Tue May 21 16:12:23 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template /usr/prog/freesurfer5.3.0/bin/recon-all -long PD_HY1_blagojevic_milan_s5 PD_HY1_blagojevic_milan_template -all subjid PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template setenv SUBJECTS_DIR /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017 FREESURFER_HOME /usr/prog/freesurfer5.3.0 Actual FREESURFER_HOME /usr/prog/freesurfer5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 4096 maxlocks unlimited maxsignal 63067 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16356376 2097808 824960 271252 13433608 13650116 Swap: 26214396 120832 26093564 ######################################## 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: 2024/05/21-14:12:23-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:24-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:25-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2024/05/21-14:12:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2024/05/21-14:12:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2024/05/21-14:12:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: dati Machine: krusty Platform: Linux PlatformVersion: 3.10.0-1160.92.1.el7.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/prog/freesurfer5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/prog/freesurfer5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### mkdir -p /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/tmp mri_map_cpdat -in /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/tmp/control.dat -out /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/tmp/control.dat -lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta --in: Using /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/tmp/control.dat as input file. --out: Using /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/tmp/control.dat as output file. --lta: Using /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta as transform. Reading 199 control points... Reading LTA Mapping control points... Writing control points... #-------------------------------------------- #@# MotionCor Tue May 21 16:12:28 CEST 2024 mri_convert -at /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta -odt uchar -rt cubic /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/orig.mgz mri_convert -at /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta -odt uchar -rt cubic /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.78434e-09, 3.32915e-09) j_ras = (6.12323e-17, 1, -6.12323e-17) k_ras = (-5.25928e-25, -8.58906e-09, 1) INFO: Reading transformation from file /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.999 0.019 -0.040 -0.477; -0.019 1.000 0.005 -2.038; 0.040 -0.005 0.999 -3.376; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/orig.mgz... mri_convert -at /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta -rt cubic /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/rawavg.mgz mri_convert -at /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta -rt cubic /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/rawavg.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.78434e-09, 3.32915e-09) j_ras = (6.12323e-17, 1, -6.12323e-17) k_ras = (-5.25928e-25, -8.58906e-09, 1) INFO: Reading transformation from file /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta... Reading transform with LTAreadEx() INFO: Applying transformation from file /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 0.999 0.019 -0.040 -0.477; -0.019 1.000 0.005 -2.038; 0.040 -0.005 0.999 -3.376; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/rawavg.mgz... mri_add_xform_to_header -c /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/talairach.xfm /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/orig.mgz /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 21 16:12:55 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cp /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/talairach.xfm /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 21 16:12:57 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7675, pval=0.6675 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Tue May 21 16:12:57 CEST 2024 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri /usr/prog/freesurfer5.3.0/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 krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue May 21 16:12:57 CEST 2024 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.19807 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19807/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19807/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, 2.85942e-17, 0) j_ras = (-1.53258e-17, 0, -1) k_ras = (1.72255e-16, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.19807/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue May 21 16:13:05 CEST 2024 nu_correct -clobber ./tmp.mri_nu_correct.mni.19807/nu0.mnc ./tmp.mri_nu_correct.mni.19807/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19807/0/ defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [dati@krusty:/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/] [2024-05-21 16:13:06] running: /usr/prog/freesurfer5.3.0/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.19807/0/ ./tmp.mri_nu_correct.mni.19807/nu0.mnc ./tmp.mri_nu_correct.mni.19807/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 14 CV of field change: 0.000979388 [dati@krusty:/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/] [2024-05-21 16:13:32] running: /usr/prog/freesurfer5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19807/nu0.mnc ./tmp.mri_nu_correct.mni.19807/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue May 21 16:13:54 CEST 2024 nu_correct -clobber ./tmp.mri_nu_correct.mni.19807/nu1.mnc ./tmp.mri_nu_correct.mni.19807/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19807/1/ defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [dati@krusty:/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/] [2024-05-21 16:13:54] running: /usr/prog/freesurfer5.3.0/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.19807/1/ ./tmp.mri_nu_correct.mni.19807/nu1.mnc ./tmp.mri_nu_correct.mni.19807/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/prog/freesurfer5.3.0/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 11 CV of field change: 0.000977252 [dati@krusty:/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/] [2024-05-21 16:14:14] running: /usr/prog/freesurfer5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19807/nu1.mnc ./tmp.mri_nu_correct.mni.19807/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.19807/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19807/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.19807/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19807/ones.mgz sysname Linux hostname krusty machine x86_64 user dati input ./tmp.mri_nu_correct.mni.19807/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.19807/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.19807/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19807/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.19807/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19807/input.mean.dat sysname Linux hostname krusty machine x86_64 user dati UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19807/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.19807/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19807/ones.mgz --i ./tmp.mri_nu_correct.mni.19807/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19807/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.19807/ones.mgz --i ./tmp.mri_nu_correct.mni.19807/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19807/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19807/output.mean.dat sysname Linux hostname krusty machine x86_64 user dati UseRobust 0 Loading ./tmp.mri_nu_correct.mni.19807/ones.mgz Loading ./tmp.mri_nu_correct.mni.19807/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.19807/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.19807/nu2.mnc ./tmp.mri_nu_correct.mni.19807/nu2.mnc mul 1.02595315878864376734 Saving result to './tmp.mri_nu_correct.mni.19807/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.19807/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.19807/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.19807/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.85942e-17, 0) j_ras = (-1.53258e-17, 0, -1) k_ras = (1.72255e-16, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 8, 137) to ( 3, 110) Tue May 21 16:15:20 CEST 2024 mri_nu_correct.mni done mri_add_xform_to_header -c /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue May 21 16:15:21 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.004 -0.012 -0.045 -0.166; 0.029 1.063 0.174 2.179; 0.038 -0.257 1.101 -5.842; 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 = 15 Starting OpenSpline(): npoints = 15 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 102 gm peak at 71 (71), valley at 57 (57) csf peak at 35, setting threshold to 59 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 98 gm peak at 69 (69), valley at 58 (58) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 9 seconds. #-------------------------------------------- #@# Skull Stripping Tue May 21 16:17:31 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/brainmask.mgz ./brainmask_PD_HY1_blagojevic_milan_template.mgz '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/brainmask.mgz' -> './brainmask_PD_HY1_blagojevic_milan_template.mgz' mri_mask -keep_mask_deletion_edits T1.mgz brainmask_PD_HY1_blagojevic_milan_template.mgz brainmask.auto.mgz Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to brainmask.auto.mgz...done. mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_PD_HY1_blagojevic_milan_template.mgz brainmask.auto.mgz transfer mask voxels=255 to dst vol Transferring mask edits ('1' voxels) to dst vol DoAbs = 0 Writing masked volume to brainmask.auto.mgz...done. cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue May 21 16:17:36 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/talairach.lta transforms/talairach.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/talairach.lta' -> 'transforms/talairach.lta' #-------------------------------------- #@# CA Normalize Tue May 21 16:17:36 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/aseg.mgz aseg_PD_HY1_blagojevic_milan_template.mgz '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/aseg.mgz' -> 'aseg_PD_HY1_blagojevic_milan_template.mgz' mri_ca_normalize -long aseg_PD_HY1_blagojevic_milan_template.mgz -mask brainmask.mgz nu.mgz /usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using longitudinal segmentation volume aseg_PD_HY1_blagojevic_milan_template.mgz to generate control points... using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 104 resetting gm mean[0]: 63 --> 63 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (51, 63, 59) --> (203, 203, 206) using (102, 110, 133) as brain centroid... mean wm in atlas = 104, using box (83,93,115) --> (120, 127,151) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 0.990 scaling channel 0 by 0.990476 using 244171 sample points... INFO: compute sample coordinates transform 0.996 -0.047 0.008 3.632; 0.044 1.112 0.222 -57.308; -0.017 -0.207 1.049 -2.385; 0.000 0.000 0.000 1.000; INFO: transform used using 99595 total control points for intensity normalization... bias field = 2.391 +- 5.223 2043 of 99595 control points discarded using 99595 total control points for intensity normalization... bias field = 0.874 +- 3.326 1370 of 99595 control points discarded using 99595 total control points for intensity normalization... bias field = 0.855 +- 3.202 1321 of 99595 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 47 seconds. #-------------------------------------- #@# CA Reg Tue May 21 16:19:24 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri mri_ca_register -nobigventricles -levels 2 -A 1 -l /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/talairach.m3z identity.nofile -align-after -mask brainmask.mgz norm.mgz /usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... levels = 2 smoothing gradient with 1 averages... reading previously computed atlas xform /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/talairach.m3z and applying inverse registration identity.nofile 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 reading input volume 'norm.mgz'... reading GCA '/usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=3.931, neg=0, invalid=96776 0001: dt=0.028000, rms=3.918 (0.316%), neg=0, invalid=96776 0002: dt=0.028000, rms=3.911 (0.185%), neg=0, invalid=96776 0003: dt=0.028000, rms=3.904 (0.183%), neg=0, invalid=96776 0004: dt=0.028000, rms=3.890 (0.349%), neg=0, invalid=96776 0005: dt=0.028000, rms=3.871 (0.501%), neg=0, invalid=96776 0006: dt=0.028000, rms=3.865 (0.164%), neg=0, invalid=96776 0007: dt=0.028000, rms=3.852 (0.314%), neg=0, invalid=96776 0008: dt=0.028000, rms=3.835 (0.448%), neg=0, invalid=96776 0009: dt=0.028000, rms=3.813 (0.566%), neg=0, invalid=96776 0010: dt=0.007000, rms=3.812 (0.034%), neg=0, invalid=96776 0011: dt=0.007000, rms=3.811 (0.034%), neg=0, invalid=96776 0012: dt=0.028000, rms=3.806 (0.135%), neg=0, invalid=96776 0013: dt=0.028000, rms=3.801 (0.133%), neg=0, invalid=96776 0014: dt=0.028000, rms=3.796 (0.130%), neg=0, invalid=96776 0015: dt=0.028000, rms=3.786 (0.247%), neg=0, invalid=96776 0016: dt=0.028000, rms=3.773 (0.349%), neg=0, invalid=96776 0017: dt=0.028000, rms=3.756 (0.442%), neg=0, invalid=96776 0018: dt=0.014000, rms=3.754 (0.052%), neg=0, invalid=96776 0019: dt=0.014000, rms=3.751 (0.102%), neg=0, invalid=96776 0020: dt=0.014000, rms=3.745 (0.143%), neg=0, invalid=96776 0021: dt=0.014000, rms=3.738 (0.182%), neg=0, invalid=96776 0022: dt=0.014000, rms=3.730 (0.215%), neg=0, invalid=96776 0023: dt=0.014000, rms=3.721 (0.244%), neg=0, invalid=96776 0024: dt=0.014000, rms=3.711 (0.269%), neg=0, invalid=96776 0025: dt=0.014000, rms=3.701 (0.290%), neg=0, invalid=96776 0026: dt=0.014000, rms=3.689 (0.306%), neg=0, invalid=96776 0027: dt=0.014000, rms=3.677 (0.320%), neg=0, invalid=96776 0028: dt=0.014000, rms=3.665 (0.329%), neg=0, invalid=96776 0029: dt=0.014000, rms=3.653 (0.330%), neg=0, invalid=96776 0030: dt=0.014000, rms=3.641 (0.329%), neg=0, invalid=96776 0031: dt=0.014000, rms=3.629 (0.332%), neg=0, invalid=96776 0032: dt=0.014000, rms=3.617 (0.323%), neg=0, invalid=96776 0033: dt=0.014000, rms=3.606 (0.312%), neg=0, invalid=96776 0034: dt=0.014000, rms=3.595 (0.300%), neg=0, invalid=96776 0035: dt=0.014000, rms=3.585 (0.289%), neg=0, invalid=96776 0036: dt=0.014000, rms=3.575 (0.273%), neg=0, invalid=96776 0037: dt=0.014000, rms=3.566 (0.259%), neg=0, invalid=96776 0038: dt=0.014000, rms=3.566 (0.007%), neg=0, invalid=96776 0039: dt=0.014000, rms=3.565 (0.010%), neg=0, invalid=96776 0040: dt=0.014000, rms=3.565 (0.014%), neg=0, invalid=96776 0041: dt=0.014000, rms=3.564 (0.019%), neg=0, invalid=96776 0042: dt=0.014000, rms=3.563 (0.025%), neg=0, invalid=96776 0043: dt=0.014000, rms=3.562 (0.030%), neg=0, invalid=96776 0044: dt=0.014000, rms=3.561 (0.034%), neg=0, invalid=96776 0045: dt=0.014000, rms=3.559 (0.042%), neg=0, invalid=96776 0046: dt=0.014000, rms=3.559 (0.008%), neg=0, invalid=96776 0047: dt=0.112000, rms=3.556 (0.076%), neg=0, invalid=96776 0048: dt=0.112000, rms=3.554 (0.080%), neg=0, invalid=96776 0049: dt=0.112000, rms=3.551 (0.082%), neg=0, invalid=96776 0050: dt=0.028000, rms=3.550 (0.020%), neg=0, invalid=96776 0051: dt=0.028000, rms=3.549 (0.022%), neg=0, invalid=96776 0052: dt=0.028000, rms=3.548 (0.039%), neg=0, invalid=96776 0053: dt=0.028000, rms=3.546 (0.058%), neg=0, invalid=96776 0054: dt=0.028000, rms=3.545 (0.021%), neg=0, invalid=96776 0055: dt=0.028000, rms=3.543 (0.041%), neg=0, invalid=96776 0056: dt=0.028000, rms=3.541 (0.059%), neg=0, invalid=96776 0057: dt=0.028000, rms=3.541 (0.022%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=3.541, neg=0, invalid=96776 0058: dt=0.096000, rms=3.539 (0.041%), neg=0, invalid=96776 0059: dt=0.096000, rms=3.538 (0.034%), neg=0, invalid=96776 0060: dt=0.096000, rms=3.537 (0.030%), neg=0, invalid=96776 0061: dt=0.048000, rms=3.536 (0.012%), neg=0, invalid=96776 0062: dt=0.024000, rms=3.536 (0.007%), neg=0, invalid=96776 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=3.519, neg=0, invalid=96776 0063: dt=0.007000, rms=3.515 (0.115%), neg=0, invalid=96776 0064: dt=0.007000, rms=3.511 (0.113%), neg=0, invalid=96776 0065: dt=0.007000, rms=3.507 (0.108%), neg=0, invalid=96776 0066: dt=0.007000, rms=3.504 (0.104%), neg=0, invalid=96776 0067: dt=0.007000, rms=3.497 (0.197%), neg=0, invalid=96776 0068: dt=0.003500, rms=3.495 (0.047%), neg=0, invalid=96776 0069: dt=0.003500, rms=3.492 (0.091%), neg=0, invalid=96776 0070: dt=0.003500, rms=3.488 (0.126%), neg=0, invalid=96776 0071: dt=0.003500, rms=3.482 (0.159%), neg=0, invalid=96776 0072: dt=0.003500, rms=3.476 (0.185%), neg=0, invalid=96776 0073: dt=0.003500, rms=3.474 (0.038%), neg=0, invalid=96776 0074: dt=0.003500, rms=3.472 (0.072%), neg=0, invalid=96776 0075: dt=0.003500, rms=3.468 (0.102%), neg=0, invalid=96776 0076: dt=0.003500, rms=3.464 (0.127%), neg=0, invalid=96776 0077: dt=0.001750, rms=3.463 (0.017%), neg=0, invalid=96776 0078: dt=0.001750, rms=3.462 (0.032%), neg=0, invalid=96776 0079: dt=0.001750, rms=3.461 (0.046%), neg=0, invalid=96776 0080: dt=0.001750, rms=3.460 (0.016%), neg=0, invalid=96776 0081: dt=0.020000, rms=3.454 (0.185%), neg=0, invalid=96776 0082: dt=0.007000, rms=3.452 (0.059%), neg=0, invalid=96776 0083: dt=0.007000, rms=3.450 (0.059%), neg=0, invalid=96776 0084: dt=0.007000, rms=3.446 (0.110%), neg=0, invalid=96776 0085: dt=0.001750, rms=3.445 (0.014%), neg=0, invalid=96776 0086: dt=0.001750, rms=3.445 (0.013%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=3.445, neg=0, invalid=96776 0087: dt=0.007000, rms=3.441 (0.109%), neg=0, invalid=96776 0088: dt=0.001500, rms=3.440 (0.020%), neg=0, invalid=96776 0089: dt=0.001500, rms=3.440 (0.022%), neg=0, invalid=96776 0090: dt=0.001500, rms=3.438 (0.041%), neg=0, invalid=96776 0091: dt=0.001500, rms=3.436 (0.060%), neg=0, invalid=96776 0092: dt=0.001500, rms=3.434 (0.073%), neg=0, invalid=96776 0093: dt=0.001500, rms=3.431 (0.086%), neg=0, invalid=96776 0094: dt=0.000375, rms=3.431 (0.004%), neg=0, invalid=96776 0095: dt=0.000375, rms=3.430 (0.008%), neg=0, invalid=96776 0096: dt=0.000375, rms=3.430 (0.013%), neg=0, invalid=96776 0097: dt=0.000375, rms=3.429 (0.016%), neg=0, invalid=96776 0098: dt=0.000375, rms=3.429 (0.019%), neg=0, invalid=96776 0099: dt=0.000375, rms=3.428 (0.021%), neg=0, invalid=96776 0100: dt=0.000375, rms=3.427 (0.024%), neg=0, invalid=96776 0101: dt=0.000375, rms=3.426 (0.026%), neg=0, invalid=96776 0102: dt=0.000375, rms=3.425 (0.027%), neg=0, invalid=96776 0103: dt=0.000375, rms=3.424 (0.029%), neg=0, invalid=96776 0104: dt=0.000375, rms=3.423 (0.030%), neg=0, invalid=96776 0105: dt=0.000375, rms=3.422 (0.031%), neg=0, invalid=96776 0106: dt=0.000375, rms=3.421 (0.032%), neg=0, invalid=96776 0107: dt=0.000375, rms=3.420 (0.033%), neg=0, invalid=96776 0108: dt=0.000375, rms=3.419 (0.034%), neg=0, invalid=96776 0109: dt=0.000375, rms=3.418 (0.033%), neg=0, invalid=96776 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 1.00000 (256) CSF peak too bright - rejecting gca peak = 0.14022 (22) mri peak = 0.25521 (256) CSF peak too bright - rejecting gca peak = 0.24234 (100) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19192 (97) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24007 (63) mri peak = 0.12641 (238) Right_Hippocampus (53): linear fit = 3.76 x + 0.0 (168 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 3.76 x + 0.0 (168 voxels, peak = 237), gca=236.6 gca peak = 0.29892 (64) mri peak = 0.51353 (256) Left_Hippocampus (17): linear fit = 3.92 x + 0.0 (547 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 3.92 x + 0.0 (547 voxels, peak = 251), gca=251.2 gca peak = 0.12541 (104) mri peak = 1.00000 (256) Right_Cerebral_White_Matter: unreasonable value (255.3/256.0), not in range [90, 130] - rejecting gca peak = 0.13686 (104) mri peak = 1.00000 (256) Left_Cerebral_White_Matter: unreasonable value (255.3/256.0), not in range [90, 130] - rejecting gca peak = 0.11691 (63) mri peak = 0.99419 (256) Left_Cerebral_Cortex: unreasonable value (251.1/256.0), not in range [40, 95] - rejecting gca peak = 0.13270 (63) mri peak = 0.98921 (256) Right_Cerebral_Cortex: unreasonable value (251.1/256.0), not in range [40, 95] - rejecting gca peak = 0.15182 (70) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14251 (76) mri peak = 1.00000 (256) Left_Caudate: unreasonable value (255.0/256.0), not in range [50, 100] - rejecting gca peak = 0.12116 (60) mri peak = 0.89208 (256) Left_Cerebellum_Cortex (8): linear fit = 3.98 x + 0.0 (15993 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 3.98 x + 0.0 (15993 voxels, peak = 239), gca=239.1 gca peak = 0.12723 (61) mri peak = 0.98061 (256) Right_Cerebellum_Cortex (47): linear fit = 3.98 x + 0.0 (13731 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 3.98 x + 0.0 (13731 voxels, peak = 243), gca=243.1 gca peak = 0.22684 (88) mri peak = 0.92423 (256) Left_Cerebellum_White_Matter (7): linear fit = 2.89 x + 0.0 (1218 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 2.89 x + 0.0 (1218 voxels, peak = 255), gca=254.8 gca peak = 0.21067 (87) mri peak = 1.00000 (256) Right_Cerebellum_White_Matter (46): linear fit = 2.93 x + 0.0 (2227 voxels, overlap=0.000) Right_Cerebellum_White_Matter (46): linear fit = 2.93 x + 0.0 (2227 voxels, peak = 255), gca=255.3 gca peak = 0.25455 (62) mri peak = 1.00000 (256) Left_Amygdala: unreasonable value (243.3/256.0), not in range [50, 90] - rejecting gca peak = 0.39668 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10129 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12071 (89) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13716 (82) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15214 (84) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.08983 (85) mri peak = 1.00000 (256) Brain_Stem: unreasonable value (254.6/256.0), not in range [80, 110] - rejecting gca peak = 0.11809 (92) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12914 (94) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 1.00000 (256) CSF peak too bright - rejecting gca peak Unknown = 0.94427 ( 0) gca peak Left_Cerebral_White_Matter = 0.13686 (104) gca peak Left_Cerebral_Cortex = 0.11691 (63) gca peak Left_Lateral_Ventricle = 0.11725 (24) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Cerebellum_White_Matter = 0.22684 (88) gca peak Left_Cerebellum_Cortex = 0.12116 (60) gca peak Left_Thalamus_Proper = 0.10129 (93) gca peak Left_Caudate = 0.14251 (76) gca peak Left_Putamen = 0.13716 (82) gca peak Left_Pallidum = 0.19192 (97) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak Brain_Stem = 0.08983 (85) gca peak Left_Hippocampus = 0.29892 (64) gca peak Left_Amygdala = 0.25455 (62) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_VentralDC = 0.12914 (94) 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_Cerebral_White_Matter = 0.12541 (104) gca peak Right_Cerebral_Cortex = 0.13270 (63) gca peak Right_Lateral_Ventricle = 0.14022 (22) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Cerebellum_White_Matter = 0.21067 (87) gca peak Right_Cerebellum_Cortex = 0.12723 (61) gca peak Right_Thalamus_Proper = 0.12071 (89) gca peak Right_Caudate = 0.15182 (70) gca peak Right_Putamen = 0.15214 (84) gca peak Right_Pallidum = 0.24234 (100) gca peak Right_Hippocampus = 0.24007 (63) gca peak Right_Amygdala = 0.39668 (62) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_VentralDC = 