invalid=96777 0047: dt=9.072000, rms=0.563 (0.011%), neg=0, invalid=96777 0048: dt=9.072000, rms=0.563 (0.002%), neg=0, invalid=96777 0049: dt=9.072000, rms=0.563 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=96777 0050: dt=82.944000, rms=0.561 (0.260%), neg=0, invalid=96777 0051: dt=36.288000, rms=0.560 (0.128%), neg=0, invalid=96777 0052: dt=36.288000, rms=0.560 (0.040%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.560 (0.060%), neg=0, invalid=96777 0054: dt=36.288000, rms=0.560 (0.059%), neg=0, invalid=96777 0055: dt=36.288000, rms=0.559 (0.038%), neg=0, invalid=96777 0056: dt=124.416000, rms=0.559 (0.030%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.580, neg=0, invalid=96777 0057: dt=8.565657, rms=0.580 (0.137%), neg=0, invalid=96777 0058: dt=4.800000, rms=0.579 (0.025%), neg=0, invalid=96777 0059: dt=4.800000, rms=0.579 (0.014%), neg=0, invalid=96777 0060: dt=4.800000, rms=0.579 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=96777 0061: dt=0.000488, rms=0.579 (0.000%), neg=0, invalid=96777 0062: dt=0.000488, rms=0.579 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0063: dt=5.596413, rms=0.618 (2.148%), neg=0, invalid=96777 0064: dt=2.486486, rms=0.617 (0.067%), neg=0, invalid=96777 0065: dt=2.486486, rms=0.617 (-0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=96777 0066: dt=0.000000, rms=0.617 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=96777 0067: dt=0.966667, rms=0.667 (0.437%), neg=0, invalid=96777 0068: dt=2.131783, rms=0.663 (0.676%), neg=0, invalid=96777 0069: dt=0.818182, rms=0.662 (0.090%), neg=0, invalid=96777 0070: dt=0.818182, rms=0.661 (0.095%), neg=0, invalid=96777 0071: dt=0.818182, rms=0.661 (0.076%), neg=0, invalid=96777 0072: dt=0.818182, rms=0.661 (-0.072%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=96777 0073: dt=1.093750, rms=0.660 (0.126%), neg=0, invalid=96777 0074: dt=0.000000, rms=0.660 (-0.003%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=96777 0075: dt=0.132962, rms=0.620 (0.717%), neg=0, invalid=96777 0076: dt=0.425439, rms=0.619 (0.198%), neg=0, invalid=96777 0077: dt=0.212719, rms=0.615 (0.616%), neg=0, invalid=96777 0078: dt=0.212719, rms=0.615 (-0.082%), neg=0, invalid=96777 0079: dt=0.006000, rms=0.615 (0.001%), neg=0, invalid=96777 0080: dt=0.000003, rms=0.615 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0081: dt=0.028000, rms=0.615 (0.037%), neg=0, invalid=96777 0082: dt=0.024000, rms=0.615 (0.005%), neg=0, invalid=96777 0083: dt=0.024000, rms=0.615 (-0.003%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11971 (20) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2003 voxels, overlap=0.485) Left_Lateral_Ventricle (4): linear fit = 0.75 x + 0.0 (2003 voxels, peak = 18), gca=18.1 gca peak = 0.14022 (22) mri peak = 0.11250 (23) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (1132 voxels, overlap=0.727) Right_Lateral_Ventricle (43): linear fit = 0.94 x + 0.0 (1132 voxels, peak = 21), gca=20.8 gca peak = 0.24234 (100) mri peak = 0.08130 (93) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (492 voxels, overlap=1.009) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (492 voxels, peak = 94), gca=93.5 gca peak = 0.19192 (97) mri peak = 0.11799 (83) Left_Pallidum (13): linear fit = 0.86 x + 0.0 (405 voxels, overlap=0.039) Left_Pallidum (13): linear fit = 0.86 x + 0.0 (405 voxels, peak = 83), gca=82.9 gca peak = 0.24007 (63) mri peak = 0.10510 (70) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (969 voxels, overlap=0.709) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (969 voxels, peak = 70), gca=69.6 gca peak = 0.29892 (64) mri peak = 0.07561 (70) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (769 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (769 voxels, peak = 68), gca=67.5 gca peak = 0.12541 (104) mri peak = 0.12031 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (67447 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (67447 voxels, peak = 108), gca=107.6 gca peak = 0.13686 (104) mri peak = 0.09866 (107) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (69004 voxels, overlap=0.583) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (69004 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.04632 (67) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (34401 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (34401 voxels, peak = 66), gca=66.5 gca peak = 0.13270 (63) mri peak = 0.05294 (68) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (37560 voxels, overlap=0.994) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (37560 voxels, peak = 65), gca=64.6 gca peak = 0.15182 (70) mri peak = 0.10033 (80) Right_Caudate (50): linear fit = 1.08 x + 0.0 (433 voxels, overlap=0.451) Right_Caudate (50): linear fit = 1.08 x + 0.0 (433 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08524 (80) Left_Caudate (11): linear fit = 1.04 x + 0.0 (805 voxels, overlap=0.817) Left_Caudate (11): linear fit = 1.04 x + 0.0 (805 voxels, peak = 79), gca=79.4 gca peak = 0.12116 (60) mri peak = 0.05578 (68) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (26997 voxels, overlap=0.501) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (26997 voxels, peak = 68), gca=68.1 gca peak = 0.12723 (61) mri peak = 0.05405 (68) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (31267 voxels, overlap=0.511) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (31267 voxels, peak = 70), gca=70.5 gca peak = 0.22684 (88) mri peak = 0.06407 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9765 voxels, overlap=0.843) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9765 voxels, peak = 93), gca=92.8 gca peak = 0.21067 (87) mri peak = 0.07919 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8652 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (8652 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.11568 (73) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (384 voxels, overlap=0.632) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (384 voxels, peak = 69), gca=68.5 gca peak = 0.39668 (62) mri peak = 0.11111 (69) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (305 voxels, overlap=0.883) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (305 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.07068 (103) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5504 voxels, overlap=0.612) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5504 voxels, peak = 102), gca=101.8 gca peak = 0.12071 (89) mri peak = 0.05467 (92) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4157 voxels, overlap=0.921) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4157 voxels, peak = 91), gca=91.2 gca peak = 0.13716 (82) mri peak = 0.04697 (87) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2567 voxels, overlap=0.971) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2567 voxels, peak = 83), gca=83.2 gca peak = 0.15214 (84) mri peak = 0.07441 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2551 voxels, overlap=0.990) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2551 voxels, peak = 84), gca=83.6 gca peak = 0.08983 (85) mri peak = 0.06983 (94) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11620 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11620 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07703 (101) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (850 voxels, overlap=0.638) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (850 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.08637 (101) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1189 voxels, overlap=0.675) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1189 voxels, peak = 100), gca=100.1 gca peak = 0.21100 (36) mri peak = 1.00000 (33) Third_Ventricle (14): linear fit = 0.88 x + 0.0 (112 voxels, overlap=2.064) Third_Ventricle (14): linear fit = 0.88 x + 0.0 (112 voxels, peak = 32), gca=31.9 gca peak = 0.13542 (27) mri peak = 0.11138 (27) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (274 voxels, overlap=0.572) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (274 voxels, peak = 21), gca=21.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.84 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.637, neg=0, invalid=96777 0084: dt=129.472000, rms=0.628 (1.507%), neg=0, invalid=96777 0085: dt=295.936000, rms=0.622 (0.849%), neg=0, invalid=96777 0086: dt=129.472000, rms=0.621 (0.213%), neg=0, invalid=96777 0087: dt=369.920000, rms=0.617 (0.623%), neg=0, invalid=96777 0088: dt=32.368000, rms=0.617 (0.087%), neg=0, invalid=96777 0089: dt=18.496000, rms=0.617 (0.015%), neg=0, invalid=96777 0090: dt=18.496000, rms=0.617 (0.009%), neg=0, invalid=96777 0091: dt=18.496000, rms=0.617 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=96777 0092: dt=129.472000, rms=0.616 (0.102%), neg=0, invalid=96777 0093: dt=295.936000, rms=0.614 (0.353%), neg=0, invalid=96777 0094: dt=32.368000, rms=0.614 (0.045%), neg=0, invalid=96777 0095: dt=32.368000, rms=0.613 (0.007%), neg=0, invalid=96777 0096: dt=32.368000, rms=0.613 (-0.037%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.614, neg=0, invalid=96777 0097: dt=124.416000, rms=0.604 (1.602%), neg=0, invalid=96777 0098: dt=36.288000, rms=0.594 (1.644%), neg=0, invalid=96777 0099: dt=20.736000, rms=0.592 (0.235%), neg=0, invalid=96777 0100: dt=497.664000, rms=0.571 (3.538%), neg=0, invalid=96777 0101: dt=36.288000, rms=0.567 (0.777%), neg=0, invalid=96777 0102: dt=36.288000, rms=0.565 (0.326%), neg=0, invalid=96777 0103: dt=82.944000, rms=0.564 (0.281%), neg=0, invalid=96777 0104: dt=36.288000, rms=0.562 (0.268%), neg=0, invalid=96777 0105: dt=36.288000, rms=0.561 (0.146%), neg=0, invalid=96777 0106: dt=82.944000, rms=0.560 (0.286%), neg=0, invalid=96777 0107: dt=25.920000, rms=0.559 (0.130%), neg=0, invalid=96777 0108: dt=331.776000, rms=0.555 (0.784%), neg=0, invalid=96777 0109: dt=20.736000, rms=0.553 (0.309%), neg=0, invalid=96777 0110: dt=36.288000, rms=0.552 (0.097%), neg=0, invalid=96777 0111: dt=124.416000, rms=0.551 (0.211%), neg=0, invalid=96777 0112: dt=20.736000, rms=0.551 (0.089%), neg=0, invalid=96777 0113: dt=124.416000, rms=0.550 (0.155%), neg=0, invalid=96777 0114: dt=31.104000, rms=0.549 (0.175%), neg=0, invalid=96777 0115: dt=25.920000, rms=0.549 (0.041%), neg=0, invalid=96777 0116: dt=25.920000, rms=0.548 (0.056%), neg=0, invalid=96777 0117: dt=25.920000, rms=0.548 (0.090%), neg=0, invalid=96777 0118: dt=25.920000, rms=0.547 (0.120%), neg=0, invalid=96777 0119: dt=25.920000, rms=0.546 (0.147%), neg=0, invalid=96777 0120: dt=25.920000, rms=0.545 (0.175%), neg=0, invalid=96777 0121: dt=25.920000, rms=0.544 (0.197%), neg=0, invalid=96777 0122: dt=25.920000, rms=0.543 (0.208%), neg=0, invalid=96777 0123: dt=25.920000, rms=0.542 (0.213%), neg=0, invalid=96777 0124: dt=25.920000, rms=0.541 (0.208%), neg=0, invalid=96777 0125: dt=25.920000, rms=0.540 (0.206%), neg=0, invalid=96777 0126: dt=25.920000, rms=0.539 (0.200%), neg=0, invalid=96777 0127: dt=25.920000, rms=0.538 (0.193%), neg=0, invalid=96777 0128: dt=25.920000, rms=0.537 (0.186%), neg=0, invalid=96777 0129: dt=25.920000, rms=0.536 (0.181%), neg=0, invalid=96777 0130: dt=25.920000, rms=0.535 (0.170%), neg=0, invalid=96777 0131: dt=25.920000, rms=0.534 (0.170%), neg=0, invalid=96777 0132: dt=25.920000, rms=0.533 (0.162%), neg=0, invalid=96777 0133: 0134: 0135: 0136: 0137: 0138: 0139: 0140: 0141: 0142: 0143: 0144: 0145: 0146: 0147: 0148: 0149: 0150: 0151: 0152: 0153: 0154: 0155: 0156: 0157: 0158: 0159: 0160: 0161: 0162: 0163: 0164: 0165: 0166: 0167: 0168: 0169: 0170: 0171: 0172: 0173: 0174: 0175: 0176: 0177: 0178: 0179: 0180: 0181: 0182: 0183: 0184: 0185: 0186: 0187: 0188: 0189: 0190: 0191: dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, dt=25.920000, rms=0.532 rms=0.531 rms=0.531 rms=0.530 rms=0.529 rms=0.529 rms=0.528 rms=0.527 rms=0.527 rms=0.526 rms=0.526 rms=0.525 rms=0.524 rms=0.524 rms=0.523 rms=0.523 rms=0.523 rms=0.522 rms=0.522 rms=0.521 rms=0.521 rms=0.520 rms=0.520 rms=0.520 rms=0.519 rms=0.519 rms=0.519 rms=0.518 rms=0.518 rms=0.518 rms=0.518 rms=0.517 rms=0.517 rms=0.517 rms=0.516 rms=0.516 rms=0.516 rms=0.516 rms=0.515 rms=0.515 rms=0.515 rms=0.515 rms=0.514 rms=0.514 rms=0.514 rms=0.514 rms=0.514 rms=0.514 rms=0.513 rms=0.513 rms=0.513 rms=0.513 rms=0.513 rms=0.512 rms=0.512 rms=0.512 rms=0.512 rms=0.512 rms=0.512 (0.153%), (0.144%), (0.139%), (0.141%), (0.128%), (0.125%), (0.123%), (0.119%), (0.119%), (0.111%), (0.104%), (0.101%), (0.096%), (0.099%), (0.092%), (0.092%), (0.085%), (0.091%), (0.080%), (0.074%), (0.084%), (0.078%), (0.070%), (0.065%), (0.061%), (0.072%), (0.073%), (0.058%), (0.057%), (0.049%), (0.058%), (0.063%), (0.054%), (0.051%), (0.050%), (0.047%), (0.050%), (0.046%), (0.046%), (0.049%), (0.047%), (0.045%), (0.042%), (0.040%), (0.038%), (0.041%), (0.034%), (0.028%), (0.045%), (0.025%), (0.034%), (0.047%), (0.043%), (0.029%), (0.017%), (0.027%), (0.039%), (0.028%), (0.027%), neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, neg=0, invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 invalid=96777 0192: dt=25.920000, rms=0.511 (0.042%), neg=0, invalid=96777 0193: dt=25.920000, rms=0.511 (0.019%), neg=0, invalid=96777 0194: dt=25.920000, rms=0.511 (0.039%), neg=0, invalid=96777 0195: dt=25.920000, rms=0.511 (0.051%), neg=0, invalid=96777 0196: dt=25.920000, rms=0.511 (0.035%), neg=0, invalid=96777 0197: dt=25.920000, rms=0.511 (0.023%), neg=0, invalid=96777 0198: dt=25.920000, rms=0.511 (0.011%), neg=0, invalid=96777 0199: dt=62.208000, rms=0.510 (0.020%), neg=0, invalid=96777 0200: dt=36.288000, rms=0.510 (0.003%), neg=0, invalid=96777 0201: dt=36.288000, rms=0.510 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=96777 0202: dt=62.208000, rms=0.509 (0.221%), neg=0, invalid=96777 0203: dt=36.288000, rms=0.509 (0.079%), neg=0, invalid=96777 0204: dt=103.680000, rms=0.509 (0.060%), neg=0, invalid=96777 0205: dt=36.288000, rms=0.508 (0.073%), neg=0, invalid=96777 0206: dt=20.736000, rms=0.508 (0.013%), neg=0, invalid=96777 0207: dt=20.736000, rms=0.508 (0.016%), neg=0, invalid=96777 0208: dt=20.736000, rms=0.508 (0.025%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.508 (0.032%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.508 (0.034%), neg=0, invalid=96777 0211: dt=20.736000, rms=0.507 (0.035%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.507 (0.032%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.507 (0.027%), neg=0, invalid=96777 0214: dt=20.736000, rms=0.507 (0.027%), neg=0, invalid=96777 0215: dt=20.736000, rms=0.507 (0.029%), neg=0, invalid=96777 0216: dt=20.736000, rms=0.507 (0.030%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.507 (0.021%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.506 (0.029%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.506 (0.037%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.506 (0.029%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.506 (0.024%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.506 (0.025%), neg=0, invalid=96777 0223: dt=20.736000, rms=0.506 (0.021%), neg=0, invalid=96777 0224: dt=20.736000, rms=0.506 (0.017%), neg=0, invalid=96777 0225: dt=36.288000, rms=0.506 (0.012%), neg=0, invalid=96777 0226: dt=36.288000, rms=0.506 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 0227: dt=11.200000, rms=0.515 (0.181%), neg=0, invalid=96777 0228: dt=44.800000, rms=0.513 (0.479%), neg=0, invalid=96777 0229: dt=11.200000, rms=0.511 (0.279%), neg=0, invalid=96777 0230: dt=11.200000, rms=0.510 (0.213%), neg=0, invalid=96777 0231: dt=32.000000, rms=0.508 (0.461%), neg=0, invalid=96777 0232: dt=9.600000, rms=0.507 (0.127%), neg=0, invalid=96777 0233: dt=11.200000, rms=0.506 (0.137%), neg=0, invalid=96777 0234: dt=9.600000, rms=0.506 (0.134%), neg=0, invalid=96777 0235: dt=44.800000, rms=0.504 (0.405%), neg=0, invalid=96777 0236: dt=2.800000, rms=0.503 (0.066%), neg=0, invalid=96777 0237: dt=2.800000, rms=0.503 (0.069%), neg=0, invalid=96777 0238: dt=2.800000, rms=0.503 (0.045%), neg=0, invalid=96777 0239: dt=2.800000, rms=0.503 (0.033%), neg=0, invalid=96777 0240: dt=2.800000, rms=0.502 (0.060%), neg=0, invalid=96777 0241: dt=2.800000, rms=0.502 (0.025%), neg=0, invalid=96777 0242: dt=2.800000, rms=0.502 (0.051%), neg=0, invalid=96777 0243: dt=2.800000, rms=0.502 (0.073%), neg=0, invalid=96777 0244: dt=2.800000, rms=0.501 (0.090%), neg=0, invalid=96777 0245: dt=2.800000, rms=0.501 (0.105%), neg=0, invalid=96777 0246: dt=2.800000, rms=0.500 (0.116%), neg=0, invalid=96777 0247: dt=1.400000, rms=0.500 (0.010%), neg=0, invalid=96777 0248: dt=0.350000, rms=0.500 (0.003%), neg=0, invalid=96777 0249: dt=0.175000, rms=0.500 (0.001%), neg=0, invalid=96777 0250: dt=0.043750, rms=0.500 (0.000%), neg=0, invalid=96777 0251: dt=0.010937, rms=0.500 (0.000%), neg=0, invalid=96777 0252: dt=0.000684, rms=0.500 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=96777 0253: dt=11.200000, rms=0.498 (0.328%), neg=0, invalid=96777 0254: dt=32.000000, rms=0.497 (0.362%), neg=0, invalid=96777 0255: dt=38.400000, rms=0.496 (0.164%), neg=0, invalid=96777 0256: dt=11.200000, rms=0.495 (0.126%), neg=0, invalid=96777 0257: dt=11.200000, rms=0.495 (0.085%), neg=0, invalid=96777 0258: dt=11.200000, rms=0.494 (0.080%), neg=0, invalid=96777 0259: dt=38.400000, rms=0.493 (0.206%), neg=0, invalid=96777 0260: dt=2.800000, rms=0.493 (0.020%), neg=0, invalid=96777 0261: dt=2.800000, rms=0.493 (0.018%), neg=0, invalid=96777 0262: dt=2.800000, rms=0.493 (0.027%), neg=0, invalid=96777 0263: dt=2.800000, rms=0.493 (0.015%), neg=0, invalid=96777 0264: dt=2.800000, rms=0.493 (0.025%), neg=0, invalid=96777 0265: dt=2.800000, rms=0.493 (0.034%), neg=0, invalid=96777 0266: dt=2.800000, rms=0.492 (0.044%), neg=0, invalid=96777 0267: dt=2.800000, rms=0.492 (0.050%), neg=0, invalid=96777 0268: dt=2.800000, rms=0.492 (0.055%), neg=0, invalid=96777 0269: dt=2.800000, rms=0.492 (0.064%), neg=0, invalid=96777 0270: dt=2.800000, rms=0.491 (0.067%), neg=0, invalid=96777 0271: dt=2.800000, rms=0.491 (0.069%), neg=0, invalid=96777 0272: dt=2.800000, rms=0.490 (0.076%), neg=0, invalid=96777 0273: dt=2.800000, rms=0.490 (0.077%), neg=0, invalid=96777 0274: dt=2.800000, rms=0.490 (0.075%), neg=0, invalid=96777 0275: dt=2.800000, rms=0.489 (0.076%), neg=0, invalid=96777 0276: dt=2.800000, rms=0.489 (0.074%), neg=0, invalid=96777 0277: dt=2.800000, rms=0.489 (0.077%), neg=0, invalid=96777 0278: dt=2.800000, rms=0.488 (0.076%), neg=0, invalid=96777 0279: dt=2.800000, rms=0.488 (0.074%), neg=0, invalid=96777 0280: dt=2.800000, rms=0.488 (0.074%), neg=0, invalid=96777 0281: dt=2.800000, rms=0.487 (0.077%), neg=0, invalid=96777 0282: dt=2.800000, rms=0.487 (0.073%), neg=0, invalid=96777 0283: dt=2.800000, rms=0.486 (0.070%), neg=0, invalid=96777 0284: dt=2.800000, rms=0.486 (0.071%), neg=0, invalid=96777 0285: dt=2.800000, rms=0.486 (0.071%), neg=0, invalid=96777 0286: dt=2.800000, rms=0.485 (0.069%), neg=0, invalid=96777 0287: dt=2.800000, rms=0.485 (0.071%), neg=0, invalid=96777 0288: dt=2.800000, rms=0.485 (0.069%), neg=0, invalid=96777 0289: dt=2.800000, rms=0.484 (0.067%), neg=0, invalid=96777 0290: dt=2.800000, rms=0.484 (0.070%), neg=0, invalid=96777 0291: dt=2.800000, rms=0.484 (0.068%), neg=0, invalid=96777 0292: dt=2.800000, rms=0.483 (0.066%), neg=0, invalid=96777 0293: dt=2.800000, rms=0.483 (0.062%), neg=0, invalid=96777 0294: dt=2.800000, rms=0.483 (0.059%), neg=0, invalid=96777 0295: dt=2.800000, rms=0.483 (0.059%), neg=0, invalid=96777 0296: dt=2.800000, rms=0.482 (0.055%), neg=0, invalid=96777 0297: dt=2.800000, rms=0.482 (0.059%), neg=0, invalid=96777 0298: dt=2.800000, rms=0.482 (0.057%), neg=0, invalid=96777 0299: dt=2.800000, rms=0.481 (0.054%), neg=0, invalid=96777 0300: dt=2.800000, rms=0.481 (0.052%), neg=0, invalid=96777 0301: dt=2.800000, rms=0.481 (0.050%), neg=0, invalid=96777 0302: dt=2.800000, rms=0.481 (0.049%), neg=0, invalid=96777 0303: 0304: 0305: 0306: 0307: 0308: 0309: 0310: 0311: 0312: 0313: 0314: 0315: 0316: 0317: 0318: 0319: 0320: 0321: 0322: 0323: 0324: 0325: 0326: 0327: 0328: 0329: 0330: 0331: 0332: 0333: 0334: 0335: 0336: 0337: 0338: 0339: 0340: 0341: 0342: 0343: 0344: 0345: 0346: 0347: 0348: 0349: 0350: 0351: 0352: 0353: 0354: 0355: 0356: 0357: 0358: 0359: 0360: 0361: dt=2.800000, rms=0.481 (0.047%), neg=0, invalid=96777 dt=2.800000, rms=0.480 (0.046%), neg=0, invalid=96777 dt=2.800000, rms=0.480 (0.046%), neg=0, invalid=96777 dt=2.800000, rms=0.480 (0.044%), neg=0, invalid=96777 dt=2.800000, rms=0.480 (0.046%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.041%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.041%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.039%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.037%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.039%), neg=0, invalid=96777 dt=2.800000, rms=0.479 (0.036%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.035%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.034%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.032%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.028%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.032%), neg=0, invalid=96777 dt=2.800000, rms=0.478 (0.029%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.030%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.030%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.029%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.028%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.027%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.026%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.025%), neg=0, invalid=96777 dt=2.800000, rms=0.477 (0.027%), neg=0, invalid=96777 dt=2.800000, rms=0.476 (0.026%), neg=0, invalid=96777 dt=2.800000, rms=0.476 (0.025%), neg=0, invalid=96777 dt=2.800000, rms=0.476 (0.026%), neg=0, invalid=96777 dt=2.800000, rms=0.476 (0.024%), neg=0, invalid=96777 dt=2.800000, rms=0.476 (0.024%), neg=0, invalid=96777 dt=128.000000, rms=0.476 (0.077%), neg=0, invalid=96777 dt=8.000000, rms=0.476 (0.014%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.012%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.008%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.010%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.014%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.021%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.028%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.031%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.026%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.030%), neg=0, invalid=96777 dt=8.000000, rms=0.475 (0.029%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.032%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.038%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.036%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.033%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.037%), neg=0, invalid=96777 dt=8.000000, rms=0.474 (0.041%), neg=0, invalid=96777 dt=8.000000, rms=0.473 (0.038%), neg=0, invalid=96777 dt=8.000000, rms=0.473 (0.037%), neg=0, invalid=96777 dt=8.000000, rms=0.473 (0.038%), neg=0, invalid=96777 dt=8.000000, rms=0.473 (0.035%), neg=0, invalid=96777 dt=8.000000, rms=0.473 (0.039%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.041%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.040%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.037%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.038%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.033%), neg=0, invalid=96777 dt=8.000000, rms=0.472 (0.034%), neg=0, invalid=96777 0362: dt=8.000000, rms=0.471 (0.038%), neg=0, invalid=96777 0363: dt=8.000000, rms=0.471 (0.034%), neg=0, invalid=96777 0364: dt=8.000000, rms=0.471 (0.033%), neg=0, invalid=96777 0365: dt=8.000000, rms=0.471 (0.033%), neg=0, invalid=96777 0366: dt=8.000000, rms=0.471 (0.027%), neg=0, invalid=96777 0367: dt=8.000000, rms=0.471 (0.028%), neg=0, invalid=96777 0368: dt=8.000000, rms=0.471 (0.029%), neg=0, invalid=96777 0369: dt=8.000000, rms=0.470 (0.032%), neg=0, invalid=96777 0370: dt=8.000000, rms=0.470 (0.029%), neg=0, invalid=96777 0371: dt=8.000000, rms=0.470 (0.028%), neg=0, invalid=96777 0372: dt=8.000000, rms=0.470 (0.024%), neg=0, invalid=96777 0373: dt=8.000000, rms=0.470 (0.026%), neg=0, invalid=96777 0374: dt=8.000000, rms=0.470 (0.029%), neg=0, invalid=96777 0375: dt=8.000000, rms=0.470 (0.024%), neg=0, invalid=96777 0376: dt=8.000000, rms=0.470 (0.024%), neg=0, invalid=96777 0377: dt=44.800000, rms=0.469 (0.007%), neg=0, invalid=96777 0378: dt=44.800000, rms=0.469 (-0.171%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=96777 0379: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=96777 0380: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=96777 0381: dt=1.171429, rms=0.529 (0.517%), neg=0, invalid=96777 0382: dt=0.320000, rms=0.529 (0.023%), neg=0, invalid=96777 0383: dt=0.320000, rms=0.529 (-0.013%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=96777 0384: dt=0.562500, rms=0.529 (0.093%), neg=0, invalid=96777 0385: dt=0.320000, rms=0.528 (0.016%), neg=0, invalid=96777 0386: dt=0.320000, rms=0.528 (-0.006%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.481, neg=0, invalid=96777 0387: dt=0.112000, rms=0.478 (0.625%), neg=0, invalid=96777 0388: dt=0.112000, rms=0.476 (0.494%), neg=0, invalid=96777 0389: dt=0.007000, rms=0.475 (0.025%), neg=0, invalid=96777 0390: dt=0.007000, rms=0.475 (0.025%), neg=0, invalid=96777 0391: dt=0.007000, rms=0.475 (0.046%), neg=0, invalid=96777 0392: dt=0.007000, rms=0.475 (0.064%), neg=0, invalid=96777 0393: dt=0.007000, rms=0.474 (0.082%), neg=0, invalid=96777 0394: dt=0.007000, rms=0.474 (0.094%), neg=0, invalid=96777 0395: dt=0.007000, rms=0.473 (0.105%), neg=0, invalid=96777 0396: dt=0.007000, rms=0.473 (0.114%), neg=0, invalid=96777 0397: dt=0.007000, rms=0.472 (0.120%), neg=0, invalid=96777 0398: dt=0.007000, rms=0.472 (0.124%), neg=0, invalid=96777 0399: dt=0.007000, rms=0.471 (0.127%), neg=0, invalid=96777 0400: dt=0.007000, rms=0.471 (0.127%), neg=0, invalid=96777 0401: dt=0.007000, rms=0.470 (0.126%), neg=0, invalid=96777 0402: dt=0.007000, rms=0.469 (0.123%), neg=0, invalid=96777 0403: dt=0.007000, rms=0.469 (0.120%), neg=0, invalid=96777 0404: dt=0.007000, rms=0.468 (0.114%), neg=0, invalid=96777 0405: dt=0.007000, rms=0.468 (0.111%), neg=0, invalid=96777 0406: dt=0.007000, rms=0.467 (0.104%), neg=0, invalid=96777 0407: dt=0.007000, rms=0.467 (0.098%), neg=0, invalid=96777 0408: dt=0.007000, rms=0.466 (0.093%), neg=0, invalid=96777 0409: dt=0.007000, rms=0.466 (0.085%), neg=0, invalid=96777 0410: dt=0.007000, rms=0.466 (0.080%), neg=0, invalid=96777 0411: dt=0.007000, rms=0.465 (0.072%), neg=0, invalid=96777 0412: dt=0.007000, rms=0.465 (0.067%), neg=0, invalid=96777 0413: dt=0.007000, rms=0.465 (0.062%), neg=0, invalid=96777 0414: dt=0.007000, rms=0.464 (0.054%), neg=0, invalid=96777 0415: dt=0.007000, rms=0.464 (0.050%), neg=0, invalid=96777 0416: dt=0.007000, rms=0.464 (0.043%), neg=0, invalid=96777 0417: dt=0.007000, rms=0.464 (0.038%), neg=0, invalid=96777 0418: dt=0.007000, rms=0.464 (0.034%), neg=0, invalid=96777 0419: dt=0.007000, rms=0.464 (0.029%), neg=0, invalid=96777 0420: dt=0.007000, rms=0.463 (0.025%), neg=0, invalid=96777 0421: dt=0.007000, rms=0.463 (-0.001%), neg=0, invalid=96777 0422: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 0423: dt=0.112000, rms=0.462 (0.203%), neg=0, invalid=96777 0424: dt=0.096000, rms=0.462 (0.133%), neg=0, invalid=96777 0425: dt=0.020000, rms=0.462 (0.022%), neg=0, invalid=96777 0426: dt=0.020000, rms=0.462 (0.024%), neg=0, invalid=96777 0427: dt=0.020000, rms=0.461 (0.040%), neg=0, invalid=96777 0428: dt=0.020000, rms=0.461 (0.056%), neg=0, invalid=96777 0429: dt=0.020000, rms=0.461 (0.068%), neg=0, invalid=96777 0430: dt=0.020000, rms=0.461 (0.075%), neg=0, invalid=96777 0431: dt=0.020000, rms=0.460 (0.012%), neg=0, invalid=96777 0432: dt=0.020000, rms=0.460 (0.026%), neg=0, invalid=96777 0433: dt=0.020000, rms=0.460 (0.032%), neg=0, invalid=96777 0434: dt=0.020000, rms=0.460 (0.040%), neg=0, invalid=96777 0435: dt=0.020000, rms=0.460 (0.010%), neg=0, invalid=96777 0436: dt=0.020000, rms=0.460 (0.018%), neg=0, invalid=96777 0437: dt=0.020000, rms=0.460 (0.024%), neg=0, invalid=96777 0438: dt=0.020000, rms=0.460 (0.031%), neg=0, invalid=96777 0439: dt=0.020000, rms=0.459 (0.034%), neg=0, invalid=96777 0440: dt=0.020000, rms=0.459 (0.036%), neg=0, invalid=96777 0441: dt=0.020000, rms=0.459 (0.040%), neg=0, invalid=96777 0442: dt=0.020000, rms=0.459 (0.041%), neg=0, invalid=96777 0443: dt=0.020000, rms=0.459 (0.038%), neg=0, invalid=96777 0444: dt=0.020000, rms=0.459 (0.037%), neg=0, invalid=96777 0445: dt=0.020000, rms=0.459 (0.003%), neg=0, invalid=96777 0446: dt=0.020000, rms=0.459 (0.004%), neg=0, invalid=96777 0447: dt=0.020000, rms=0.459 (0.007%), neg=0, invalid=96777 0448: dt=0.020000, rms=0.458 (0.007%), neg=0, invalid=96777 0449: dt=0.112000, rms=0.458 (0.012%), neg=0, invalid=96777 0450: dt=0.112000, rms=0.458 (0.014%), neg=0, invalid=96777 0451: dt=0.112000, rms=0.458 (0.016%), neg=0, invalid=96777 0452: dt=0.112000, rms=0.458 (0.012%), neg=0, invalid=96777 0453: dt=0.112000, rms=0.458 (0.012%), neg=0, invalid=96777 0454: dt=0.028000, rms=0.458 (0.002%), neg=0, invalid=96777 0455: dt=0.028000, rms=0.458 (0.005%), neg=0, invalid=96777 0456: dt=0.028000, rms=0.458 (0.005%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) *********************************************************************************** ********** *********************************************************************************** ********** *********************************************************************************** ********** ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** *********************************************************************************** ********** *********************************************************************************** ********** *********************************************************************************** ********** **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=96777 0457: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=96777 0458: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=96777 0459: dt=369.920000, rms=0.456 (0.086%), neg=0, invalid=96777 0460: dt=32.368000, rms=0.456 (0.020%), neg=0, invalid=96777 0461: dt=32.368000, rms=0.456 (0.006%), neg=0, invalid=96777 0462: dt=32.368000, rms=0.456 (0.000%), neg=0, invalid=96777 0463: dt=32.368000, rms=0.456 (0.005%), neg=0, invalid=96777 0464: dt=32.368000, rms=0.456 (0.015%), neg=0, invalid=96777 0465: dt=32.368000, rms=0.456 (0.023%), neg=0, invalid=96777 0466: dt=32.368000, rms=0.456 (0.026%), neg=0, invalid=96777 0467: dt=32.368000, rms=0.456 (0.018%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=96777 0468: dt=9.072000, rms=0.455 (0.019%), neg=0, invalid=96777 0469: dt=9.072000, rms=0.455 (0.005%), neg=0, invalid=96777 0470: dt=9.072000, rms=0.455 (0.004%), neg=0, invalid=96777 0471: dt=9.072000, rms=0.455 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=96777 0472: dt=36.288000, rms=0.454 (0.248%), neg=0, invalid=96777 0473: dt=62.208000, rms=0.454 (0.143%), neg=0, invalid=96777 0474: dt=62.208000, rms=0.453 (0.168%), neg=0, invalid=96777 0475: dt=62.208000, rms=0.452 (0.262%), neg=0, invalid=96777 0476: dt=62.208000, rms=0.451 (0.237%), neg=0, invalid=96777 0477: dt=62.208000, rms=0.449 (0.371%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0478: dt=62.208000, rms=0.448 (0.250%), neg=0, invalid=96777 0479: dt=62.208000, rms=0.448 (0.038%), neg=0, invalid=96777 0480: dt=62.208000, rms=0.447 (0.246%), neg=0, invalid=96777 0481: dt=62.208000, rms=0.446 (0.147%), neg=0, invalid=96777 0482: dt=62.208000, rms=0.446 (0.045%), neg=0, invalid=96777 0483: dt=62.208000, rms=0.445 (0.104%), neg=0, invalid=96777 0484: dt=62.208000, rms=0.445 (0.103%), neg=0, invalid=96777 0485: dt=20.736000, rms=0.444 (0.060%), neg=0, invalid=96777 0486: dt=20.736000, rms=0.444 (0.012%), neg=0, invalid=96777 0487: dt=20.736000, rms=0.444 (0.012%), neg=0, invalid=96777 0488: dt=20.736000, rms=0.444 (0.022%), neg=0, invalid=96777 0489: dt=20.736000, rms=0.444 (0.033%), neg=0, invalid=96777 0490: dt=20.736000, rms=0.444 (0.034%), neg=0, invalid=96777 0491: dt=20.736000, rms=0.444 (0.032%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=96777 0492: dt=6.400000, rms=0.444 (0.050%), neg=0, invalid=96777 0493: dt=8.000000, rms=0.444 (0.027%), neg=0, invalid=96777 0494: dt=8.000000, rms=0.444 (0.045%), neg=0, invalid=96777 0495: dt=8.000000, rms=0.444 (0.066%), neg=0, invalid=96777 0496: dt=8.000000, rms=0.443 (0.073%), neg=0, invalid=96777 0497: dt=8.000000, rms=0.443 (0.103%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0498: dt=8.000000, rms=0.442 (0.132%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0499: dt=8.000000, rms=0.442 (0.149%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0500: dt=8.000000, rms=0.441 (0.164%), neg=0, invalid=96777 0501: dt=8.000000, rms=0.440 (0.166%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0502: dt=8.000000, rms=0.440 (0.177%), neg=0, invalid=96777 0503: dt=8.000000, rms=0.439 (0.191%), neg=0, invalid=96777 0504: dt=8.000000, rms=0.438 (0.200%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0505: dt=8.000000, rms=0.437 (0.200%), neg=0, invalid=96777 0506: dt=8.000000, rms=0.436 (0.173%), neg=0, invalid=96777 0507: dt=8.000000, rms=0.435 (0.160%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0508: dt=8.000000, rms=0.435 (0.144%), neg=0, invalid=96777 0509: dt=8.000000, rms=0.434 (0.127%), neg=0, invalid=96777 0510: dt=8.000000, rms=0.434 (0.116%), neg=0, invalid=96777 0511: dt=8.000000, rms=0.433 (0.121%), neg=0, invalid=96777 0512: dt=8.000000, rms=0.433 (0.123%), neg=0, invalid=96777 0513: dt=8.000000, rms=0.432 (0.106%), neg=0, invalid=96777 0514: dt=25.600000, rms=0.432 (0.019%), neg=0, invalid=96777 0515: dt=25.600000, rms=0.432 (0.087%), neg=0, invalid=96777 0516: dt=25.600000, rms=0.432 (0.027%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0517: dt=25.600000, rms=0.432 (0.011%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=96777 0518: dt=19.200000, rms=0.429 (0.558%), neg=0, invalid=96777 0519: dt=11.200000, rms=0.428 (0.183%), neg=0, invalid=96777 0520: dt=11.200000, rms=0.428 (0.119%), neg=0, invalid=96777 0521: dt=11.200000, rms=0.427 (0.201%), neg=0, invalid=96777 0522: dt=11.200000, rms=0.426 (0.177%), neg=0, invalid=96777 0523: dt=11.200000, rms=0.426 (0.124%), neg=0, invalid=96777 0524: dt=11.200000, rms=0.425 (0.088%), neg=0, invalid=96777 0525: dt=11.200000, rms=0.425 (0.073%), neg=0, invalid=96777 0526: dt=11.200000, rms=0.425 (0.029%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0527: dt=11.200000, rms=0.425 (0.048%), neg=0, invalid=96777 0528: dt=11.200000, rms=0.424 (0.081%), neg=0, invalid=96777 0529: dt=11.200000, rms=0.424 (0.050%), neg=0, invalid=96777 0530: dt=11.200000, rms=0.424 (0.028%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 0531: dt=0.180000, rms=0.430 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 iter 0, gcam->neg = 8 after 18 iterations, nbhd size=2, neg = 0 0532: dt=4.500000, rms=0.430 (0.143%), neg=0, invalid=96777 0533: dt=1.933333, rms=0.430 (0.026%), neg=0, invalid=96777 0534: dt=1.933333, rms=0.429 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0535: dt=1.933333, rms=0.429 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 19 iterations, nbhd size=2, neg = 0 0536: dt=1.933333, rms=0.429 (-0.032%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=96777 0537: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0538: dt=1.280000, rms=0.437 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0539: dt=0.320000, rms=0.437 (0.010%), neg=0, invalid=96777 0540: dt=0.320000, rms=0.437 (0.003%), neg=0, invalid=96777 0541: dt=0.320000, rms=0.437 (-0.005%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 iter 0, gcam->neg = 338 after 15 iterations, nbhd size=1, neg = 0 0542: dt=1.769096, rms=0.403 (5.551%), neg=0, invalid=96777 0543: dt=0.000250, rms=0.403 (-0.003%), neg=0, invalid=96777 0544: dt=0.000250, rms=0.403 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0545: dt=0.000250, rms=0.403 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0546: dt=0.001750, rms=0.403 (0.001%), neg=0, invalid=96777 0547: dt=0.000438, rms=0.403 (-0.000%), neg=0, invalid=96777 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 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0548: dt=0.000000, rms=0.393 (-0.256%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0549: dt=73.984000, rms=0.393 (0.023%), neg=0, invalid=96777 0550: dt=129.472000, rms=0.393 (0.014%), neg=0, invalid=96777 0551: dt=129.472000, rms=0.393 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0552: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0553: dt=103.680000, rms=0.392 (0.088%), neg=0, invalid=96777 0554: dt=36.288000, rms=0.392 (0.032%), neg=0, invalid=96777 0555: dt=36.288000, rms=0.392 (0.026%), neg=0, invalid=96777 0556: dt=36.288000, rms=0.392 (0.037%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.392 (0.040%), neg=0, invalid=96777 0558: dt=36.288000, rms=0.392 (0.037%), neg=0, invalid=96777 0559: dt=36.288000, rms=0.392 (0.035%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0560: dt=2.400000, rms=0.392 (0.006%), neg=0, invalid=96777 0561: dt=0.700000, rms=0.392 (0.001%), neg=0, invalid=96777 0562: dt=0.700000, rms=0.392 (0.000%), neg=0, invalid=96777 0563: dt=0.700000, rms=0.392 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 18 iterations, nbhd size=2, neg = 0 0564: dt=38.400000, rms=0.391 (0.386%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0565: dt=11.200000, rms=0.390 (0.181%), neg=0, invalid=96777 0566: dt=11.200000, rms=0.390 (-0.085%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0567: dt=0.036000, rms=0.392 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0568: dt=5.043478, rms=0.391 (0.172%), neg=0, invalid=96777 0569: dt=1.008000, rms=0.391 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0570: dt=1.008000, rms=0.391 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0571: dt=1.008000, rms=0.391 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0572: dt=0.864000, rms=0.391 (0.062%), neg=0, invalid=96777 iter 0, gcam->neg = 51 after 21 iterations, nbhd size=2, neg = 0 0573: dt=9.216000, rms=0.388 (0.765%), neg=0, invalid=96777 0574: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0575: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0576: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0577: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0578: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0579: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0580: dt=0.003375, rms=0.388 (0.000%), neg=0, invalid=96777 0581: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0582: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0583: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0584: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0585: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0586: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0587: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0588: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0589: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0590: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0591: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0592: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0593: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0594: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0595: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0596: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0597: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0598: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0599: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0600: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0601: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0602: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0603: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0604: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0605: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0606: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0607: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 0608: dt=0.003375, rms=0.388 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 9 iterations, nbhd size=1, neg = 0 0609: dt=11.520000, rms=0.387 (0.260%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=1, neg = 0 0610: dt=0.864000, rms=0.387 (0.023%), neg=0, invalid=96777 0611: dt=0.864000, rms=0.386 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0612: dt=0.864000, rms=0.386 (0.058%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0613: dt=0.864000, rms=0.386 (0.068%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0614: dt=0.864000, rms=0.386 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0615: dt=0.864000, rms=0.385 (0.055%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0616: dt=2.880000, rms=0.385 (0.018%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0617: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0618: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.382, neg=0, invalid=96777 iter 0, gcam->neg = 319 after 25 iterations, nbhd size=2, neg = 0 0619: dt=0.885811, rms=0.373 (2.370%), neg=0, invalid=96777 0620: dt=0.000078, rms=0.373 (0.002%), neg=0, invalid=96777 0621: dt=0.000078, rms=0.373 (0.000%), neg=0, invalid=96777 0622: dt=0.000078, rms=0.373 (0.000%), neg=0, invalid=96777 0623: dt=0.000078, rms=0.373 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=96777 0624: dt=0.005001, rms=0.373 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0625: dt=0.028000, rms=0.373 (0.011%), neg=0, invalid=96777 0626: dt=0.007000, rms=0.373 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0627: dt=0.007000, rms=0.373 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=1, neg = 0 0628: dt=0.007000, rms=0.373 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0629: dt=0.007000, rms=0.373 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0630: dt=0.007000, rms=0.373 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0631: dt=0.007000, rms=0.373 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0632: dt=0.007000, rms=0.373 (0.003%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 14 minutes and 10 seconds. #-------------------------------------#@# CA Reg Inv Wed Feb 9 07:30:26 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------#@# Remove Neck Wed Feb 9 07:32:09 AST 2022 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-0326.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11186419 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 39 seconds. #-------------------------------------#@# SkullLTA Wed Feb 9 07:33:48 AST 2022 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_withskull_2008-0326.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (50, 10, 25) --> (210, 150, 219) using (103, 57, 122) as brain centroid... mean wm in atlas = 126, using box (83,40,98) --> (122, 74,145) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.091 0.066 0.075 -30.797; -0.081 1.278 0.169 8.049; -0.073 -0.189 1.045 9.861; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.091 0.066 0.075 -30.797; -0.081 1.278 0.169 8.049; -0.073 -0.189 1.045 9.861; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.093 0.024 0.069 -25.139; -0.045 1.280 0.171 2.987; -0.071 -0.185 1.025 11.664; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.093 0.024 0.069 -25.139; -0.045 1.280 0.171 2.987; -0.071 -0.185 1.025 11.664; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.093 0.026 0.061 -24.837; -0.046 1.283 0.180 1.801; -0.062 -0.196 1.028 10.604; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.093 0.026 0.061 -24.837; -0.046 1.280 0.180 2.081; -0.062 -0.196 1.026 10.827; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09342 0.02575 0.06068 -24.83692; -0.04584 1.27986 0.17960 2.08052; -0.06204 -0.19597 1.02552 10.82732; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09342 0.02575 0.06068 -24.83692; -0.04584 1.27986 0.17960 2.08052; -0.06204 -0.19597 1.02552 10.82732; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.093 0.026 0.061 -24.837; -0.046 1.280 0.180 2.081; -0.062 -0.196 1.026 10.827; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.0) transform before final EM align: 1.093 0.026 0.061 -24.837; -0.046 -0.062 0.000 1.280 -0.196 0.000 0.180 1.026 0.000 2.081; 10.827; 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09342 0.02575 0.06068 -24.83692; -0.04584 1.27986 0.17960 2.08052; -0.06204 -0.19597 1.02552 10.82732; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09342 0.02575 0.06068 -24.83692; -0.04584 1.27986 0.17960 2.08052; -0.06204 -0.19597 1.02552 10.82732; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000 final transform: 1.093 0.026 0.061 -24.837; -0.046 1.280 0.180 2.081; -0.062 -0.196 1.026 10.827; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 31 minutes and 42 seconds. #-------------------------------------#@# SubCort Seg Wed Feb 9 08:05:29 AST 2022 mri_ca_label -align norm.mgz transforms/talairach.m3z /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname kcn109 machine x86_64 setenv SUBJECTS_DIR /fefs1/fcit/Rbahathiq0001/freesurfer/subjects cd /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /fefs1/fcit/Rbahathiq0001/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.13984 (21) Left_Lateral_Ventricle (4): linear fit = 0.79 x + 0.0 (486 voxels, overlap=0.376) Left_Lateral_Ventricle (4): linear fit = 0.79 x + 0.0 (486 voxels, peak = 21), gca=21.2 gca peak = 0.14982 (20) mri peak = 0.14742 (22) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1341 voxels, overlap=0.767) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (1341 voxels, peak = 20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.11498 (95) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (287 voxels, overlap=0.982) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (287 voxels, peak = 92), gca=91.7 gca peak = 0.18160 (96) mri peak = 0.08982 (93) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (329 voxels, overlap=0.839) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (329 voxels, peak = 92), gca=91.7 gca peak = 0.27536 (62) mri peak = 0.10660 (70) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (902 voxels, overlap=0.555) Right_Hippocampus (53): linear fit = 1.11 x + 0.0 (902 voxels, peak = 69), gca=68.5 gca peak = 0.32745 (63) mri peak = 0.10609 (71) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (761 voxels, overlap=0.972) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (761 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.13166 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29361 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (29361 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.10197 (109) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (30805 voxels, overlap=0.504) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (30805 voxels, peak = 110), gca=109.7 gca peak = 0.07826 (63) mri peak = 0.05023 (66) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (45474 voxels, overlap=0.955) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (45474 voxels, peak = 65), gca=64.6 gca peak = 0.08598 (64) mri peak = 0.05660 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (43228 voxels, overlap=0.939) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (43228 voxels, peak = 66), gca=65.6 gca peak = 0.24164 (71) mri peak = 0.10577 (80) Right_Caudate (50): linear fit = 1.12 x + 0.0 (832 voxels, overlap=0.448) Right_Caudate (50): linear fit = 1.12 x + 0.0 (832 voxels, peak = 79), gca=79.2 gca peak = 0.18227 (75) mri peak = 0.11634 (81) Left_Caudate (11): linear fit = 1.03 x + 0.0 (765 voxels, overlap=0.990) Left_Caudate (11): linear fit = 1.03 x + 0.0 (765 voxels, peak = 78), gca=77.6 gca peak = 0.10629 (62) mri peak = 0.06199 (71) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (26954 voxels, overlap=0.549) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (26954 voxels, peak = 70), gca=70.4 gca peak = 0.11668 (59) mri peak = 0.06188 (68) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (27324 voxels, overlap=0.425) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (27324 voxels, peak = 68), gca=68.1 gca peak = 0.17849 (88) mri peak = 0.09422 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5550 voxels, overlap=0.875) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5550 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.09820 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4808 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4808 voxels, peak = 91), gca=90.7 gca peak = 0.41688 (64) mri peak = 0.11927 (72) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (327 voxels, overlap=0.145) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (327 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.11674 (71) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (325 voxels, overlap=0.470) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (325 voxels, peak = 69), gca=68.5 gca peak = 0.10041 (96) mri peak = 0.07055 (95) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3671 voxels, overlap=0.776) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (3671 voxels, peak = 101), gca=101.3 gca peak = 0.13978 (88) mri peak = 0.07176 (92) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3436 voxels, overlap=0.988) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3436 voxels, peak = 91), gca=91.1 gca peak = 0.08514 (81) mri peak = 0.09709 (84) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1411 voxels, overlap=0.776) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1411 voxels, peak = 83), gca=83.0 gca peak = 0.09624 (82) mri peak = 0.09117 (84) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1766 voxels, overlap=0.985) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1766 voxels, peak = 83), gca=83.2 gca peak = 0.07543 (88) mri peak = 0.07160 (94) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10120 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10120 voxels, peak = 93), gca=92.8 gca peak = 0.12757 (95) mri peak = 0.07205 (103) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1054 voxels, overlap=0.785) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1054 voxels, peak = 100), gca=100.2 gca peak = 0.17004 (92) mri peak = 0.08648 (103) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1027 voxels, overlap=0.785) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1027 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.10300 (27) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (115 voxels, overlap=0.710) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (115 voxels, peak = 20), gca=20.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.89 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15518 (22) mri peak = 0.13984 (21) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (486 voxels, overlap=0.912) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (486 voxels, peak = 21), gca=21.5 gca peak = 0.19377 (21) mri peak = 0.14742 (22) Right_Lateral_Ventricle (43): linear fit = 0.89 x + 0.0 (1341 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 0.89 x + 0.0 (1341 voxels, peak = 19), gca=18.8 gca peak = 0.30116 (92) mri peak = 0.11498 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (287 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (287 voxels, peak = 93), gca=93.4 gca peak = 0.16589 (93) mri peak = 0.08982 (93) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (329 voxels, overlap=1.001) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (329 voxels, peak = 93), gca=93.0 gca peak = 0.23406 (68) mri peak = 0.10660 (70) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (902 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (902 voxels, peak = 68), gca=68.0 gca peak = 0.28940 (67) mri peak = 0.10609 (71) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (761 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (761 voxels, peak = 69), gca=69.3 gca peak = 0.08343 (108) mri peak = 0.13166 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29361 voxels, overlap=0.652) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (29361 voxels, peak = 108), gca=108.0 gca peak = 0.08545 (110) mri peak = 0.10197 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30805 voxels, overlap=0.644) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30805 voxels, peak = 111), gca=110.6 gca peak = 0.07454 (65) mri peak = 0.05023 (66) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (45474 voxels, overlap=0.922) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (45474 voxels, peak = 65), gca=65.0 gca peak = 0.08746 (65) mri peak = 0.05660 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (43228 voxels, overlap=0.907) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (43228 voxels, peak = 64), gca=64.0 gca peak = 0.24794 (82) mri peak = 0.10577 (80) Right_Caudate (50): linear fit = 1.00 x + 0.0 (832 voxels, overlap=1.004) Right_Caudate (50): linear fit = 1.00 x + 0.0 (832 voxels, peak = 82), gca=82.0 gca peak = 0.17675 (77) mri peak = 0.11634 (81) Left_Caudate (11): linear fit = 1.01 x + 0.0 (765 voxels, overlap=0.944) Left_Caudate (11): linear fit = 1.01 x + 0.0 (765 voxels, peak = 78), gca=78.2 gca peak = 0.09500 (69) mri peak = 0.06199 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26954 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26954 voxels, peak = 69), gca=69.0 gca peak = 0.10990 (69) mri peak = 0.06188 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27324 voxels, overlap=0.986) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27324 voxels, peak = 69), gca=69.0 gca peak = 0.17071 (92) mri peak = 0.09422 (91) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5550 voxels, overlap=0.992) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (5550 voxels, peak = 91), gca=90.6 gca peak = 0.16436 (91) mri peak = 0.09820 (93) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4808 voxels, overlap=0.990) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4808 voxels, peak = 90), gca=89.6 gca peak = 0.30692 (70) mri peak = 0.11927 (72) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (327 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (327 voxels, peak = 71), gca=71.0 gca peak = 0.36178 (69) mri peak = 0.11674 (71) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (325 voxels, overlap=1.009) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (325 voxels, peak = 70), gca=70.0 gca peak = 0.11086 (101) mri peak = 0.07055 (95) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3671 voxels, overlap=0.959) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3671 voxels, peak = 102), gca=101.5 gca peak = 0.13039 (91) mri peak = 0.07176 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3436 voxels, overlap=0.970) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3436 voxels, peak = 91), gca=91.5 gca peak = 0.08396 (83) mri peak = 0.09709 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1411 voxels, overlap=0.883) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1411 voxels, peak = 83), gca=83.0 gca peak = 0.10295 (77) mri peak = 0.09117 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1766 voxels, overlap=0.965) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1766 voxels, peak = 77), gca=77.0 gca peak = 0.06936 (93) mri peak = 0.07160 (94) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10120 voxels, overlap=0.817) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10120 voxels, peak = 93), gca=92.5 gca peak = 0.13199 (100) mri peak = 0.07205 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1054 voxels, overlap=0.841) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1054 voxels, peak = 100), gca=100.5 gca peak = 0.16366 (99) mri peak = 0.08648 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1027 voxels, overlap=0.849) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1027 voxels, peak = 99), gca=99.5 gca peak = 0.21185 (32) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24174 (20) mri peak = 0.10300 (27) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (115 voxels, overlap=0.845) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (115 voxels, peak = 22), gca=22.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.20910 (38) gca peak Third_Ventricle = 0.21185 (32) gca peak CSF = 0.17404 (41) gca peak Left_Accumbens_area = 0.44003 (72) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65116 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.28428 (35) gca peak Right_Accumbens_area = 0.31820 (80) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (38) gca peak WM_hypointensities = 0.17700 (84) gca peak non_WM_hypointensities = 0.09425 (54) gca peak Optic_Chiasm = 0.34763 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 15869 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 652 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 71199 changed. image ll: -2.158, PF=1.000 pass 2: 11883 changed. image ll: -2.155, PF=1.000 pass 3: 4036 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 18 minutes and 46 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri/ transforms/cc_up.lta sub-28962_ses-1_run-1_T1w will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/transforms/cc_up.lta reading aseg from /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/aseg.auto_noCCseg.mgz reading norm from /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/mri/norm.mgz 51626 voxels in left wm, 63681 in right wm, xrange [124, 136] searching rotation angles z=[-9 5], y=[-4 10] searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 global minimum found at slice 130.3, rotations (3.44, -2.40) final transformation (x=130.3, yr=3.435, zr=-2.403): 0.997 0.042 0.060 -11.603; -0.042 0.999 -0.003 69.803; -0.060 0.000 0.998 19.016; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 148 106 eigenvectors: 0.002 -0.010 1.000; 0.004 -1.000 -0.010; 1.000 0.004 -0.002; error in mid anterior detected - correcting... writing aseg with callosum to /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.2 minutes #-------------------------------------#@# Merge ASeg Wed Feb 9 08:25:31 AST 2022 cp aseg.auto.mgz aseg.mgz #-------------------------------------------#@# Intensity Normalization2 Wed Feb 9 08:25:31 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2107 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 111 white matter peak found at 110 gm peak at 70 (70), valley at 36 (36) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 33 (33) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------writing output to brain.mgz 3D bias adjustment took 4 minutes and 9 seconds. #-------------------------------------------- #@# Mask BFS Wed Feb 9 08:29:42 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1663907 voxels in mask (pct= 9.92) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------#@# WM Segmentation Wed Feb 9 08:29:45 AST 2022 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.0 +- 6.5 [80.0 --> 125.0] GM (73.0) : 72.6 +- 9.1 [30.0 --> 96.0] setting bottom of white matter range to 81.7 setting top of gray matter range to 90.8 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... 5865 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5809 filled 100 bright non-wm voxels segmented. 3281 diagonally connected voxels added... white matter segmentation took 1.9 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.75 minutes reading wm segmentation from wm.seg.mgz... 957 voxels added to wm to prevent paths from MTL structures to cortex 1760 additional wm voxels added 0 additional wm voxels added SEG EDIT: 40803 voxels turned on, 54590 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 34 found pass 2 (xy+): 0 found pass 1 (xy-): 27 found - 34 modified 34 modified 27 modified | | | TOTAL: TOTAL: TOTAL: 34 34 61 pass 2 (xy-): 0 found - 27 modified pass 1 (yz+): 22 found - 22 modified pass 2 (yz+): 0 found - 22 modified pass 1 (yz-): 42 found - 42 modified pass 2 (yz-): 0 found - 42 modified pass 1 (xz+): 18 found - 18 modified pass 2 (xz+): 0 found - 18 modified pass 1 (xz-): 26 found - 26 modified pass 2 (xz-): 0 found - 26 modified Iteration Number : 1 pass 1 (+++): 13 found - 13 modified pass 2 (+++): 0 found - 13 modified pass 1 (+++): 8 found 8 modified pass 2 (+++): 0 found 8 modified pass 1 (+++): 7 found 7 modified pass 2 (+++): 0 found 7 modified pass 1 (+++): 14 found - 14 modified pass 2 (+++): 0 found - 14 modified Iteration Number : 1 pass 1 (++): 138 found - 138 modified pass 2 (++): 0 found - 138 modified pass 1 (+-): 144 found - 144 modified pass 2 (+-): 0 found - 144 modified pass 1 (--): 167 found - 167 modified pass 2 (--): 0 found - 167 modified pass 1 (-+): 166 found - 166 modified pass 2 (-+): 0 found - 166 modified Iteration Number : 2 pass 1 (xy+): 5 found 5 modified pass 2 (xy+): 0 found 5 modified pass 1 (xy-): 6 found 6 modified pass 2 (xy-): 0 found 6 modified pass 1 (yz+): 6 found 6 modified pass 2 (yz+): 0 found 6 modified pass 1 (yz-): 7 found 7 modified pass 2 (yz-): 0 found 7 modified pass 1 (xz+): 9 found 9 modified pass 2 (xz+): 0 found 9 modified pass 1 (xz-): 0 found 0 modified Iteration Number : 2 pass 1 (+++): 0 found 0 modified pass 1 (+++): 1 found 1 modified pass 2 (+++): 0 found 1 modified pass 1 (+++): 2 found 2 modified pass 2 (+++): 0 found 2 modified pass 1 (+++): 2 found 2 modified pass 2 (+++): 0 found 2 modified Iteration Number : 2 pass 1 (++): 3 found 3 modified pass 2 (++): 0 found 3 modified pass 1 (+-): 3 found 3 modified pass 2 (+-): 0 found 3 modified pass 1 (--): 2 found 2 modified pass 2 (--): 0 found 2 modified pass 1 (-+): 0 found 0 modified Iteration Number : 3 pass 1 (xy+): 0 found 0 modified pass 1 (xy-): 0 found 0 modified pass 1 (yz+): 0 found 0 modified | | | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 61 83 83 125 125 143 143 169 169 | | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 13 13 21 21 28 28 42 42 | | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 138 138 282 282 449 449 615 615 | | | | | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 5 5 11 11 17 17 24 24 33 33 33 | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 0 1 1 3 3 5 5 | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: | | | TOTAL: TOTAL: TOTAL: 3 3 6 6 8 8 8 0 0 0 pass 1 (yz-): pass 2 (yz-): pass 1 (xz+): pass 2 (xz+): pass 1 (xz-): pass 2 (xz-): Iteration Number pass 1 (+++): pass 1 (+++): pass 1 (+++): pass 1 (+++): Iteration Number pass 1 (++): pass 1 (+-): pass 1 (--): pass 2 (--): pass 1 (-+): Iteration Number pass 1 (xy+): pass 1 (xy-): pass 1 (yz+): pass 1 (yz-): pass 1 (xz+): pass 1 (xz-): Iteration Number pass 1 (+++): pass 1 (+++): pass 1 (+++): pass 1 (+++): Iteration Number pass 1 (++): pass 1 (+-): pass 1 (--): pass 1 (-+): 1 0 1 0 2 0 found found found found found found - : 3 0 found 0 found 0 found 0 found : 3 0 found 0 found 1 found 0 found 0 found : 4 0 found 0 found 0 found 0 found 0 found 0 found : 4 0 found 0 found 0 found 0 found : 4 0 found 0 found 0 found 0 found - 1 1 1 1 2 2 modified modified modified modified modified modified | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 1 1 2 2 4 4 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 1 1 0 modified modified modified modified modified | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 0 0 1 1 1 modified modified modified modified modified modified | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 Total Number of Modified Voxels = 877 (out of 512421: 0.171148) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------#@# Fill Wed Feb 9 08:32:28 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/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 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.025 0.062 0.070 -21.415; -0.076 1.202 0.159 14.825; -0.068 -0.176 0.972 16.571; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1334 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (124, 106, 100), TAL = (4.0, -28.0, 22.0) talairach voxel to voxel transform 0.967 -0.059 -0.060 22.574; 0.051 0.810 -0.136 -8.657; 0.076 0.142 1.000 -17.047; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 106, 100) --> (4.0, -28.0, 22.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (4.00, -28.00, 22.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -28.00, 22.00) SRC: (112.81, 69.00, 106.16) search lh wm seed point around talairach space (-14.00, -28.00, 22.00), SRC: (147.62, 70.84, 108.92) 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 Wed Feb 9 08:33:25 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number pass 1 (xy+): pass 1 (xy-): pass 2 (xy-): pass 1 (yz+): pass 2 (yz+): pass 1 (yz-): pass 2 (yz-): pass 1 (xz+): pass 1 (xz-): Iteration Number pass 1 (+++): pass 1 (+++): pass 1 (+++): pass 1 (+++): Iteration Number pass 1 (++): pass 1 (+-): pass 1 (--): pass 1 (-+): Iteration Number pass 1 (xy+): : 1 0 found 2 found 0 found 2 found 0 found 2 found 0 found 0 found 0 found : 1 0 found 0 found 0 found 0 found : 1 0 found 0 found 0 found 0 found : 2 0 found - modified modified modified modified modified modified modified modified modified | | | | | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 0 2 2 4 4 6 6 6 6 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 0 0 0 2 2 2 2 2 2 0 0 modified modified modified modified 0 modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: | TOTAL: 0 0 0 0 0 pass 1 (xy-): pass 1 (yz+): pass 1 (yz-): pass 1 (xz+): pass 1 (xz-): Iteration Number pass 1 (+++): pass 1 (+++): pass 1 (+++): pass 1 (+++): Iteration Number pass 1 (++): pass 1 (+-): pass 1 (--): pass 1 (-+): 0 0 0 0 0 found found found found found - : 2 0 found 0 found 0 found 0 found : 2 0 found 0 found 0 found 0 found - modified modified modified modified modified | | | | | TOTAL: TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 0 0 0 0 0 0 0 0 0 modified modified modified modified | | | | TOTAL: TOTAL: TOTAL: TOTAL: 0 0 0 0 Total Number of Modified Voxels = 6 (out of 243740: 0.002462) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 170 vertices, 200 faces slice 50: 3680 vertices, 3867 faces slice 60: 11225 vertices, 11540 faces slice 70: 21327 vertices, 21693 faces slice 80: 32282 vertices, 32698 faces slice 90: 43340 vertices, 43691 faces slice 100: 54519 vertices, 54936 faces slice 110: 66918 vertices, 67349 faces slice 120: 78927 vertices, 79375 faces slice 130: 90150 vertices, 90553 faces slice 140: 101721 vertices, 102151 faces slice 150: 111399 vertices, 111765 faces slice 160: 120143 vertices, 120474 faces slice 170: 127553 vertices, 127868 faces slice 180: 134291 vertices, 134587 faces slice 190: 139692 vertices, 139922 faces slice 200: 142979 vertices, 143087 faces slice 210: 143234 vertices, 143306 faces slice 220: 143234 vertices, 143306 faces slice 230: 143234 vertices, 143306 faces slice 240: 143234 vertices, 143306 faces slice 250: 143234 vertices, 143306 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 143234 voxel in cpt #1: X=-72 [v=143234,e=429918,f=286612] located at (30.343996, -13.415851, 53.224422) For the whole surface: X=-72 [v=143234,e=429918,f=286612] One single component has been found nothing to do done #-------------------------------------------#@# Smooth1 lh Wed Feb 9 08:33:33 AST 2022 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------#@# Inflation1 lh Wed Feb 9 08:33:37 AST 2022 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts avg radius = 46.3 mm, total surface area = 75677 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.044 (target=0.015) step 025: RMS=0.040 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------#@# QSphere lh Wed Feb 9 08:34:07 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->6.70) (max @ vno 96791 --> 97949) face area 0.02 +- 0.03 (-0.13-->0.58) scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.972, avgs=0 005/300: dt: 0.9000, rms radial error=176.712, avgs=0 010/300: dt: 0.9000, rms radial error=176.154, avgs=0 015/300: 020/300: 025/300: 030/300: 035/300: 040/300: 045/300: 050/300: 055/300: 060/300: 065/300: 070/300: 075/300: 080/300: 085/300: 090/300: 095/300: 100/300: 105/300: 110/300: 115/300: 120/300: 125/300: 130/300: 135/300: 140/300: 145/300: 150/300: 155/300: 160/300: 165/300: 170/300: 175/300: 180/300: 185/300: 190/300: 195/300: 200/300: 205/300: 210/300: 215/300: 220/300: 225/300: 230/300: 235/300: 240/300: 245/300: 250/300: 255/300: 260/300: 265/300: 270/300: 275/300: 280/300: 285/300: 290/300: 295/300: 300/300: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: dt: 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, 0.9000, rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms rms radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial radial error=175.421, error=174.587, error=173.695, error=172.773, error=171.835, error=170.889, error=169.940, error=168.991, error=168.046, error=167.104, error=166.167, error=165.234, error=164.305, error=163.383, error=162.466, error=161.554, error=160.647, error=159.745, error=158.848, error=157.955, error=157.068, error=156.185, error=155.307, error=154.434, error=153.565, error=152.701, error=151.842, error=150.988, error=150.138, error=149.293, error=148.453, error=147.617, error=146.786, error=145.959, error=145.138, error=144.321, error=143.509, error=142.701, error=141.898, error=141.100, error=140.306, error=139.517, error=138.732, error=137.952, error=137.175, error=136.404, error=135.636, error=134.873, error=134.114, error=133.359, error=132.608, error=131.862, error=131.120, error=130.382, error=129.648, error=128.918, error=128.192, error=127.471, avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16931.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2889.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 307.29 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00721 epoch 4 (K=640.0), pass 1, starting sse = 20.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00949 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------#@# Fix Topology lh Wed Feb 9 08:39:44 AST 2022 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-28962_ses-1_run1_T1w 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-72 (nv=143234, nf=286612, ne=429918, g=37) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 6353 ambiguous faces found in tessellation segmenting defects... 43 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 43 defects to be corrected 0 vertices coincident reading input surface /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5922 (-4.7961) -vertex loglikelihood: -6.0458 (-3.0229) -normal dot loglikelihood: -3.6198 (-3.6198) -quad curv loglikelihood: -6.4594 (-3.2297) Total Loglikelihood : -25.7172 CORRECTING DEFECT 0 (vertices=62, convex hull=68) After retessellation of defect 0, euler #=-40 (139416,416764,277308) : difference with theory (-40) = 0 CORRECTING DEFECT 1 (vertices=102, convex hull=113) After retessellation of defect 1, euler #=-39 (139463,416956,277454) : difference with theory (-39) = 0 CORRECTING DEFECT 2 (vertices=26, convex hull=65) After retessellation of defect 2, euler #=-38 (139471,417007,277498) : difference with theory (-38) = 0 CORRECTING DEFECT 3 (vertices=31, convex hull=67) After retessellation of defect 3, euler #=-37 (139490,417094,277567) : difference with theory (-37) = 0 CORRECTING DEFECT 4 (vertices=819, convex hull=404) After retessellation of defect 4, euler #=-36 (139818,418306,278452) : difference with theory (-36) = 0 CORRECTING DEFECT 5 (vertices=17, convex hull=21) After retessellation of defect 5, euler #=-35 (139819,418316,278462) : difference with theory (-35) = 0 CORRECTING DEFECT 6 (vertices=35, convex hull=57) After retessellation of defect 6, euler #=-34 (139838,418399,278527) : difference with theory (-34) = 0 CORRECTING DEFECT 7 (vertices=83, convex hull=86) After retessellation of defect 7, euler #=-33 (139859,418499,278607) : difference with theory (-33) = 0 CORRECTING DEFECT 8 (vertices=13, convex hull=27) After retessellation of defect 8, euler #=-32 (139860,418512,278620) : difference with theory (-32) = 0 CORRECTING DEFECT 9 (vertices=70, convex hull=88) After retessellation of defect 9, euler #=-31 (139892,418645,278722) : difference with theory (-31) = 0 CORRECTING DEFECT 10 (vertices=6, convex hull=32) After retessellation of defect 10, euler #=-30 (139894,418661,278737) : difference with theory (-30) = 0 CORRECTING DEFECT 11 (vertices=23, convex hull=70) After retessellation of defect 11, euler #=-29 (139908,418730,278793) : difference with theory (-29) = 0 CORRECTING DEFECT 12 (vertices=45, convex hull=84) After retessellation of defect 12, euler #=-28 (139935,418848,278885) : difference with theory (-28) = 0 CORRECTING DEFECT 13 (vertices=17, convex hull=44) After retessellation of defect 13, euler #=-27 (139942,418884,278915) : difference with theory (-27) = 0 CORRECTING DEFECT 14 (vertices=19, convex hull=25) After retessellation of defect 14, euler #=-26 (139944,418896,278926) : difference with theory (-26) = 0 CORRECTING DEFECT 15 (vertices=66, convex hull=87) After retessellation of defect 15, euler #=-25 (139990,419069,279054) : difference with theory (-25) = 0 CORRECTING DEFECT 16 (vertices=73, convex hull=79) After retessellation of defect 16, euler #=-24 (140035,419239,279180) : difference with theory (-24) = 0 CORRECTING DEFECT 17 (vertices=31, convex hull=37) After retessellation of defect 17, euler #=-23 (140052,419303,279228) : difference with theory (-23) = 0 CORRECTING DEFECT 18 (vertices=8, convex hull=20) After retessellation of defect 18, euler #=-22 (140054,419315,279239) : difference with theory (-22) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=24) After retessellation of defect 19, euler #=-21 (140060,419342,279261) : difference with theory (-21) = 0 CORRECTING DEFECT 20 (vertices=26, convex hull=56) After retessellation of defect 20, euler #=-20 (140074,419404,279310) : difference with theory (-20) = 0 CORRECTING DEFECT 21 (vertices=234, convex hull=114) After retessellation of defect 21, euler #=-19 (140117,419587,279451) : difference with theory (-19) = 0 CORRECTING DEFECT 22 (vertices=36, convex hull=22) After retessellation of defect 22, euler #=-18 (140122,419608,279468) : difference with theory (-18) = 0 CORRECTING DEFECT 23 (vertices=186, convex hull=188) After retessellation of defect 23, euler #=-17 (140187,419898,279694) : difference with theory (-17) = 0 CORRECTING DEFECT 24 (vertices=45, convex hull=59) After retessellation of defect 24, euler #=-16 (140210,419990,279764) : difference with theory (-16) = 0 CORRECTING DEFECT 25 (vertices=120, convex hull=68) After retessellation of defect 25, euler #=-15 (140235,420093,279843) : difference with theory (-15) = 0 CORRECTING DEFECT 26 (vertices=35, convex hull=44) After retessellation of defect 26, euler #=-14 (140245,420139,279880) : difference with theory (-14) = 0 CORRECTING DEFECT 27 (vertices=66, convex hull=51) After retessellation of defect 27, euler #=-13 (140263,420214,279938) : difference with theory (-13) = 0 CORRECTING DEFECT 28 (vertices=82, convex hull=50) After retessellation of defect 28, euler #=-12 (140276,420279,279991) : difference with theory (-12) = 0 CORRECTING DEFECT 29 (vertices=602, convex hull=214) After retessellation of defect 29, euler #=-11 (140360,420648,280277) : difference with theory (-11) = 0 CORRECTING DEFECT 30 (vertices=52, convex hull=86) After retessellation of defect 30, euler #=-10 (140389,420771,280372) : difference with theory (-10) = 0 CORRECTING DEFECT 31 (vertices=43, convex hull=91) After retessellation of defect 31, euler #=-9 (140412,420881,280460) : difference with theory (-9) = 0 CORRECTING DEFECT 32 (vertices=39, convex hull=42) After retessellation of defect 32, euler #=-8 (140422,420928,280498) : difference with theory (-8) = 0 CORRECTING DEFECT 33 (vertices=11, convex hull=24) After retessellation of defect 33, euler #=-7 (140422,420936,280507) : difference with theory (-7) = 0 CORRECTING DEFECT 34 (vertices=31, convex hull=77) After retessellation of defect 34, euler #=-6 (140437,421011,280568) : difference with theory (-6) = 0 CORRECTING DEFECT 35 (vertices=19, convex hull=22) After retessellation of defect 35, euler #=-5 (140439,421021,280577) : difference with theory (-5) = 0 CORRECTING DEFECT 36 (vertices=320, convex hull=235) After retessellation of defect 36, euler #=-4 (140502,421332,280826) : difference with theory (-4) = 0 CORRECTING DEFECT 37 (vertices=32, convex hull=74) After retessellation of defect 37, euler #=-3 (140519,421412,280890) : difference with theory (-3) = 0 CORRECTING DEFECT 38 (vertices=38, convex hull=50) After retessellation of defect 38, euler #=-2 (140535,421479,280942) : difference with theory (-2) = 0 CORRECTING DEFECT 39 (vertices=166, convex hull=83) After retessellation of defect 39, euler #=-1 (140552,421567,281014) : difference with theory (-1) = 0 CORRECTING DEFECT 40 (vertices=18, convex hull=62) After retessellation of defect 40, euler #=0 (140561,421620,281059) : difference with theory (0) = 0 CORRECTING DEFECT 41 (vertices=32, convex hull=61) After retessellation of defect 41, euler #=1 (140579,421698,281120) : difference with theory (1) = 0 CORRECTING DEFECT 42 (vertices=37, convex hull=79) After retessellation of defect 42, euler #=2 (140589,421761,281174) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->10.18) (max @ vno 120580 --> 124584) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->10.18) (max @ vno 120580 --> 124584) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 137 mutations (34.5%), 260 crossovers (65.5%), 189 vertices were eliminated building final representation... 2645 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140589, nf=281174, ne=421761, g=0) writing corrected surface to /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 32.2 minutes 0 defective edges removing intersecting faces 000: 324 intersecting 001: 23 intersecting 002: 4 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 140589 - 421761 + 281174 = 2 --> 0 holes F =2V-4: 281174 = 281178-4 (0) 2E=3F: 843522 = 843522 (0) total defect index = 0 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 39 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------#@# Make White Surf lh Wed Feb 9 09:12:05 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-28962_ses1_run-1_T1w lh only generating white matter surface 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/filled.mgz... reading volume /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/brain.finalsurfs.mgz... reading volume /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/wm.mgz... 12038 bright wm thresholded. 132 bright non-wm voxels segmented. reading original surface position from /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/surf/ lh.orig... computing class statistics... border white: 251314 voxels (1.50%) border gray 299349 voxels (1.78%) WM (95.0): 95.8 +- 8.0 [70.0 --> 110.0] GM (82.0) : 81.0 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.5 (was 70) setting MAX_BORDER_WHITE to 113.0 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 50.0 (was 40) setting MAX_GRAY to 97.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run1_T1w/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.07) (max @ vno 140461 --> 140487) face area 0.28 +- 0.12 (0.00-->4.11) mean absolute distance = 0.61 +- 0.72 5076 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=71 mean inside = 95.3, mean outside = 78.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.9, 115 (115) missing vertices, mean dist 0.3 [0.4 (%35.6)->0.7 (%64.4))] %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kcn10, 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 0.91 +- 0.26 (0.05-->5.14) (max @ vno 105739 --> 104806) face area 0.28 +- 0.13 (0.00-->3.79) mean absolute distance = 0.30 +- 0.43 2703 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4845488.5, rms=9.09 001: dt: 0.5000, sse=5732802.0, rms=6.381 (0.000%) 002: dt: 0.5000, sse=6244819.5, rms=4.997 (0.000%) 003: dt: 0.5000, sse=6609198.0, rms=4.257 (0.000%) 004: dt: 0.5000, sse=6846506.0, rms=3.800 (0.000%) 005: dt: 0.5000, sse=7009731.5, rms=3.575 (0.000%) 006: dt: 0.5000, sse=7042031.5, rms=3.408 (0.000%) 007: dt: 0.5000, sse=7120460.5, rms=3.346 (0.000%) 008: dt: 0.5000, sse=7096570.5, rms=3.260 (0.000%) rms = 3.24, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7136871.0, rms=3.243 (0.000%) 010: dt: 0.2500, sse=4411054.5, rms=2.205 (0.000%) 011: dt: 0.2500, sse=4069184.5, rms=1.957 (0.000%) 012: dt: 0.2500, sse=3907296.0, rms=1.898 (0.000%) rms = 1.86, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3866690.5, rms=1.862 (0.000%) rms = 1.83, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3800698.0, rms=1.830 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.2, 100 (32) missing vertices, mean dist -0.2 [0.3 (%79.4)->0.3 (%20.6))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kcn10, 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 +- 0.25 (0.07-->5.06) (max @ vno 105739 --> 104806) face area 0.35 +- 0.16 (0.00-->4.70) mean absolute distance = 0.20 +- 0.31 3256 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4356682.5, rms=4.41 015: dt: 0.5000, sse=4791971.0, rms=2.664 (0.000%) rms = 2.82, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4470640.0, rms=2.062 (0.000%) 017: dt: 0.2500, sse=4290504.0, rms=1.671 (0.000%) 018: dt: 0.2500, sse=4212207.0, rms=1.533 (0.000%) rms = 1.51, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4159858.0, rms=1.505 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=4113109.5, rms=1.476 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 79 (22) missing vertices, mean dist -0.1 [0.2 (%68.7)->0.2 (%31.3))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kcn10, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.09-->4.97) (max @ vno 105739 --> 104806) face area 0.34 +- 0.16 (0.00-->4.56) mean absolute distance = 0.18 +- 0.28 3308 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4205161.0, rms=2.48 021: dt: 0.5000, sse=4669755.5, rms=2.300 (0.000%) rms = 2.64, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4392143.0, rms=1.649 (0.000%) 023: dt: 0.2500, sse=4288895.0, rms=1.400 (0.000%) 024: dt: 0.2500, sse=4258634.0, rms=1.345 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... rms = 1.33, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4236333.5, rms=1.332 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.3, 90 (15) missing vertices, mean dist -0.0 [0.2 (%54.4)->0.2 (%45.6))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kcn10, 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 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4234831.5, rms=1.39 rms = 1.56, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4322471.0, rms=1.115 (0.000%) 027: dt: 0.2500, sse=4537979.5, rms=1.023 (0.000%) rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4537979.5, rms=1.023 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group generating cortex label... 20 non-cortical segments detected only using segment with 2184 vertices erasing segment 0 (vno[0] = 28597) erasing segment 2 (vno[0] = 61493) erasing segment 3 (vno[0] = 64093) erasing segment 4 (vno[0] = 76094) erasing segment 5 (vno[0] = 81781) erasing segment 6 (vno[0] = 81840) erasing segment 7 (vno[0] = 85967) erasing segment 8 (vno[0] = 89621) erasing segment 9 (vno[0] = 93963) erasing segment 10 (vno[0] = 94001) erasing segment 11 (vno[0] = 95953) erasing segment 12 (vno[0] = 96140) erasing segment 13 (vno[0] = 96885) erasing segment 14 (vno[0] = 97152) erasing segment 15 (vno[0] = 97930) erasing segment 16 (vno[0] = 99888) erasing segment 17 (vno[0] = 99997) erasing segment 18 (vno[0] = 100798) erasing segment 19 (vno[0] = 101813) writing cortex label to /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub28962_ses-1_run-1_T1w/label/lh.cortex.label... writing curvature file /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/surf/lh.curv writing smoothed area to lh.area writing curvature file /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses1_run-1_T1w/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.97) (max @ vno 104806 --> 105739) face area 0.34 +- 0.16 (0.00-->4.46) refinement took 6.6 minutes #-------------------------------------------- #@# Smooth2 lh Wed Feb 9 09:18:42 AST 2022 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts 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 Wed Feb 9 09:18:46 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.4 mm, total surface area = 86668 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.6 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 151 vertices thresholded to be in k1 ~ [-0.21 0.78], k2 ~ [-0.11 0.06] total integrated curvature = 0.520*4pi (6.530) --> 0 handles ICI = 1.5, FI = 11.2, variation=185.156 115 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 111 vertices thresholded to be in [-0.12 0.20] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------#@# Curvature Stats lh Wed Feb 9 09:20:54 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-28962_ses-1_run-1_T1w lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-28962_ses-1_run-1_T1w/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... Setting texture Reading texture...Gb_filter = 0 [ ok ] [ sulc ] [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 284 ] Gb_filter = 0 WARN: WARN: S lookup min: S explicit min: -1.841328 0.000000 vertex = 688 WARN: C lookup max: 119.458923 WARN: C explicit max: 99.775620vertex = 140057 #-------------------------------------------#@# Sphere lh Wed Feb 9 09:20:59 AST 2022 /fefs1/fcit/Rbahathiq0001/freesurfer/subjects/sub-28962_ses-1_run-1_T1w/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.280... MRISunfold() max_passes = 1 ------tol=5.0e-01, sigma=0.0, host=kcn10, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.51 pass 1: epoch 2 of 3 starting distance error %19.49 unfolding complete - removing small folds... starting distance error %19.43 removing remaining folds... final distance error %19.45 MRISunfold() return, current seed 1234