0.11809 (92) 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 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=3.416, neg=0, invalid=96776 0110: dt=0.028000, rms=3.406 (0.277%), neg=0, invalid=96776 0111: dt=0.028000, rms=3.397 (0.274%), neg=0, invalid=96776 0112: dt=0.028000, rms=3.388 (0.273%), neg=0, invalid=96776 0113: dt=0.028000, rms=3.379 (0.270%), neg=0, invalid=96776 0114: dt=0.028000, rms=3.370 (0.267%), neg=0, invalid=96776 0115: dt=0.028000, rms=3.361 (0.267%), neg=0, invalid=96776 0116: dt=0.007000, rms=3.358 (0.066%), neg=0, invalid=96776 0117: dt=0.028000, rms=3.350 (0.263%), neg=0, invalid=96776 0118: dt=0.096000, rms=3.319 (0.900%), neg=0, invalid=96776 0119: dt=0.001750, rms=3.319 (0.014%), neg=0, invalid=96776 0120: dt=0.001750, rms=3.318 (0.016%), neg=0, invalid=96776 0121: dt=0.001750, rms=3.317 (0.030%), neg=0, invalid=96776 0122: dt=0.001750, rms=3.316 (0.043%), neg=0, invalid=96776 0123: dt=0.001750, rms=3.314 (0.055%), neg=0, invalid=96776 0124: dt=0.001750, rms=3.312 (0.065%), neg=0, invalid=96776 0125: dt=0.001750, rms=3.310 (0.074%), neg=0, invalid=96776 0126: dt=0.001750, rms=3.307 (0.082%), neg=0, invalid=96776 0127: dt=0.001750, rms=3.304 (0.090%), neg=0, invalid=96776 0128: dt=0.001750, rms=3.301 (0.096%), neg=0, invalid=96776 0129: dt=0.001750, rms=3.297 (0.102%), neg=0, invalid=96776 0130: dt=0.001750, rms=3.294 (0.107%), neg=0, invalid=96776 0131: dt=0.001750, rms=3.290 (0.113%), neg=0, invalid=96776 0132: dt=0.001750, rms=3.286 (0.117%), neg=0, invalid=96776 0133: dt=0.001750, rms=3.282 (0.121%), neg=0, invalid=96776 0134: dt=0.001750, rms=3.278 (0.124%), neg=0, invalid=96776 0135: dt=0.001750, rms=3.274 (0.127%), neg=0, invalid=96776 0136: dt=0.001750, rms=3.270 (0.130%), neg=0, invalid=96776 0137: dt=0.001750, rms=3.265 (0.132%), neg=0, invalid=96776 0138: dt=0.001750, rms=3.261 (0.134%), neg=0, invalid=96776 0139: dt=0.001750, rms=3.257 (0.136%), neg=0, invalid=96776 0140: dt=0.001750, rms=3.252 (0.137%), neg=0, invalid=96776 0141: dt=0.001750, rms=3.248 (0.138%), neg=0, invalid=96776 0142: dt=0.001750, rms=3.243 (0.139%), neg=0, invalid=96776 0143: dt=0.001750, rms=3.239 (0.140%), neg=0, invalid=96776 0144: dt=0.001750, rms=3.234 (0.141%), neg=0, invalid=96776 0145: dt=0.001750, rms=3.229 (0.143%), neg=0, invalid=96776 0146: dt=0.001750, rms=3.225 (0.142%), neg=0, invalid=96776 0147: dt=0.001750, rms=3.220 (0.142%), neg=0, invalid=96776 0148: dt=0.001750, rms=3.216 (0.142%), neg=0, invalid=96776 0149: dt=0.001750, rms=3.211 (0.144%), neg=0, invalid=96776 0150: dt=0.001750, rms=3.206 (0.143%), neg=0, invalid=96776 0151: dt=0.001750, rms=3.202 (0.143%), neg=0, invalid=96776 0152: dt=0.001750, rms=3.197 (0.142%), neg=0, invalid=96776 0153: dt=0.001750, rms=3.193 (0.142%), neg=0, invalid=96776 0154: dt=0.001750, rms=3.188 (0.142%), neg=0, invalid=96776 0155: dt=0.001750, rms=3.184 (0.141%), neg=0, invalid=96776 0156: dt=0.001750, rms=3.179 (0.140%), neg=0, invalid=96776 0157: dt=0.001750, rms=3.175 (0.140%), neg=0, invalid=96776 0158: dt=0.001750, rms=3.170 (0.139%), neg=0, invalid=96776 0159: dt=0.001750, rms=3.166 (0.139%), neg=0, invalid=96776 0160: dt=0.001750, rms=3.162 (0.138%), neg=0, invalid=96776 0161: dt=0.001750, rms=3.157 (0.137%), neg=0, invalid=96776 0162: dt=0.001750, rms=3.153 (0.136%), neg=0, invalid=96776 0163: dt=0.001750, rms=3.149 (0.136%), neg=0, invalid=96776 0164: dt=0.001750, rms=3.145 (0.135%), neg=0, invalid=96776 0165: dt=0.001750, rms=3.140 (0.135%), neg=0, invalid=96776 0166: dt=0.001750, rms=3.136 (0.133%), neg=0, invalid=96776 0167: dt=0.001750, rms=3.132 (0.132%), neg=0, invalid=96776 0168: dt=0.001750, rms=3.128 (0.132%), neg=0, invalid=96776 0169: dt=0.001750, rms=3.124 (0.131%), neg=0, invalid=96776 0170: dt=0.001750, rms=3.120 (0.130%), neg=0, invalid=96776 0171: dt=0.001750, rms=3.116 (0.129%), neg=0, invalid=96776 0172: dt=0.001750, rms=3.112 (0.129%), neg=0, invalid=96776 0173: dt=0.001750, rms=3.108 (0.127%), neg=0, invalid=96776 0174: dt=0.001750, rms=3.104 (0.127%), neg=0, invalid=96776 0175: dt=0.001750, rms=3.100 (0.126%), neg=0, invalid=96776 0176: dt=0.001750, rms=3.096 (0.126%), neg=0, invalid=96776 0177: dt=0.001750, rms=3.092 (0.123%), neg=0, invalid=96776 0178: dt=0.001750, rms=3.088 (0.124%), neg=0, invalid=96776 0179: dt=0.001750, rms=3.084 (0.123%), neg=0, invalid=96776 0180: dt=0.001750, rms=3.081 (0.122%), neg=0, invalid=96776 0181: dt=0.001750, rms=3.077 (0.122%), neg=0, invalid=96776 0182: dt=0.001750, rms=3.073 (0.121%), neg=0, invalid=96776 0183: dt=0.001750, rms=3.070 (0.120%), neg=0, invalid=96776 0184: dt=0.001750, rms=3.066 (0.119%), neg=0, invalid=96776 0185: dt=0.001750, rms=3.062 (0.119%), neg=0, invalid=96776 0186: dt=0.001750, rms=3.059 (0.118%), neg=0, invalid=96776 0187: dt=0.001750, rms=3.055 (0.118%), neg=0, invalid=96776 0188: dt=0.001750, rms=3.051 (0.117%), neg=0, invalid=96776 0189: dt=0.001750, rms=3.048 (0.116%), neg=0, invalid=96776 0190: dt=0.001750, rms=3.044 (0.115%), neg=0, invalid=96776 0191: dt=0.001750, rms=3.041 (0.114%), neg=0, invalid=96776 0192: dt=0.001750, rms=3.038 (0.113%), neg=0, invalid=96776 0193: dt=0.001750, rms=3.034 (0.111%), neg=0, invalid=96776 0194: dt=0.001750, rms=3.031 (0.113%), neg=0, invalid=96776 0195: dt=0.001750, rms=3.027 (0.111%), neg=0, invalid=96776 0196: dt=0.001750, rms=3.024 (0.110%), neg=0, invalid=96776 0197: dt=0.001750, rms=3.021 (0.110%), neg=0, invalid=96776 0198: dt=0.001750, rms=3.017 (0.109%), neg=0, invalid=96776 0199: dt=0.001750, rms=3.014 (0.108%), neg=0, invalid=96776 0200: dt=0.001750, rms=3.011 (0.105%), neg=0, invalid=96776 0201: dt=0.001750, rms=3.008 (0.107%), neg=0, invalid=96776 0202: dt=0.001750, rms=3.005 (0.105%), neg=0, invalid=96776 0203: dt=0.001750, rms=3.001 (0.105%), neg=0, invalid=96776 0204: dt=0.001750, rms=2.998 (0.103%), neg=0, invalid=96776 0205: dt=0.001750, rms=2.995 (0.104%), neg=0, invalid=96776 0206: dt=0.001750, rms=2.992 (0.103%), neg=0, invalid=96776 0207: dt=0.001750, rms=2.989 (0.101%), neg=0, invalid=96776 0208: dt=0.001750, rms=2.986 (0.102%), neg=0, invalid=96776 0209: dt=0.001750, rms=2.983 (0.101%), neg=0, invalid=96776 0210: dt=0.001750, rms=2.980 (0.099%), neg=0, invalid=96776 0211: dt=0.001750, rms=2.977 (0.100%), neg=0, invalid=96776 0212: dt=0.001750, rms=2.974 (0.100%), neg=0, invalid=96776 0213: dt=0.001750, rms=2.971 (0.097%), neg=0, invalid=96776 0214: dt=0.001750, rms=2.968 (0.098%), neg=0, invalid=96776 0215: dt=0.001750, rms=2.966 (0.094%), neg=0, invalid=96776 0216: dt=0.001750, rms=2.963 (0.096%), neg=0, invalid=96776 0217: dt=0.001750, rms=2.960 (0.096%), neg=0, invalid=96776 0218: dt=0.001750, rms=2.957 (0.095%), neg=0, invalid=96776 0219: dt=0.001750, rms=2.954 (0.095%), neg=0, invalid=96776 0220: dt=0.001750, rms=2.951 (0.094%), neg=0, invalid=96776 0221: dt=0.001750, rms=2.949 (0.094%), neg=0, invalid=96776 0222: dt=0.001750, rms=2.946 (0.093%), neg=0, invalid=96776 0223: dt=0.001750, rms=2.943 (0.093%), neg=0, invalid=96776 0224: dt=0.001750, rms=2.941 (0.091%), neg=0, invalid=96776 0225: dt=0.001750, rms=2.938 (0.091%), neg=0, invalid=96776 0226: dt=0.001750, rms=2.935 (0.087%), neg=0, invalid=96776 0227: dt=0.001750, rms=2.933 (0.088%), neg=0, invalid=96776 0228: dt=0.001750, rms=2.930 (0.089%), neg=0, invalid=96776 0229: dt=0.001750, rms=2.927 (0.090%), neg=0, invalid=96776 0230: dt=0.001750, rms=2.925 (0.087%), neg=0, invalid=96776 0231: dt=0.001750, rms=2.922 (0.089%), neg=0, invalid=96776 0232: dt=0.001750, rms=2.920 (0.087%), neg=0, invalid=96776 0233: dt=0.001750, rms=2.917 (0.085%), neg=0, invalid=96776 0234: dt=0.001750, rms=2.915 (0.086%), neg=0, invalid=96776 0235: dt=0.001750, rms=2.912 (0.085%), neg=0, invalid=96776 0236: dt=0.001750, rms=2.910 (0.085%), neg=0, invalid=96776 0237: dt=0.001750, rms=2.907 (0.084%), neg=0, invalid=96776 0238: dt=0.001750, rms=2.905 (0.085%), neg=0, invalid=96776 0239: dt=0.001750, rms=2.903 (0.082%), neg=0, invalid=96776 0240: dt=0.001750, rms=2.900 (0.082%), neg=0, invalid=96776 0241: dt=0.001750, rms=2.898 (0.079%), neg=0, invalid=96776 0242: dt=0.001750, rms=2.896 (0.081%), neg=0, invalid=96776 0243: dt=0.001750, rms=2.893 (0.080%), neg=0, invalid=96776 0244: dt=0.001750, rms=2.891 (0.080%), neg=0, invalid=96776 0245: dt=0.001750, rms=2.889 (0.081%), neg=0, invalid=96776 0246: dt=0.001750, rms=2.886 (0.079%), neg=0, invalid=96776 0247: dt=0.001750, rms=2.884 (0.080%), neg=0, invalid=96776 0248: dt=0.001750, rms=2.882 (0.078%), neg=0, invalid=96776 0249: dt=0.001750, rms=2.879 (0.078%), neg=0, invalid=96776 0250: dt=0.001750, rms=2.877 (0.077%), neg=0, invalid=96776 0251: dt=0.001750, rms=2.875 (0.077%), neg=0, invalid=96776 0252: dt=0.001750, rms=2.873 (0.076%), neg=0, invalid=96776 0253: dt=0.001750, rms=2.871 (0.076%), neg=0, invalid=96776 0254: dt=0.001750, rms=2.868 (0.076%), neg=0, invalid=96776 0255: dt=0.001750, rms=2.866 (0.074%), neg=0, invalid=96776 0256: dt=0.001750, rms=2.864 (0.075%), neg=0, invalid=96776 0257: dt=0.001750, rms=2.862 (0.075%), neg=0, invalid=96776 0258: dt=0.001750, rms=2.860 (0.074%), neg=0, invalid=96776 0259: dt=0.001750, rms=2.858 (0.072%), neg=0, invalid=96776 0260: dt=0.001750, rms=2.856 (0.073%), neg=0, invalid=96776 0261: dt=0.001750, rms=2.854 (0.072%), neg=0, invalid=96776 0262: dt=0.001750, rms=2.852 (0.072%), neg=0, invalid=96776 0263: dt=0.001750, rms=2.850 (0.070%), neg=0, invalid=96776 0264: dt=0.001750, rms=2.848 (0.071%), neg=0, invalid=96776 0265: dt=0.001750, rms=2.846 (0.070%), neg=0, invalid=96776 0266: dt=0.001750, rms=2.844 (0.070%), neg=0, invalid=96776 0267: dt=0.001750, rms=2.842 (0.070%), neg=0, invalid=96776 0268: dt=0.001750, rms=2.840 (0.069%), neg=0, invalid=96776 0269: dt=0.001750, rms=2.838 (0.069%), neg=0, invalid=96776 0270: dt=0.001750, rms=2.836 (0.068%), neg=0, invalid=96776 0271: dt=0.001750, rms=2.834 (0.067%), neg=0, invalid=96776 0272: dt=0.001750, rms=2.832 (0.067%), neg=0, invalid=96776 0273: dt=0.001750, rms=2.830 (0.067%), neg=0, invalid=96776 0274: dt=0.001750, rms=2.828 (0.067%), neg=0, invalid=96776 0275: dt=0.001750, rms=2.826 (0.067%), neg=0, invalid=96776 0276: dt=0.001750, rms=2.824 (0.066%), neg=0, invalid=96776 0277: dt=0.001750, rms=2.823 (0.066%), neg=0, invalid=96776 0278: dt=0.001750, rms=2.821 (0.069%), neg=0, invalid=96776 0279: dt=0.001750, rms=2.819 (0.065%), neg=0, invalid=96776 0280: dt=0.001750, rms=2.817 (0.064%), neg=0, invalid=96776 0281: dt=0.001750, rms=2.815 (0.064%), neg=0, invalid=96776 0282: dt=0.001750, rms=2.813 (0.063%), neg=0, invalid=96776 0283: dt=0.001750, rms=2.812 (0.063%), neg=0, invalid=96776 0284: dt=0.001750, rms=2.810 (0.064%), neg=0, invalid=96776 0285: dt=0.001750, rms=2.808 (0.062%), neg=0, invalid=96776 0286: dt=0.001750, rms=2.806 (0.062%), neg=0, invalid=96776 0287: dt=0.001750, rms=2.805 (0.062%), neg=0, invalid=96776 0288: dt=0.001750, rms=2.803 (0.062%), neg=0, invalid=96776 0289: dt=0.001750, rms=2.801 (0.062%), neg=0, invalid=96776 0290: dt=0.001750, rms=2.799 (0.061%), neg=0, invalid=96776 0291: dt=0.001750, rms=2.798 (0.060%), neg=0, invalid=96776 0292: dt=0.001750, 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rms=2.575 (0.074%), neg=0, invalid=96776 0493: dt=0.007000, rms=2.573 (0.076%), neg=0, invalid=96776 0494: dt=0.007000, rms=2.571 (0.072%), neg=0, invalid=96776 0495: dt=0.007000, rms=2.569 (0.073%), neg=0, invalid=96776 0496: dt=0.007000, rms=2.567 (0.072%), neg=0, invalid=96776 0497: dt=0.007000, rms=2.565 (0.072%), neg=0, invalid=96776 0498: dt=0.007000, rms=2.564 (0.072%), neg=0, invalid=96776 0499: dt=0.007000, rms=2.562 (0.072%), neg=0, invalid=96776 0500: dt=0.007000, rms=2.560 (0.069%), neg=0, invalid=96776 0501: dt=0.007000, rms=2.558 (0.069%), neg=0, invalid=96776 0502: dt=0.007000, rms=2.557 (0.066%), neg=0, invalid=96776 0503: dt=0.007000, rms=2.555 (0.068%), neg=0, invalid=96776 0504: dt=0.007000, rms=2.553 (0.064%), neg=0, invalid=96776 0505: dt=0.007000, rms=2.551 (0.069%), neg=0, invalid=96776 0506: dt=0.007000, rms=2.550 (0.062%), neg=0, invalid=96776 0507: dt=0.007000, rms=2.548 (0.067%), neg=0, invalid=96776 0508: dt=0.007000, rms=2.546 (0.064%), neg=0, invalid=96776 0509: dt=0.007000, rms=2.545 (0.061%), neg=0, invalid=96776 0510: dt=0.007000, rms=2.543 (0.061%), neg=0, invalid=96776 0511: dt=0.007000, rms=2.542 (0.061%), neg=0, invalid=96776 0512: dt=0.007000, rms=2.540 (0.059%), neg=0, invalid=96776 0513: dt=0.007000, rms=2.539 (0.057%), neg=0, invalid=96776 0514: dt=0.007000, rms=2.537 (0.061%), neg=0, invalid=96776 0515: dt=0.007000, rms=2.536 (0.057%), neg=0, invalid=96776 0516: dt=0.007000, rms=2.534 (0.057%), neg=0, invalid=96776 0517: dt=0.007000, rms=2.533 (0.056%), neg=0, invalid=96776 0518: dt=0.007000, rms=2.532 (0.053%), neg=0, invalid=96776 0519: dt=0.007000, rms=2.530 (0.055%), neg=0, invalid=96776 0520: dt=0.007000, rms=2.529 (0.050%), neg=0, invalid=96776 0521: dt=0.007000, rms=2.528 (0.051%), neg=0, invalid=96776 0522: dt=0.007000, rms=2.526 (0.052%), neg=0, invalid=96776 0523: dt=0.007000, rms=2.525 (0.049%), neg=0, invalid=96776 0524: dt=0.007000, rms=2.524 (0.050%), neg=0, invalid=96776 0525: dt=0.007000, rms=2.523 (0.049%), neg=0, invalid=96776 0526: dt=0.007000, rms=2.521 (0.048%), neg=0, invalid=96776 0527: dt=0.007000, rms=2.520 (0.047%), neg=0, invalid=96776 0528: dt=0.007000, rms=2.519 (0.045%), neg=0, invalid=96776 0529: dt=0.007000, rms=2.518 (0.043%), neg=0, invalid=96776 0530: dt=0.007000, rms=2.517 (0.047%), neg=0, invalid=96776 0531: dt=0.007000, rms=2.516 (0.045%), neg=0, invalid=96776 0532: dt=0.007000, rms=2.515 (0.042%), neg=0, invalid=96776 0533: dt=0.007000, rms=2.514 (0.042%), neg=0, invalid=96776 0534: dt=0.007000, rms=2.513 (0.043%), neg=0, invalid=96776 0535: dt=0.007000, rms=2.511 (0.045%), neg=0, invalid=96776 0536: dt=0.007000, rms=2.510 (0.039%), neg=0, invalid=96776 0537: dt=0.007000, rms=2.509 (0.041%), neg=0, invalid=96776 0538: dt=0.007000, rms=2.509 (0.037%), neg=0, invalid=96776 0539: dt=0.007000, rms=2.507 (0.041%), neg=0, invalid=96776 0540: dt=0.007000, rms=2.506 (0.041%), neg=0, invalid=96776 0541: dt=0.007000, rms=2.505 (0.040%), neg=0, invalid=96776 0542: dt=0.007000, rms=2.505 (0.035%), neg=0, invalid=96776 0543: dt=0.007000, rms=2.504 (0.039%), neg=0, invalid=96776 0544: dt=0.007000, rms=2.503 (0.037%), neg=0, invalid=96776 0545: dt=0.007000, rms=2.502 (0.035%), neg=0, invalid=96776 0546: dt=0.007000, rms=2.501 (0.037%), neg=0, invalid=96776 0547: dt=0.007000, rms=2.500 (0.039%), neg=0, invalid=96776 0548: dt=0.007000, rms=2.499 (0.035%), neg=0, invalid=96776 0549: dt=0.007000, rms=2.498 (0.035%), neg=0, invalid=96776 0550: dt=0.007000, rms=2.497 (0.034%), neg=0, invalid=96776 0551: dt=0.007000, rms=2.496 (0.033%), neg=0, invalid=96776 0552: dt=0.007000, rms=2.496 (0.032%), neg=0, invalid=96776 0553: dt=0.007000, rms=2.495 (0.033%), neg=0, invalid=96776 0554: dt=0.007000, rms=2.494 (0.031%), neg=0, invalid=96776 0555: dt=0.007000, rms=2.493 (0.034%), neg=0, invalid=96776 0556: dt=0.007000, rms=2.492 (0.032%), neg=0, invalid=96776 0557: dt=0.007000, rms=2.492 (0.032%), neg=0, invalid=96776 0558: dt=0.007000, rms=2.491 (0.031%), neg=0, invalid=96776 0559: dt=0.007000, rms=2.490 (0.032%), neg=0, invalid=96776 0560: dt=0.007000, rms=2.489 (0.030%), neg=0, invalid=96776 0561: dt=0.007000, rms=2.489 (0.030%), neg=0, invalid=96776 0562: dt=0.007000, rms=2.488 (0.030%), neg=0, invalid=96776 0563: dt=0.007000, rms=2.487 (0.029%), neg=0, invalid=96776 0564: dt=0.007000, rms=2.486 (0.029%), neg=0, invalid=96776 0565: dt=0.007000, rms=2.486 (0.027%), neg=0, invalid=96776 0566: dt=0.007000, rms=2.485 (0.030%), neg=0, invalid=96776 0567: dt=0.007000, rms=2.484 (0.029%), neg=0, invalid=96776 0568: dt=0.007000, rms=2.484 (0.028%), neg=0, invalid=96776 0569: dt=0.007000, rms=2.483 (0.028%), neg=0, invalid=96776 0570: dt=0.007000, rms=2.482 (0.029%), neg=0, invalid=96776 0571: dt=0.007000, rms=2.481 (0.027%), neg=0, invalid=96776 0572: dt=0.007000, rms=2.481 (0.026%), neg=0, invalid=96776 0573: dt=0.007000, rms=2.480 (0.027%), neg=0, invalid=96776 0574: dt=0.007000, rms=2.479 (0.027%), neg=0, invalid=96776 0575: dt=0.007000, rms=2.479 (0.026%), neg=0, invalid=96776 0576: dt=0.007000, rms=2.478 (0.026%), neg=0, invalid=96776 0577: dt=0.007000, rms=2.478 (0.026%), neg=0, invalid=96776 0578: dt=0.007000, rms=2.477 (0.028%), neg=0, invalid=96776 0579: dt=0.007000, rms=2.476 (0.025%), neg=0, invalid=96776 0580: dt=0.007000, rms=2.476 (0.025%), neg=0, invalid=96776 0581: dt=0.007000, rms=2.475 (0.023%), neg=0, invalid=96776 0582: dt=0.007000, rms=2.474 (0.025%), neg=0, invalid=96776 0583: dt=0.007000, rms=2.474 (0.027%), neg=0, invalid=96776 0584: dt=0.007000, rms=2.473 (0.024%), neg=0, invalid=96776 0585: dt=0.007000, rms=2.473 (0.024%), neg=0, invalid=96776 0586: dt=0.007000, rms=2.472 (0.024%), neg=0, invalid=96776 0587: dt=0.028000, rms=2.472 (0.008%), neg=0, invalid=96776 0588: dt=0.028000, rms=2.472 (0.006%), neg=0, invalid=96776 0589: dt=0.028000, rms=2.471 (0.016%), neg=0, invalid=96776 0590: dt=0.028000, rms=2.471 (0.021%), neg=0, invalid=96776 0591: dt=0.028000, rms=2.470 (0.028%), neg=0, invalid=96776 0592: dt=0.028000, rms=2.469 (0.032%), neg=0, invalid=96776 0593: dt=0.028000, rms=2.468 (0.037%), neg=0, invalid=96776 0594: dt=0.007000, rms=2.468 (0.002%), neg=0, invalid=96776 0595: dt=0.007000, rms=2.468 (0.004%), neg=0, invalid=96776 0596: dt=0.007000, rms=2.468 (0.004%), neg=0, invalid=96776 0597: dt=0.028000, rms=2.468 (0.009%), neg=0, invalid=96776 0598: dt=0.020000, rms=2.468 (0.006%), neg=0, invalid=96776 0599: dt=0.010000, rms=2.468 (0.001%), neg=0, invalid=96776 0600: dt=0.010000, rms=2.468 (0.007%), neg=0, invalid=96776 0601: dt=0.010000, rms=2.467 (0.007%), neg=0, invalid=96776 0602: dt=0.010000, rms=2.467 (0.010%), neg=0, invalid=96776 0603: dt=0.010000, rms=2.467 (0.002%), neg=0, invalid=96776 0604: dt=0.010000, rms=2.467 (0.006%), neg=0, invalid=96776 0605: dt=0.010000, rms=2.467 (0.007%), neg=0, invalid=96776 0606: dt=0.010000, rms=2.466 (0.009%), neg=0, invalid=96776 0607: dt=0.010000, rms=2.466 (0.012%), neg=0, invalid=96776 0608: dt=0.010000, rms=2.466 (0.013%), neg=0, invalid=96776 0609: dt=0.010000, rms=2.466 (0.014%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.466, neg=0, invalid=96776 0610: dt=0.028000, rms=2.465 (0.002%), neg=0, invalid=96776 0611: dt=0.024000, rms=2.465 (0.004%), neg=0, invalid=96776 0612: dt=0.007000, rms=2.465 (-0.000%), neg=0, invalid=96776 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.431, neg=0, invalid=96776 0613: dt=0.005000, rms=2.428 (0.132%), neg=0, invalid=96776 0614: dt=0.005000, rms=2.425 (0.132%), neg=0, invalid=96776 0615: dt=0.001500, rms=2.424 (0.039%), neg=0, invalid=96776 0616: dt=0.001500, rms=2.423 (0.038%), neg=0, invalid=96776 0617: dt=0.001500, rms=2.421 (0.074%), neg=0, invalid=96776 0618: dt=0.001500, rms=2.420 (0.040%), neg=0, invalid=96776 0619: dt=0.001500, rms=2.419 (0.074%), neg=0, invalid=96776 0620: dt=0.001500, rms=2.416 (0.105%), neg=0, invalid=96776 0621: dt=0.001500, rms=2.413 (0.133%), neg=0, invalid=96776 0622: dt=0.001500, rms=2.409 (0.158%), neg=0, invalid=96776 0623: dt=0.001500, rms=2.405 (0.180%), neg=0, invalid=96776 0624: dt=0.000375, rms=2.404 (0.010%), neg=0, invalid=96776 0625: dt=0.000375, rms=2.404 (0.009%), neg=0, invalid=96776 0626: dt=0.007000, rms=2.400 (0.175%), neg=0, invalid=96776 0627: dt=0.000438, rms=2.400 (0.010%), neg=0, invalid=96776 0628: dt=0.000438, rms=2.399 (0.011%), neg=0, invalid=96776 0629: dt=0.000438, rms=2.399 (0.021%), neg=0, invalid=96776 0630: dt=0.000438, rms=2.398 (0.030%), neg=0, invalid=96776 0631: dt=0.000438, rms=2.397 (0.037%), neg=0, invalid=96776 0632: dt=0.000438, rms=2.396 (0.044%), neg=0, invalid=96776 0633: dt=0.000438, rms=2.396 (0.011%), neg=0, invalid=96776 0634: dt=0.000438, rms=2.396 (0.010%), neg=0, invalid=96776 0635: dt=0.001750, rms=2.395 (0.043%), neg=0, invalid=96776 0636: dt=0.000438, rms=2.395 (0.010%), neg=0, invalid=96776 0637: dt=0.000438, rms=2.394 (0.011%), neg=0, invalid=96776 0638: dt=0.000438, rms=2.394 (0.011%), neg=0, invalid=96776 0639: dt=0.000438, rms=2.394 (0.018%), neg=0, invalid=96776 0640: dt=0.000438, rms=2.393 (0.031%), neg=0, invalid=96776 0641: dt=0.000438, rms=2.392 (0.037%), neg=0, invalid=96776 0642: dt=0.000438, rms=2.391 (0.042%), neg=0, invalid=96776 0643: dt=0.000438, rms=2.390 (0.051%), neg=0, invalid=96776 0644: dt=0.000438, rms=2.388 (0.055%), neg=0, invalid=96776 0645: dt=0.000027, rms=2.388 (-0.002%), neg=0, invalid=96776 0646: dt=0.000027, rms=2.388 (0.001%), neg=0, invalid=96776 0647: dt=0.001750, rms=2.387 (0.042%), neg=0, invalid=96776 0648: dt=0.001750, rms=2.386 (0.044%), neg=0, invalid=96776 0649: dt=0.005000, rms=2.384 (0.119%), neg=0, invalid=96776 0650: dt=0.001250, rms=2.383 (0.030%), neg=0, invalid=96776 0651: dt=0.000313, rms=2.383 (0.008%), neg=0, invalid=96776 0652: dt=0.000313, rms=2.382 (0.014%), neg=0, invalid=96776 0653: dt=0.000313, rms=2.382 (0.020%), neg=0, invalid=96776 0654: dt=0.000313, rms=2.382 (0.006%), neg=0, invalid=96776 0655: dt=0.000313, rms=2.381 (0.014%), neg=0, invalid=96776 0656: dt=0.000313, rms=2.381 (0.021%), neg=0, invalid=96776 0657: dt=0.000313, rms=2.380 (0.025%), neg=0, invalid=96776 0658: dt=0.000313, rms=2.380 (0.030%), neg=0, invalid=96776 0659: dt=0.000313, rms=2.379 (0.035%), neg=0, invalid=96776 0660: dt=0.000313, rms=2.378 (0.037%), neg=0, invalid=96776 0661: dt=0.000313, rms=2.377 (0.043%), neg=0, invalid=96776 0662: dt=0.000313, rms=2.376 (0.045%), neg=0, invalid=96776 0663: dt=0.000313, rms=2.375 (0.047%), neg=0, invalid=96776 0664: dt=0.000313, rms=2.373 (0.051%), neg=0, invalid=96776 0665: dt=0.000313, rms=2.372 (0.052%), neg=0, invalid=96776 0666: dt=0.000313, rms=2.371 (0.054%), neg=0, invalid=96776 0667: dt=0.000313, rms=2.370 (0.056%), neg=0, invalid=96776 0668: dt=0.000313, rms=2.368 (0.056%), neg=0, invalid=96776 0669: dt=0.000313, rms=2.367 (0.060%), neg=0, invalid=96776 0670: dt=0.000313, rms=2.365 (0.059%), neg=0, invalid=96776 0671: dt=0.000313, rms=2.364 (0.061%), neg=0, invalid=96776 0672: dt=0.000313, rms=2.363 (0.063%), neg=0, invalid=96776 0673: dt=0.000313, rms=2.361 (0.063%), neg=0, invalid=96776 0674: dt=0.000313, rms=2.360 (0.063%), neg=0, invalid=96776 0675: dt=0.000313, rms=2.358 (0.066%), neg=0, invalid=96776 0676: dt=0.000313, rms=2.356 (0.065%), neg=0, invalid=96776 0677: dt=0.000313, rms=2.355 (0.066%), neg=0, invalid=96776 0678: dt=0.000313, rms=2.353 (0.064%), neg=0, invalid=96776 0679: dt=0.000313, rms=2.352 (0.066%), neg=0, invalid=96776 0680: dt=0.000313, rms=2.350 (0.066%), neg=0, invalid=96776 0681: dt=0.000313, rms=2.349 (0.066%), neg=0, invalid=96776 0682: dt=0.000313, rms=2.347 (0.068%), neg=0, invalid=96776 0683: dt=0.000313, rms=2.346 (0.065%), neg=0, invalid=96776 0684: dt=0.000313, rms=2.344 (0.065%), neg=0, invalid=96776 0685: dt=0.000313, rms=2.343 (0.068%), neg=0, invalid=96776 0686: dt=0.000313, rms=2.341 (0.067%), neg=0, invalid=96776 0687: dt=0.000313, rms=2.339 (0.064%), neg=0, invalid=96776 0688: dt=0.000313, rms=2.338 (0.067%), neg=0, invalid=96776 0689: dt=0.000313, rms=2.336 (0.067%), neg=0, invalid=96776 0690: dt=0.000313, rms=2.335 (0.065%), neg=0, invalid=96776 0691: dt=0.000313, rms=2.333 (0.066%), neg=0, invalid=96776 0692: dt=0.000313, rms=2.332 (0.064%), neg=0, invalid=96776 0693: dt=0.000313, rms=2.330 (0.067%), neg=0, invalid=96776 0694: dt=0.000313, rms=2.329 (0.064%), neg=0, invalid=96776 0695: dt=0.000313, rms=2.327 (0.065%), neg=0, invalid=96776 0696: dt=0.000313, rms=2.326 (0.066%), neg=0, invalid=96776 0697: dt=0.000313, rms=2.324 (0.064%), neg=0, invalid=96776 0698: dt=0.000313, rms=2.323 (0.064%), neg=0, invalid=96776 0699: dt=0.000313, rms=2.321 (0.063%), neg=0, invalid=96776 0700: dt=0.000313, rms=2.320 (0.063%), neg=0, invalid=96776 0701: dt=0.000313, rms=2.318 (0.063%), neg=0, invalid=96776 0702: dt=0.000313, rms=2.317 (0.063%), neg=0, invalid=96776 0703: dt=0.000313, rms=2.315 (0.063%), neg=0, invalid=96776 0704: dt=0.000313, rms=2.314 (0.062%), neg=0, invalid=96776 0705: dt=0.000313, rms=2.313 (0.062%), neg=0, invalid=96776 0706: dt=0.000313, rms=2.311 (0.061%), neg=0, invalid=96776 0707: dt=0.000313, rms=2.310 (0.064%), neg=0, invalid=96776 0708: dt=0.000313, rms=2.308 (0.061%), neg=0, invalid=96776 0709: dt=0.000313, rms=2.307 (0.060%), neg=0, invalid=96776 0710: dt=0.000313, rms=2.305 (0.060%), neg=0, invalid=96776 0711: dt=0.000313, rms=2.304 (0.059%), neg=0, invalid=96776 0712: dt=0.000313, rms=2.303 (0.059%), neg=0, invalid=96776 0713: dt=0.000313, rms=2.301 (0.059%), neg=0, invalid=96776 0714: dt=0.000313, rms=2.300 (0.060%), neg=0, invalid=96776 0715: dt=0.000313, rms=2.299 (0.059%), neg=0, invalid=96776 0716: dt=0.000313, rms=2.297 (0.059%), neg=0, invalid=96776 0717: dt=0.000313, rms=2.296 (0.057%), neg=0, invalid=96776 0718: dt=0.000313, rms=2.295 (0.059%), neg=0, invalid=96776 0719: dt=0.000313, rms=2.293 (0.058%), neg=0, invalid=96776 0720: dt=0.000313, rms=2.292 (0.055%), neg=0, invalid=96776 0721: dt=0.000313, rms=2.291 (0.057%), neg=0, invalid=96776 0722: dt=0.000313, rms=2.289 (0.055%), neg=0, invalid=96776 0723: dt=0.000313, rms=2.288 (0.056%), neg=0, invalid=96776 0724: dt=0.000313, rms=2.287 (0.056%), neg=0, invalid=96776 0725: dt=0.000313, rms=2.286 (0.055%), neg=0, invalid=96776 0726: dt=0.000313, rms=2.284 (0.058%), neg=0, invalid=96776 0727: dt=0.000313, rms=2.283 (0.053%), neg=0, invalid=96776 0728: dt=0.000313, rms=2.283 (0.005%), neg=0, invalid=96776 0729: dt=0.000313, rms=2.283 (0.008%), neg=0, invalid=96776 0730: dt=0.000313, rms=2.283 (0.013%), neg=0, invalid=96776 0731: dt=0.000313, rms=2.282 (0.017%), neg=0, invalid=96776 0732: dt=0.000313, rms=2.282 (0.023%), neg=0, invalid=96776 0733: dt=0.000313, rms=2.281 (0.023%), neg=0, invalid=96776 0734: dt=0.005000, rms=2.279 (0.078%), neg=0, invalid=96776 0735: dt=0.001750, rms=2.279 (0.031%), neg=0, invalid=96776 0736: dt=0.000438, rms=2.278 (0.007%), neg=0, invalid=96776 0737: dt=0.000438, rms=2.278 (0.013%), neg=0, invalid=96776 0738: dt=0.000438, rms=2.278 (0.006%), neg=0, invalid=96776 0739: dt=0.000438, rms=2.278 (0.013%), neg=0, invalid=96776 0740: dt=0.000438, rms=2.278 (0.008%), neg=0, invalid=96776 0741: dt=0.001250, rms=2.277 (0.018%), neg=0, invalid=96776 0742: dt=0.000438, rms=2.277 (0.008%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.277, neg=0, invalid=96776 0743: dt=0.000313, rms=2.277 (0.008%), neg=0, invalid=96776 0744: dt=0.001750, rms=2.276 (0.044%), neg=0, invalid=96776 0745: dt=0.000438, rms=2.275 (0.012%), neg=0, invalid=96776 0746: dt=0.000438, rms=2.275 (0.012%), neg=0, invalid=96776 0747: dt=0.000438, rms=2.275 (0.019%), neg=0, invalid=96776 0748: dt=0.000438, rms=2.274 (0.030%), neg=0, invalid=96776 0749: dt=0.000438, rms=2.273 (0.038%), neg=0, invalid=96776 0750: dt=0.000438, rms=2.272 (0.048%), neg=0, invalid=96776 0751: dt=0.000219, rms=2.272 (0.005%), neg=0, invalid=96776 0752: dt=0.000219, rms=2.272 (0.009%), neg=0, invalid=96776 0753: dt=0.000219, rms=2.271 (0.015%), neg=0, invalid=96776 0754: dt=0.000219, rms=2.271 (0.019%), neg=0, invalid=96776 0755: dt=0.000219, rms=2.271 (0.022%), neg=0, invalid=96776 0756: dt=0.000219, rms=2.270 (0.027%), neg=0, invalid=96776 0757: dt=0.000219, rms=2.269 (0.028%), neg=0, invalid=96776 0758: dt=0.000219, rms=2.269 (0.032%), neg=0, invalid=96776 0759: dt=0.000219, rms=2.268 (0.032%), neg=0, invalid=96776 0760: dt=0.000219, rms=2.267 (0.037%), neg=0, invalid=96776 0761: dt=0.000219, rms=2.266 (0.038%), neg=0, invalid=96776 0762: dt=0.000219, rms=2.265 (0.037%), neg=0, invalid=96776 0763: dt=0.000219, rms=2.264 (0.043%), neg=0, invalid=96776 0764: dt=0.000219, rms=2.263 (0.042%), neg=0, invalid=96776 0765: dt=0.000219, rms=2.262 (0.040%), neg=0, invalid=96776 0766: dt=0.000219, rms=2.261 (0.047%), neg=0, invalid=96776 0767: dt=0.000219, rms=2.260 (0.045%), neg=0, invalid=96776 0768: dt=0.000219, rms=2.259 (0.046%), neg=0, invalid=96776 0769: dt=0.000219, rms=2.258 (0.045%), neg=0, invalid=96776 0770: dt=0.000219, rms=2.257 (0.049%), neg=0, invalid=96776 0771: dt=0.000219, rms=2.256 (0.045%), neg=0, invalid=96776 0772: dt=0.000219, rms=2.255 (0.052%), neg=0, invalid=96776 0773: dt=0.000219, rms=2.254 (0.049%), neg=0, invalid=96776 0774: dt=0.000219, rms=2.253 (0.049%), neg=0, invalid=96776 0775: dt=0.000219, rms=2.252 (0.049%), neg=0, invalid=96776 0776: dt=0.000219, rms=2.251 (0.048%), neg=0, invalid=96776 0777: dt=0.000219, rms=2.249 (0.053%), neg=0, invalid=96776 0778: dt=0.000219, rms=2.248 (0.051%), neg=0, invalid=96776 0779: dt=0.000219, rms=2.247 (0.050%), neg=0, invalid=96776 0780: dt=0.000219, rms=2.246 (0.050%), neg=0, invalid=96776 0781: dt=0.000219, rms=2.245 (0.050%), neg=0, invalid=96776 0782: dt=0.000219, rms=2.244 (0.051%), neg=0, invalid=96776 0783: dt=0.000219, rms=2.243 (0.049%), neg=0, invalid=96776 0784: dt=0.000219, rms=2.242 (0.051%), neg=0, invalid=96776 0785: dt=0.000219, rms=2.240 (0.050%), neg=0, invalid=96776 0786: dt=0.000219, rms=2.239 (0.052%), neg=0, invalid=96776 0787: dt=0.000219, rms=2.238 (0.050%), neg=0, invalid=96776 0788: dt=0.000219, rms=2.237 (0.049%), neg=0, invalid=96776 0789: dt=0.000219, rms=2.236 (0.050%), neg=0, invalid=96776 0790: dt=0.000219, rms=2.235 (0.050%), neg=0, invalid=96776 0791: dt=0.000219, rms=2.234 (0.051%), neg=0, invalid=96776 0792: dt=0.000219, rms=2.233 (0.051%), neg=0, invalid=96776 0793: dt=0.000219, rms=2.231 (0.049%), neg=0, invalid=96776 0794: dt=0.000219, rms=2.230 (0.048%), neg=0, invalid=96776 0795: dt=0.000219, rms=2.229 (0.048%), neg=0, invalid=96776 0796: dt=0.000219, rms=2.228 (0.050%), neg=0, invalid=96776 0797: dt=0.000219, rms=2.227 (0.051%), neg=0, invalid=96776 0798: dt=0.000219, rms=2.226 (0.049%), neg=0, invalid=96776 0799: dt=0.000219, rms=2.225 (0.049%), neg=0, invalid=96776 0800: dt=0.000219, rms=2.224 (0.049%), neg=0, invalid=96776 0801: dt=0.000219, rms=2.223 (0.047%), neg=0, invalid=96776 0802: dt=0.000219, rms=2.222 (0.049%), neg=0, invalid=96776 0803: dt=0.000219, rms=2.221 (0.043%), neg=0, invalid=96776 0804: dt=0.000219, rms=2.220 (0.047%), neg=0, invalid=96776 0805: dt=0.000219, rms=2.218 (0.051%), neg=0, invalid=96776 0806: dt=0.000219, rms=2.218 (0.006%), neg=0, invalid=96776 0807: dt=0.000219, rms=2.218 (0.009%), neg=0, invalid=96776 0808: dt=0.000219, rms=2.218 (0.009%), neg=0, invalid=96776 0809: dt=0.001750, rms=2.217 (0.040%), neg=0, invalid=96776 0810: dt=0.001750, rms=2.216 (0.035%), neg=0, invalid=96776 0811: dt=0.000875, rms=2.216 (0.018%), neg=0, invalid=96776 0812: dt=0.000438, rms=2.216 (0.009%), neg=0, invalid=96776 0813: dt=0.000219, rms=2.216 (0.004%), neg=0, invalid=96776 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=2.213, neg=0, invalid=96776 0814: dt=2.400000, rms=2.212 (0.052%), neg=0, invalid=96776 0815: dt=1.734000, rms=2.212 (0.010%), neg=0, invalid=96776 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.004, neg=3, removing folds in lattice.... iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.004 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0816: dt=1.734000, rms=2.212 (0.000%), neg=0, invalid=96776 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.004, neg=3, removing folds in lattice.... iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.004 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0817: dt=1.734000, rms=2.212 (0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.212, neg=0, invalid=96776 0818: dt=0.505750, rms=2.212 (0.001%), neg=0, invalid=96776 0819: dt=0.305556, rms=2.212 (-0.000%), neg=0, invalid=96776 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.212, neg=0, invalid=96776 iter 0, gcam->neg = 101 after 200 iterations, nbhd size=2, neg = 16 starting rms=0.010, neg=16, removing folds in lattice.... iter 1, dt=0.000000: new neg 16, old_neg 16, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0820: dt=2.268000, rms=2.212 (0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.212, neg=0, invalid=96776 iter 0, gcam->neg = 116 after 200 iterations, nbhd size=4, neg = 22 starting rms=0.011, neg=22, removing folds in lattice.... iter 1, dt=0.000000: new neg 22, old_neg 22, delta 0, rms=0.011 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0821: dt=4.516129, rms=2.212 (0.000%), neg=0, invalid=96776 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=2.212, neg=0, invalid=96776 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.004, neg=3, removing folds in lattice.... iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.004 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0822: dt=0.505750, rms=2.217 (-0.211%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.217, neg=0, invalid=96776 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0823: dt=0.433500, rms=2.217 (0.000%), neg=0, invalid=96776 0824: dt=0.433500, rms=2.217 (-0.000%), neg=0, invalid=96776 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=2.217, neg=0, invalid=96776 iter 0, gcam->neg = 224 after 200 iterations, nbhd size=3, neg = 42 starting rms=0.013, neg=42, removing folds in lattice.... iter 1, dt=0.000000: new neg 42, old_neg 42, delta 0, rms=0.013 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0825: dt=3.294118, rms=2.217 (0.000%), neg=0, invalid=96776 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=2.217, neg=0, invalid=96776 iter 0, gcam->neg = 109 after 200 iterations, nbhd size=2, neg = 20 starting rms=0.011, neg=20, removing folds in lattice.... iter 1, dt=0.000000: new neg 20, old_neg 20, delta 0, rms=0.011 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0826: dt=4.495868, rms=2.217 (0.000%), neg=0, invalid=96776 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 29 minutes and 25 seconds. #-------------------------------------- #@# CA Reg Inv Tue May 21 18:48:51 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue May 21 18:50:04 CEST 2024 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/prog/freesurfer5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11096629 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 13 seconds. #-------------------------------------- #@# SkullLTA Tue May 21 18:51:18 CEST 2024 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/prog/freesurfer5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 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 '/usr/prog/freesurfer5.3.0/average/RB_all_withskull_2008-03-26.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=17.0 skull bounding box = (43, 63, 26) --> (214, 218, 210) using (100, 115, 118) as brain centroid... mean wm in atlas = 126, using box (79,96,95) --> (121, 134,140) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.212 scaling channel 0 by 1.21154 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.3, old_max_log_p =-4.8 (thresh=-4.8) 1.057 0.107 0.017 -26.841; -0.097 1.294 0.072 -55.982; -0.012 -0.082 1.070 2.408; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.3 (thresh=-4.2) 0.978 0.099 0.016 -15.395; -0.105 1.367 0.227 -82.176; 0.001 -0.269 1.130 27.938; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 0.978 0.099 0.016 -15.395; -0.105 1.367 0.227 -82.176; 0.001 -0.269 1.130 27.938; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 0.981 0.052 0.008 -8.408; -0.072 1.318 0.219 -78.736; 0.001 -0.254 1.067 28.597; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 0.981 0.052 0.008 -8.408; -0.072 1.318 0.219 -78.736; 0.001 -0.254 1.067 28.597; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 0.981 0.042 0.006 -6.768; -0.064 1.315 0.228 -80.220; 0.001 -0.264 1.064 29.854; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 0.981 0.042 0.006 -6.768; -0.064 1.312 0.227 -79.748; 0.001 -0.265 1.065 29.765; 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 0.98134 0.04159 0.00633 -6.76756; -0.06361 1.31194 0.22710 -79.74818; 0.00143 -0.26478 1.06543 29.76540; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98134 0.04159 0.00633 -6.76756; -0.06361 1.31194 0.22710 -79.74818; 0.00143 -0.26478 1.06543 29.76540; 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: 0.981 0.042 0.006 -6.768; -0.064 1.312 0.227 -79.748; 0.001 -0.265 1.065 29.765; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.8) transform before final EM align: 0.981 0.042 0.006 -6.768; -0.064 1.312 0.227 -79.748; 0.001 -0.265 1.065 29.765; 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 0.98134 0.04159 0.00633 -6.76756; -0.06361 1.31194 0.22710 -79.74818; 0.00143 -0.26478 1.06543 29.76540; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98134 0.04159 0.00633 -6.76756; -0.06361 1.31194 0.22710 -79.74818; 0.00143 -0.26478 1.06543 29.76540; 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) = 4.5 tol 0.000000 final transform: 0.981 0.042 0.006 -6.768; -0.064 1.312 0.227 -79.748; 0.001 -0.265 1.065 29.765; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 30 minutes and 32 seconds. #-------------------------------------- #@# SubCort Seg Tue May 21 19:21:50 CEST 2024 /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s1_to_PD_HY1_blagojevic_milan_template.lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s1_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s1_to_PD_HY1_blagojevic_milan_template.lta' -> '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s1_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta' cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s2_to_PD_HY1_blagojevic_milan_template.lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s2_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s2_to_PD_HY1_blagojevic_milan_template.lta' -> '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s2_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta' cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s3_to_PD_HY1_blagojevic_milan_template.lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s3_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s3_to_PD_HY1_blagojevic_milan_template.lta' -> '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s3_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta' cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s4_to_PD_HY1_blagojevic_milan_template.lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s4_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s4_to_PD_HY1_blagojevic_milan_template.lta' -> '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s4_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta' cp -vf /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_template.lta' -> '/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/transforms/PD_HY1_blagojevic_milan_s5_to_PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template.lta' mri_fuse_segmentations -a aseg.mgz -c aseg.auto_noCCseg.mgz -n norm.mgz PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template PD_HY1_blagojevic_milan_s1 PD_HY1_blagojevic_milan_s2 PD_HY1_blagojevic_milan_s3 PD_HY1_blagojevic_milan_s4 PD_HY1_blagojevic_milan_s5 aseg.fused.mgz mghRead(/snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s1/mri/aseg.mgz, -1): could not open file using aseg.mgz as aseg volume using aseg.auto_noCCseg.mgz as aseg no-CC-label volume using norm.mgz as norm volume reading /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template/mri/norm.mgz and processing 5 timepoints, writing to aseg.fused.mgz loading data for subject PD_HY1_blagojevic_milan_s1 ... mri_fuse_segmentations: could not read input volume /snap/home2/dati/BELGRADO_1.5Philips/PD-Demenze/group_analysis/Freesurfer_PD_HY_LONG_2017/PD_HY1_blagojevic_milan_s1/mri/aseg.mgz Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PD_HY1_blagojevic_milan_s5.long.PD_HY1_blagojevic_milan_template exited with ERRORS at Tue May 21 19:21:52 CEST 2024 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting