Fri 15 Mar 2024 09:29:11 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -i LS5K/ses-01/anat/FS/UNI_reo_out.nii -s LS5K subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 74889276 66302188 92428 253663776 317246548 Swap: 9765884 9765112 772 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_convert /data/pt_02321/1_Analysen/2_CROSSING/Recon-all/LS5K/ses-01/anat/FS/UNI_reo_out.nii /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz mri_convert.bin /data/pt_02321/1_Analysen/2_CROSSING/Recon-all/LS5K/ses-01/anat/FS/UNI_reo_out.nii /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/pt_02321/1_Analysen/2_CROSSING/Recon-all/LS5K/ses-01/anat/FS/UNI_reo_out.nii... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996779, 0, 0.080199) j_ras = (0, 1, 0) k_ras = (-0.080199, 0, 0.996779) writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz... Started at Fri 15 Mar 2024 09:29:11 AM CET Ended at Fri 15 Mar 2024 09:29:24 AM CET #@#%# recon-all-run-time-hours 0.004 recon-all -s LS5K finished without error at Fri 15 Mar 2024 09:29:24 AM CET New invocation of recon-all Fri 15 Mar 2024 09:29:25 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -motioncor subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 74954424 66227732 91404 253673084 317182424 Swap: 9765884 9765112 772 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:27-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri 15 Mar 2024 09:29:28 AM CET Found 1 runs /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_convert /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform mri_convert.bin /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996779, 0, 0.080199) j_ras = (0, 1, 0) k_ras = (-0.080199, 0, 0.996779) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz... mri_add_xform_to_header -c /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/talairach.xfm /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz INFO: extension is mgz Started at Fri 15 Mar 2024 09:29:25 AM CET Ended at Fri 15 Mar 2024 09:29:39 AM CET #@#%# recon-all-run-time-hours 0.004 recon-all -s LS5K finished without error at Fri 15 Mar 2024 09:29:39 AM CET New invocation of recon-all Fri 15 Mar 2024 09:29:40 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -normalization -skullstrip subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 75062716 66097120 91916 253695404 317073648 Swap: 9765884 9765112 772 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:40-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:29:41-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization Fri 15 Mar 2024 09:29:41 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.17259 -0.15608 0.06831 0.88898; 0.16758 1.14045 -0.10487 -9.39799; -0.03649 0.10201 1.09959 -51.21169; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 7 Starting OpenSpline(): npoints = 7 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 109 white matter peak found at 89 gm peak at 61 (61), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 60 (60), valley at 0 (-1) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 4 minutes and 27 seconds. #-------------------------------------------- #@# Skull Stripping Fri 15 Mar 2024 09:34:09 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_em_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=63.2 skull bounding box = (39, 52, 31) --> (216, 225, 224) using (98, 110, 128) as brain centroid... mean wm in atlas = 108, using box (76,89,104) --> (119, 131,151) to find MRI wm before smoothing, mri peak at 178 robust fit to distribution - 178 +- 10.3 after smoothing, mri peak at 179, scaling input intensities by 0.603 scaling channel 0 by 0.603352 initial log_p = -5.284 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.520784 @ (-27.273, 9.091, -9.091) max log p = -4.485068 @ (13.636, 4.545, -31.818) max log p = -4.485068 @ (0.000, 0.000, 0.000) max log p = -4.470833 @ (-1.136, 3.409, 5.682) max log p = -4.456766 @ (-2.841, -0.568, -0.568) max log p = -4.456766 @ (0.000, 0.000, 0.000) Found translation: (-17.6, 16.5, -35.8): log p = -4.457 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.373, old_max_log_p =-4.457 (thresh=-4.5) 0.98999 0.10298 -0.37533 23.73407; -0.00989 1.19857 0.30274 -47.61812; 0.42066 -0.25885 1.03853 -83.21642; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.341, old_max_log_p =-4.373 (thresh=-4.4) 0.98999 0.10298 -0.37533 23.73407; -0.01138 1.37835 0.34816 -76.08696; 0.42066 -0.25885 1.03853 -83.21642; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.341, old_max_log_p =-4.341 (thresh=-4.3) 0.98999 0.10298 -0.37533 23.73407; -0.01138 1.37835 0.34816 -76.08696; 0.42066 -0.25885 1.03853 -83.21642; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.289, old_max_log_p =-4.341 (thresh=-4.3) 1.06979 0.17962 -0.30190 -8.61828; -0.05308 1.37586 0.43779 -78.06145; 0.33675 -0.34839 0.99720 -53.74004; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.289, old_max_log_p =-4.289 (thresh=-4.3) 1.07601 0.24135 -0.32428 -13.24965; -0.07807 1.38214 0.48987 -83.16069; 0.36613 -0.37988 0.95372 -47.69850; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.269, old_max_log_p =-4.289 (thresh=-4.3) 1.07548 0.22178 -0.34025 -8.87981; -0.06659 1.39520 0.46993 -83.29255; 0.37317 -0.35499 0.95773 -52.26730; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.267, old_max_log_p =-4.269 (thresh=-4.3) 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.267 (old=-5.284) transform before final EM align: 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.6 tol 0.000000 final transform: 1.07674 0.22204 -0.34065 -9.03655; -0.06651 1.39356 0.46938 -83.02833; 0.37360 -0.35541 0.95886 -52.45853; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 528.843559 mri_em_register stimesec 1.663835 mri_em_register ru_maxrss 614432 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 221621 mri_em_register ru_majflt 7 mri_em_register ru_nswap 0 mri_em_register ru_inblock 80168 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 241 mri_em_register ru_nivcsw 4420 registration took 8 minutes and 52 seconds. mri_watershed -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_watershed.dat -T1 -brain_atlas /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=170 y=102 z=143 r=98 first estimation of the main basin volume: 4024304 voxelsWM coord (293, 106, 239) out of bounds (256, 256, 256), normalization failed? mri_watershed Error: indices out of bounds Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux recon-all -s LS5K exited with ERRORS at Fri 15 Mar 2024 09:43:03 AM CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri 15 Mar 2024 09:43:03 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -autorecon2 -autorecon3 -s LS5K subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 69368304 68524616 91896 256962320 322768052 Swap: 9765884 9765096 788 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:43:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Fri 15 Mar 2024 09:43:03 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_em_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... mghRead(/data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/brainmask.mgz, -1): could not open file mri_em_register: could not open mask volume brainmask.mgz. Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux recon-all -s LS5K exited with ERRORS at Fri 15 Mar 2024 09:43:05 AM CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri 15 Mar 2024 09:50:25 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -motioncor subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 69374764 68517388 92408 256963088 322761080 Swap: 9765884 9765088 796 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:26-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri 15 Mar 2024 09:50:26 AM CET Found 1 runs /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_convert /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform mri_convert.bin /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996779, 0, 0.080199) j_ras = (0, 1, 0) k_ras = (-0.080199, 0, 0.996779) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz... mri_add_xform_to_header -c /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/talairach.xfm /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz INFO: extension is mgz Started at Fri 15 Mar 2024 09:50:25 AM CET Ended at Fri 15 Mar 2024 09:50:32 AM CET #@#%# recon-all-run-time-hours 0.002 recon-all -s LS5K finished without error at Fri 15 Mar 2024 09:50:32 AM CET New invocation of recon-all Fri 15 Mar 2024 09:50:32 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -normalization -skullstrip subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 69378568 68514092 91896 256962580 322757788 Swap: 9765884 9765088 796 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:50:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization Fri 15 Mar 2024 09:50:33 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_normalize -g 1 -f /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat -mprage nu.mgz T1.mgz using max gradient = 1.000 using control points from file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... Reading 11 control points... only using 11 control points from file, mean 177.0, scaling by 0.62... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... talairach transform 1.17259 -0.15608 0.06831 0.88898; 0.16758 1.14045 -0.10487 -9.39799; -0.03649 0.10201 1.09959 -51.21169; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 9 Starting OpenSpline(): npoints = 9 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 89 gm peak at 65 (65), valley at 0 (-1) csf peak at 32, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 64 (64), valley at 0 (-1) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 59 seconds. #-------------------------------------------- #@# Skull Stripping Fri 15 Mar 2024 09:52:33 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_watershed -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_watershed.dat -T1 -brain_atlas /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=137 y=106 z=124 r=91 first estimation of the main basin volume: 3188021 voxels Looking for seedpoints 2 found in the cerebellum 10 found in the rest of the brain global maximum in x=156, y=104, z=114, Imax=255 CSF=14, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=1422113672 voxels, voxel volume =1.000 = 1422113672 mmm3 = 1422113.664 cm3 done. PostAnalyze...Basin Prior 158 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=138,y=146, z=141, r=10567 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 33005 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1031143109 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1103184272 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1053909623 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1098835940 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1082262334 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 6, 34, 41 after analyzing : 3, 24, 34, 28 RIGHT_CER before analyzing : 3, 6, 34, 41 after analyzing : 3, 24, 34, 28 LEFT_CER before analyzing : 3, 6, 34, 41 after analyzing : 3, 24, 34, 28 RIGHT_BRAIN before analyzing : 3, 6, 34, 41 after analyzing : 3, 24, 34, 28 LEFT_BRAIN before analyzing : 3, 6, 34, 41 after analyzing : 3, 24, 34, 28 OTHER before analyzing : 3, 5, 30, 41 after analyzing : 3, 21, 30, 26 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.009, std = 0.008 curvature mean = 96.613, std = 9.626 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 32.98, sigma = 84.08 after rotation: sse = 32.98, sigma = 84.08 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 39.66, its var is 62.34 before Erosion-Dilatation 43.76% of inacurate vertices after Erosion-Dilatation 64.83% of inacurate vertices 50.90% of 'positive' inacurate vertices 49.10% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...58 iterations mri_strip_skull: done peeling brain Brain Size = 4066721 voxels, voxel volume = 1.000 mm3 = 4066721 mmm3 = 4066.721 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 15.497559 mri_watershed stimesec 0.459571 mri_watershed ru_maxrss 840148 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208393 mri_watershed ru_majflt 4 mri_watershed ru_nswap 0 mri_watershed ru_inblock 12136 mri_watershed ru_oublock 6448 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 231 mri_watershed ru_nivcsw 38 mri_watershed done cp brainmask.auto.mgz brainmask.mgz Started at Fri 15 Mar 2024 09:50:32 AM CET Ended at Fri 15 Mar 2024 09:52:50 AM CET #@#%# recon-all-run-time-hours 0.038 recon-all -s LS5K finished without error at Fri 15 Mar 2024 09:52:50 AM CET New invocation of recon-all Fri 15 Mar 2024 09:52:50 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -autorecon2 -autorecon3 -s LS5K subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 69376864 68507168 90904 256971208 322760484 Swap: 9765884 9765088 796 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-08:52:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Fri 15 Mar 2024 09:52:51 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_em_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (37, 51, 52) --> (217, 228, 225) using (97, 110, 139) as brain centroid... mean wm in atlas = 107, using box (75,88,118) --> (119, 131,160) to find MRI wm before smoothing, mri peak at 175 robust fit to distribution - 176 +- 10.8 after smoothing, mri peak at 176, scaling input intensities by 0.608 scaling channel 0 by 0.607955 initial log_p = -5.058 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.610537 @ (0.000, 0.000, 0.000) max log p = -4.583787 @ (-4.545, 4.545, -4.545) max log p = -4.545241 @ (-25.000, 11.364, -6.818) max log p = -4.525362 @ (-1.136, 5.682, 1.136) max log p = -4.525362 @ (0.000, 0.000, 0.000) max log p = -4.525362 @ (0.000, 0.000, 0.000) Found translation: (-30.7, 21.6, -10.2): log p = -4.525 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.344, old_max_log_p =-4.525 (thresh=-4.5) 0.82465 -0.01459 -0.21064 23.60643; -0.00238 1.13004 0.07663 -14.09931; 0.19056 0.06611 0.78076 -24.79320; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.318, old_max_log_p =-4.344 (thresh=-4.3) 0.85696 -0.32957 -0.24004 56.76225; 0.21114 1.08776 0.01950 -28.74636; 0.19056 0.06611 0.78076 -24.79320; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.309, old_max_log_p =-4.318 (thresh=-4.3) 0.81418 -0.17099 -0.20550 42.79114; 0.12937 1.20486 0.16291 -45.43729; 0.14927 -0.07070 0.71367 3.87868; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.309, old_max_log_p =-4.309 (thresh=-4.3) 0.81418 -0.17099 -0.20550 42.79114; 0.12937 1.20486 0.16291 -45.43729; 0.14927 -0.07070 0.71367 3.87868; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.266, old_max_log_p =-4.309 (thresh=-4.3) 0.86637 -0.25843 -0.07173 31.25897; 0.16997 1.17092 0.10644 -45.11323; -0.00390 0.04743 0.76301 3.67657; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.252, old_max_log_p =-4.266 (thresh=-4.3) 0.87614 -0.30360 -0.10197 40.31824; 0.19821 1.16180 0.10322 -48.03854; 0.02491 0.03968 0.77451 -1.35859; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.250, old_max_log_p =-4.252 (thresh=-4.2) 0.88417 -0.34901 -0.13301 47.92775; 0.22248 1.12962 0.09715 -47.47406; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.223, old_max_log_p =-4.250 (thresh=-4.2) 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.223, old_max_log_p =-4.223 (thresh=-4.2) 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.223 (old=-5.058) transform before final EM align: 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.88770 -0.33048 -0.13140 45.20975; 0.20749 1.13252 0.09908 -45.77450; 0.05356 0.02973 0.77076 -4.12895; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 012: -log(p) = 144.0 after pass:transform: ( 0.89, -0.33, -0.13, 45.21) ( 0.21, 1.13, 0.10, -45.77) ( 0.05, 0.03, 0.77, -4.13) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 014: -log(p) = 144.0 tol 0.000000 final transform: 0.88813 -0.33003 -0.13063 45.20975; 0.20850 1.13371 0.10005 -45.77450; 0.05463 0.03065 0.77168 -4.12895; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 580.298517 mri_em_register stimesec 2.655901 mri_em_register ru_maxrss 604264 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161972 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 29 mri_em_register ru_nivcsw 1480 registration took 9 minutes and 43 seconds. #-------------------------------------- #@# CA Normalize Fri 15 Mar 2024 10:02:34 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (37, 51, 52) --> (217, 228, 225) using (97, 110, 139) as brain centroid... mean wm in atlas = 107, using box (75,88,118) --> (119, 131,160) to find MRI wm before smoothing, mri peak at 175 robust fit to distribution - 176 +- 10.8 after smoothing, mri peak at 176, scaling input intensities by 0.608 scaling channel 0 by 0.607955 using 246344 sample points... INFO: compute sample coordinates transform 0.88813 -0.33003 -0.13063 45.20975; 0.20850 1.13371 0.10005 -45.77450; 0.05463 0.03065 0.77168 -4.12895; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (133, 47, 22) --> (225, 143, 241) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 87 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 54, 25) --> (165, 155, 243) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 217 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (153, 126, 49) --> (213, 159, 120) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 127, 48) --> (157, 167, 124) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 10 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (139, 115, 93) --> (182, 176, 137) Brain_Stem: limiting intensities to 103.0 --> 132.0 1 of 15 (6.7%) samples deleted using 340 total control points for intensity normalization... bias field = 0.969 +- 0.085 5 of 339 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (133, 47, 22) --> (225, 143, 241) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 167 (28.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 54, 25) --> (165, 155, 243) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 5 of 290 (1.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (153, 126, 49) --> (213, 159, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 127, 48) --> (157, 167, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 26 (61.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (139, 115, 93) --> (182, 176, 137) Brain_Stem: limiting intensities to 93.0 --> 132.0 38 of 58 (65.5%) samples deleted using 549 total control points for intensity normalization... bias field = 1.018 +- 0.082 5 of 437 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (133, 47, 22) --> (225, 143, 241) Left_Cerebral_White_Matter: limiting intensities to 118.0 --> 132.0 158 of 178 (88.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (75, 54, 25) --> (165, 155, 243) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 115.0 18 of 328 (5.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (153, 126, 49) --> (213, 159, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 17 (88.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (113, 127, 48) --> (157, 167, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 47 of 55 (85.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (139, 115, 93) --> (182, 176, 137) Brain_Stem: limiting intensities to 88.0 --> 132.0 31 of 57 (54.4%) samples deleted using 635 total control points for intensity normalization... bias field = 0.998 +- 0.085 0 of 363 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Fri 15 Mar 2024 10:03:38 AM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.83 (predicted orig area = 9.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.202, neg=0, invalid=762 0001: dt=517.888000, rms=1.121 (6.785%), neg=0, invalid=762 0002: dt=613.680141, rms=1.074 (4.163%), neg=0, invalid=762 0003: dt=517.888000, rms=1.051 (2.159%), neg=0, invalid=762 0004: dt=443.904000, rms=1.034 (1.574%), neg=0, invalid=762 0005: dt=443.904000, rms=1.023 (1.101%), neg=0, invalid=762 0006: dt=369.920000, rms=1.017 (0.601%), neg=0, invalid=762 0007: dt=517.888000, rms=1.010 (0.639%), neg=0, invalid=762 0008: dt=295.936000, rms=1.007 (0.273%), neg=0, invalid=762 0009: dt=517.888000, rms=1.002 (0.511%), neg=0, invalid=762 0010: dt=295.936000, rms=1.001 (0.127%), neg=0, invalid=762 0011: dt=295.936000, rms=0.998 (0.250%), neg=0, invalid=762 0012: dt=295.936000, rms=0.996 (0.298%), neg=0, invalid=762 0013: dt=295.936000, rms=0.993 (0.299%), neg=0, invalid=762 0014: dt=295.936000, rms=0.990 (0.284%), neg=0, invalid=762 0015: dt=295.936000, rms=0.987 (0.287%), neg=0, invalid=762 0016: dt=295.936000, rms=0.985 (0.200%), neg=0, invalid=762 0017: dt=295.936000, rms=0.984 (0.065%), neg=0, invalid=762 0018: dt=295.936000, rms=0.982 (0.237%), neg=0, invalid=762 0019: dt=295.936000, rms=0.978 (0.367%), neg=0, invalid=762 0020: dt=295.936000, rms=0.977 (0.127%), neg=0, invalid=762 0021: dt=295.936000, rms=0.975 (0.189%), neg=0, invalid=762 0022: dt=295.936000, rms=0.973 (0.235%), neg=0, invalid=762 0023: dt=295.936000, rms=0.972 (0.066%), neg=0, invalid=762 0024: dt=295.936000, rms=0.970 (0.221%), neg=0, invalid=762 0025: dt=295.936000, rms=0.967 (0.288%), neg=0, invalid=762 0026: dt=295.936000, rms=0.967 (0.052%), neg=0, invalid=762 0027: dt=295.936000, rms=0.964 (0.319%), neg=0, invalid=762 0028: dt=295.936000, rms=0.962 (0.219%), neg=0, invalid=762 0029: dt=295.936000, rms=0.962 (-0.134%), neg=0, invalid=762 0030: dt=0.000000, rms=0.962 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.963, neg=0, invalid=762 0031: dt=129.472000, rms=0.960 (0.233%), neg=0, invalid=762 0032: dt=295.936000, rms=0.960 (0.076%), neg=0, invalid=762 0033: dt=295.936000, rms=0.959 (0.041%), neg=0, invalid=762 0034: dt=295.936000, rms=0.959 (0.033%), neg=0, invalid=762 0035: dt=295.936000, rms=0.959 (0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.990, neg=0, invalid=762 0036: dt=84.645161, rms=0.984 (0.591%), neg=0, invalid=762 0037: dt=88.760656, rms=0.973 (1.065%), neg=0, invalid=762 0038: dt=31.104000, rms=0.970 (0.333%), neg=0, invalid=762 0039: dt=145.152000, rms=0.964 (0.613%), neg=0, invalid=762 0040: dt=62.693878, rms=0.958 (0.631%), neg=0, invalid=762 0041: dt=18.196078, rms=0.957 (0.071%), neg=0, invalid=762 0042: dt=18.196078, rms=0.957 (0.036%), neg=0, invalid=762 0043: dt=18.196078, rms=0.956 (0.061%), neg=0, invalid=762 0044: dt=18.196078, rms=0.955 (0.127%), neg=0, invalid=762 0045: dt=18.196078, rms=0.953 (0.237%), neg=0, invalid=762 0046: dt=18.196078, rms=0.950 (0.294%), neg=0, invalid=762 0047: dt=18.196078, rms=0.947 (0.272%), neg=0, invalid=762 0048: dt=18.196078, rms=0.945 (0.239%), neg=0, invalid=762 0049: dt=18.196078, rms=0.943 (0.218%), neg=0, invalid=762 0050: dt=18.196078, rms=0.942 (0.153%), neg=0, invalid=762 0051: dt=18.196078, rms=0.941 (0.119%), neg=0, invalid=762 0052: dt=18.196078, rms=0.939 (0.145%), neg=0, invalid=762 0053: dt=18.196078, rms=0.937 (0.204%), neg=0, invalid=762 0054: dt=18.196078, rms=0.935 (0.204%), neg=0, invalid=762 0055: dt=18.196078, rms=0.934 (0.180%), neg=0, invalid=762 0056: dt=18.196078, rms=0.932 (0.145%), neg=0, invalid=762 0057: dt=18.196078, rms=0.931 (0.123%), neg=0, invalid=762 0058: dt=18.196078, rms=0.930 (0.096%), neg=0, invalid=762 0059: dt=145.152000, rms=0.928 (0.236%), neg=0, invalid=762 0060: dt=0.000354, rms=0.928 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.929, neg=0, invalid=762 0061: dt=36.288000, rms=0.927 (0.231%), neg=0, invalid=762 0062: dt=0.000000, rms=0.927 (0.004%), neg=0, invalid=762 0063: dt=0.450000, rms=0.927 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.015, neg=0, invalid=762 0064: dt=16.457143, rms=1.010 (0.467%), neg=0, invalid=762 0065: dt=11.200000, rms=1.005 (0.497%), neg=0, invalid=762 0066: dt=44.800000, rms=0.996 (0.889%), neg=0, invalid=762 0067: dt=32.000000, rms=0.989 (0.675%), neg=0, invalid=762 0068: dt=11.200000, rms=0.987 (0.167%), neg=0, invalid=762 0069: dt=11.200000, rms=0.986 (0.165%), neg=0, invalid=762 0070: dt=11.200000, rms=0.983 (0.287%), neg=0, invalid=762 0071: dt=11.200000, rms=0.979 (0.368%), neg=0, invalid=762 0072: dt=11.200000, rms=0.975 (0.401%), neg=0, invalid=762 0073: dt=11.200000, rms=0.971 (0.428%), neg=0, invalid=762 0074: dt=11.200000, rms=0.967 (0.403%), neg=0, invalid=762 0075: dt=11.200000, rms=0.964 (0.348%), neg=0, invalid=762 0076: dt=11.200000, rms=0.961 (0.305%), neg=0, invalid=762 0077: dt=11.200000, rms=0.959 (0.244%), neg=0, invalid=762 0078: dt=11.200000, rms=0.957 (0.187%), neg=0, invalid=762 0079: dt=11.200000, rms=0.955 (0.160%), neg=0, invalid=762 0080: dt=11.200000, rms=0.954 (0.155%), neg=0, invalid=762 0081: dt=11.200000, rms=0.953 (0.146%), neg=0, invalid=762 0082: dt=11.200000, rms=0.952 (0.101%), neg=0, invalid=762 0083: dt=11.200000, rms=0.951 (0.099%), neg=0, invalid=762 0084: dt=25.600000, rms=0.950 (0.032%), neg=0, invalid=762 0085: dt=25.600000, rms=0.950 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.951, neg=0, invalid=762 0086: dt=0.000000, rms=0.950 (0.109%), neg=0, invalid=762 0087: dt=0.000000, rms=0.950 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.069, neg=0, invalid=762 0088: dt=0.045000, rms=1.068 (0.087%), neg=0, invalid=762 0089: dt=0.015750, rms=1.068 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.069, neg=0, invalid=762 0090: dt=0.144000, rms=1.068 (0.088%), neg=0, invalid=762 0091: dt=0.045000, rms=1.068 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.281, neg=0, invalid=762 0092: dt=1.990291, rms=1.254 (2.145%), neg=0, invalid=762 0093: dt=1.792000, rms=1.239 (1.166%), neg=0, invalid=762 0094: dt=1.280000, rms=1.231 (0.668%), neg=0, invalid=762 0095: dt=1.536000, rms=1.224 (0.547%), neg=0, invalid=762 0096: dt=1.280000, rms=1.218 (0.464%), neg=0, invalid=762 0097: dt=1.536000, rms=1.214 (0.401%), neg=0, invalid=762 0098: dt=1.024000, rms=1.209 (0.373%), neg=0, invalid=762 0099: dt=1.792000, rms=1.204 (0.395%), neg=0, invalid=762 0100: dt=1.024000, rms=1.201 (0.285%), neg=0, invalid=762 0101: dt=1.792000, rms=1.197 (0.343%), neg=0, invalid=762 0102: dt=1.024000, rms=1.194 (0.240%), neg=0, invalid=762 0103: dt=1.024000, rms=1.191 (0.236%), neg=0, invalid=762 0104: dt=1.024000, rms=1.187 (0.346%), neg=0, invalid=762 0105: dt=1.024000, rms=1.181 (0.490%), neg=0, invalid=762 0106: dt=1.024000, rms=1.176 (0.462%), neg=0, invalid=762 0107: dt=1.024000, rms=1.170 (0.514%), neg=0, invalid=762 0108: dt=1.024000, rms=1.164 (0.444%), neg=0, invalid=762 0109: dt=1.024000, rms=1.159 (0.460%), neg=0, invalid=762 0110: dt=1.024000, rms=1.154 (0.401%), neg=0, invalid=762 0111: dt=1.024000, rms=1.150 (0.385%), neg=0, invalid=762 0112: dt=1.024000, rms=1.146 (0.375%), neg=0, invalid=762 0113: dt=1.024000, rms=1.142 (0.328%), neg=0, invalid=762 0114: dt=1.024000, rms=1.138 (0.308%), neg=0, invalid=762 0115: dt=1.024000, rms=1.135 (0.269%), neg=0, invalid=762 0116: dt=1.024000, rms=1.132 (0.277%), neg=0, invalid=762 0117: dt=1.024000, rms=1.130 (0.230%), neg=0, invalid=762 0118: dt=1.024000, rms=1.127 (0.221%), neg=0, invalid=762 0119: dt=1.024000, rms=1.125 (0.209%), neg=0, invalid=762 0120: dt=1.024000, rms=1.123 (0.165%), neg=0, invalid=762 0121: dt=1.024000, rms=1.122 (0.115%), neg=0, invalid=762 0122: dt=1.024000, rms=1.120 (0.100%), neg=0, invalid=762 0123: dt=1.024000, rms=1.120 (0.032%), neg=0, invalid=762 0124: dt=1.024000, rms=1.120 (0.024%), neg=0, invalid=762 0125: dt=1.024000, rms=1.119 (0.027%), neg=0, invalid=762 0126: dt=1.024000, rms=1.119 (0.033%), neg=0, invalid=762 0127: dt=1.024000, rms=1.119 (0.047%), neg=0, invalid=762 0128: dt=1.024000, rms=1.118 (0.062%), neg=0, invalid=762 0129: dt=1.024000, rms=1.117 (0.062%), neg=0, invalid=762 0130: dt=1.024000, rms=1.117 (0.055%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.118, neg=0, invalid=762 0131: dt=1.024000, rms=1.116 (0.142%), neg=0, invalid=762 0132: dt=0.000000, rms=1.116 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.092, neg=0, invalid=762 0133: dt=0.895194, rms=1.071 (1.955%), neg=0, invalid=762 0134: dt=0.096000, rms=1.070 (0.092%), neg=0, invalid=762 0135: dt=0.096000, rms=1.070 (-0.030%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.071, neg=0, invalid=762 0136: dt=0.080000, rms=1.069 (0.145%), neg=0, invalid=762 0137: dt=0.005000, rms=1.069 (0.000%), neg=0, invalid=762 0138: dt=0.005000, rms=1.069 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.05792 (42) Left_Lateral_Ventricle (4): linear fit = 2.07 x + 0.0 (2483 voxels, overlap=0.038) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2483 voxels, peak = 41), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.08461 (51) Right_Lateral_Ventricle (43): linear fit = 2.87 x + 0.0 (1992 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1992 voxels, peak = 46), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.07857 (95) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (973 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (973 voxels, peak = 97), gca=97.4 gca peak = 0.20183 (93) mri peak = 0.05777 (85) Left_Pallidum (13): linear fit = 1.14 x + 0.0 (555 voxels, overlap=0.102) Left_Pallidum (13): linear fit = 1.14 x + 0.0 (555 voxels, peak = 106), gca=106.5 gca peak = 0.21683 (55) mri peak = 0.04392 (56) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1489 voxels, overlap=0.986) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1489 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.12165 (50) Left_Hippocampus (17): linear fit = 0.87 x + 0.0 (1134 voxels, overlap=0.704) Left_Hippocampus (17): linear fit = 0.87 x + 0.0 (1134 voxels, peak = 50), gca=50.2 gca peak = 0.11430 (101) mri peak = 0.06880 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (59553 voxels, overlap=0.902) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (59553 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.06792 (90) Left_Cerebral_White_Matter (2): linear fit = 0.94 x + 0.0 (52230 voxels, overlap=0.392) Left_Cerebral_White_Matter (2): linear fit = 0.94 x + 0.0 (52230 voxels, peak = 95), gca=95.4 gca peak = 0.14995 (59) mri peak = 0.03151 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24108 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (24108 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.03694 (50) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (32544 voxels, overlap=0.464) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (32544 voxels, peak = 52), gca=51.9 gca peak = 0.14161 (67) mri peak = 0.07163 (52) Right_Caudate (50): linear fit = 0.76 x + 0.0 (799 voxels, overlap=0.018) Right_Caudate (50): linear fit = 0.76 x + 0.0 (799 voxels, peak = 51), gca=51.3 gca peak = 0.15243 (71) mri peak = 0.07009 (80) Left_Caudate (11): linear fit = 1.04 x + 0.0 (473 voxels, overlap=0.687) Left_Caudate (11): linear fit = 1.04 x + 0.0 (473 voxels, peak = 74), gca=74.2 gca peak = 0.13336 (57) mri peak = 0.02655 (57) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31451 voxels, overlap=0.415) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (31451 voxels, peak = 56), gca=56.1 gca peak = 0.13252 (56) mri peak = 0.03307 (54) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (38822 voxels, overlap=0.830) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (38822 voxels, peak = 55), gca=55.2 gca peak = 0.18181 (84) mri peak = 0.03723 (37) Left_Cerebellum_White_Matter (7): linear fit = 0.44 x + 0.0 (10503 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 0.44 x + 0.0 (10503 voxels, peak = 37), gca=37.4 gca peak = 0.20573 (83) mri peak = 0.03364 (54) Right_Cerebellum_White_Matter (46): linear fit = 0.63 x + 0.0 (10731 voxels, overlap=0.002) Right_Cerebellum_White_Matter (46): linear fit = 0.63 x + 0.0 (10731 voxels, peak = 53), gca=52.7 gca peak = 0.21969 (57) mri peak = 0.04678 (68) Left_Amygdala (18): linear fit = 1.49 x + 0.0 (151 voxels, overlap=0.164) Left_Amygdala (18): linear fit = 1.49 x + 0.0 (151 voxels, peak = 85), gca=84.6 gca peak = 0.39313 (56) mri peak = 0.07603 (54) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (681 voxels, overlap=0.876) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (681 voxels, peak = 53), gca=52.9 gca peak = 0.14181 (85) mri peak = 0.08485 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6421 voxels, overlap=0.980) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6421 voxels, peak = 86), gca=86.3 gca peak = 0.11978 (83) mri peak = 0.09058 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4852 voxels, overlap=0.248) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4852 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.05615 (69) Left_Putamen (12): linear fit = 0.93 x + 0.0 (915 voxels, overlap=0.690) Left_Putamen (12): linear fit = 0.93 x + 0.0 (915 voxels, peak = 73), gca=73.1 gca peak = 0.14159 (79) mri peak = 0.04079 (92) Right_Putamen (51): linear fit = 1.26 x + 0.0 (2191 voxels, overlap=0.016) Right_Putamen (51): linear fit = 1.26 x + 0.0 (2191 voxels, peak = 100), gca=99.9 gca peak = 0.10025 (80) mri peak = 0.11214 (81) Brain_Stem (16): linear fit = 1.10 x + 0.0 (17604 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (17604 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07833 (86) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2555 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2555 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.16106 (83) Left_VentralDC (28): linear fit = 0.93 x + 0.0 (2344 voxels, overlap=0.463) Left_VentralDC (28): linear fit = 0.93 x + 0.0 (2344 voxels, peak = 82), gca=82.3 gca peak = 0.20494 (23) mri peak = 0.11236 (49) Third_Ventricle (14): linear fit = 1.93 x + 0.0 (122 voxels, overlap=0.036) Third_Ventricle (14): linear fit = 1.93 x + 0.0 (122 voxels, peak = 45), gca=44.5 gca peak = 0.15061 (21) mri peak = 0.06707 (37) Fourth_Ventricle (15): linear fit = 1.98 x + 0.0 (1128 voxels, overlap=0.038) Fourth_Ventricle (15): linear fit = 1.98 x + 0.0 (1128 voxels, peak = 41), gca=41.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_White_Matter = 0.18181 (84) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_White_Matter = 0.20573 (83) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.04 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Pallidum too bright - rescaling by 0.910 (from 1.145) to 97.0 (was 106.5) Right_Putamen too bright - rescaling by 0.900 (from 1.265) to 90.0 (was 99.9) Right_Pallidum too bright - rescaling by 0.995 (from 1.015) to 97.0 (was 97.4) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.054, neg=0, invalid=762 0139: dt=443.904000, rms=1.036 (1.697%), neg=0, invalid=762 0140: dt=308.310259, rms=1.022 (1.311%), neg=0, invalid=762 0141: dt=369.920000, rms=1.013 (0.874%), neg=0, invalid=762 0142: dt=221.952000, rms=1.008 (0.501%), neg=0, invalid=762 0143: dt=517.888000, rms=1.000 (0.828%), neg=0, invalid=762 0144: dt=129.472000, rms=0.998 (0.242%), neg=0, invalid=762 0145: dt=1479.680000, rms=0.988 (0.987%), neg=0, invalid=762 0146: dt=148.000000, rms=0.983 (0.471%), neg=0, invalid=762 0147: dt=369.920000, rms=0.981 (0.163%), neg=0, invalid=762 0148: dt=32.368000, rms=0.981 (0.031%), neg=0, invalid=762 0149: dt=0.252875, rms=0.981 (0.001%), neg=0, invalid=762 0150: dt=0.126438, rms=0.981 (0.000%), neg=0, invalid=762 0151: dt=0.031609, rms=0.981 (0.000%), neg=0, invalid=762 0152: dt=0.022578, rms=0.981 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.982, neg=0, invalid=762 0153: dt=0.000000, rms=0.981 (0.116%), neg=0, invalid=762 0154: dt=0.000000, rms=0.981 (0.000%), neg=0, invalid=762 0155: dt=0.000415, rms=0.981 (0.000%), neg=0, invalid=762 0156: dt=0.000052, rms=0.981 (0.000%), neg=0, invalid=762 0157: dt=0.000013, rms=0.981 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.984, neg=0, invalid=762 0158: dt=0.000000, rms=0.982 (0.116%), neg=0, invalid=762 0159: dt=0.000000, rms=0.982 (0.000%), neg=0, invalid=762 0160: dt=0.000000, rms=0.982 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.984, neg=0, invalid=762 0161: dt=0.000000, rms=0.982 (0.116%), neg=0, invalid=762 0162: dt=0.000000, rms=0.982 (0.000%), neg=0, invalid=762 0163: dt=0.000000, rms=0.982 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.988, neg=0, invalid=762 0164: dt=11.200000, rms=0.971 (1.762%), neg=0, invalid=762 0165: dt=0.700000, rms=0.970 (0.090%), neg=0, invalid=762 0166: dt=0.043750, rms=0.970 (0.006%), neg=0, invalid=762 0167: dt=0.021875, rms=0.970 (0.003%), neg=0, invalid=762 0168: dt=0.005469, rms=0.970 (0.001%), neg=0, invalid=762 0169: dt=0.002734, rms=0.970 (0.000%), neg=0, invalid=762 0170: dt=0.000000, rms=0.970 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.971, neg=0, invalid=762 0171: dt=0.000000, rms=0.970 (0.112%), neg=0, invalid=762 0172: dt=0.000000, rms=0.970 (0.000%), neg=0, invalid=762 0173: dt=0.000244, rms=0.970 (0.000%), neg=0, invalid=762 0174: dt=0.000122, rms=0.970 (0.000%), neg=0, invalid=762 0175: dt=0.000061, rms=0.970 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.987, neg=0, invalid=762 0176: dt=0.000000, rms=0.986 (0.108%), neg=0, invalid=762 0177: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 0178: dt=0.000001, rms=0.986 (0.000%), neg=0, invalid=762 0179: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 0180: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.987, neg=0, invalid=762 0181: dt=0.000000, rms=0.986 (0.108%), neg=0, invalid=762 0182: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 0183: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 0184: dt=0.000000, rms=0.986 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.019, neg=0, invalid=762 0185: dt=1.280000, rms=0.999 (1.989%), neg=0, invalid=762 0186: dt=1.792000, rms=0.978 (2.110%), neg=0, invalid=762 0187: dt=1.792000, rms=0.965 (1.350%), neg=0, invalid=762 0188: dt=0.448000, rms=0.963 (0.209%), neg=0, invalid=762 0189: dt=0.448000, rms=0.961 (0.193%), neg=0, invalid=762 0190: dt=0.320000, rms=0.960 (0.129%), neg=0, invalid=762 0191: dt=0.028000, rms=0.959 (0.011%), neg=0, invalid=762 0192: dt=0.014000, rms=0.959 (0.005%), neg=0, invalid=762 0193: dt=0.003500, rms=0.959 (0.001%), neg=0, invalid=762 0194: dt=0.000438, rms=0.959 (0.000%), neg=0, invalid=762 0195: dt=0.000109, rms=0.959 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.960, neg=0, invalid=762 0196: dt=0.000313, rms=0.959 (0.104%), neg=0, invalid=762 0197: dt=0.000000, rms=0.959 (0.000%), neg=0, invalid=762 0198: dt=0.000002, rms=0.959 (0.000%), neg=0, invalid=762 0199: dt=0.000002, rms=0.959 (0.000%), neg=0, invalid=762 0200: dt=0.000000, rms=0.959 (0.000%), neg=0, invalid=762 0201: dt=0.000000, rms=0.959 (-0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.899, neg=0, invalid=762 0202: dt=0.384000, rms=0.881 (2.023%), neg=0, invalid=762 0203: dt=0.384000, rms=0.871 (1.069%), neg=0, invalid=762 0204: dt=0.384000, rms=0.865 (0.672%), neg=0, invalid=762 0205: dt=0.384000, rms=0.862 (0.400%), neg=0, invalid=762 0206: dt=0.384000, rms=0.859 (0.293%), neg=0, invalid=762 0207: dt=0.384000, rms=0.858 (0.188%), neg=0, invalid=762 0208: dt=0.384000, rms=0.856 (0.175%), neg=0, invalid=762 0209: dt=0.384000, rms=0.855 (0.118%), neg=0, invalid=762 0210: dt=0.384000, rms=0.854 (0.121%), neg=0, invalid=762 0211: dt=0.384000, rms=0.854 (0.072%), neg=0, invalid=762 0212: dt=0.384000, rms=0.853 (0.088%), neg=0, invalid=762 0213: dt=0.384000, rms=0.852 (0.054%), neg=0, invalid=762 0214: dt=0.384000, rms=0.852 (0.076%), neg=0, invalid=762 0215: dt=0.384000, rms=0.852 (0.033%), neg=0, invalid=762 0216: dt=0.384000, rms=0.851 (0.065%), neg=0, invalid=762 0217: dt=0.384000, rms=0.850 (0.081%), neg=0, invalid=762 0218: dt=0.192000, rms=0.850 (0.020%), neg=0, invalid=762 0219: dt=0.192000, rms=0.850 (0.057%), neg=0, invalid=762 0220: dt=0.192000, rms=0.849 (0.027%), neg=0, invalid=762 0221: dt=0.192000, rms=0.849 (0.034%), neg=0, invalid=762 0222: dt=0.192000, rms=0.849 (0.037%), neg=0, invalid=762 0223: dt=0.192000, rms=0.848 (0.054%), neg=0, invalid=762 0224: dt=0.192000, rms=0.848 (0.018%), neg=0, invalid=762 0225: dt=0.192000, rms=0.848 (0.020%), neg=0, invalid=762 0226: dt=0.192000, rms=0.848 (0.004%), neg=0, invalid=762 0227: dt=0.112000, rms=0.848 (0.009%), neg=0, invalid=762 0228: dt=0.112000, rms=0.848 (0.009%), neg=0, invalid=762 0229: dt=0.112000, rms=0.848 (0.007%), neg=0, invalid=762 0230: dt=0.112000, rms=0.848 (0.013%), neg=0, invalid=762 0231: dt=0.112000, rms=0.848 (0.014%), neg=0, invalid=762 0232: dt=0.112000, rms=0.847 (0.018%), neg=0, invalid=762 0233: dt=0.112000, rms=0.847 (0.021%), neg=0, invalid=762 0234: dt=0.112000, rms=0.847 (0.020%), neg=0, invalid=762 0235: dt=0.112000, rms=0.847 (0.022%), neg=0, invalid=762 0236: dt=0.112000, rms=0.847 (0.022%), neg=0, invalid=762 0237: dt=0.112000, rms=0.847 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.848, neg=0, invalid=762 0238: dt=0.112000, rms=0.844 (0.406%), neg=0, invalid=762 0239: dt=0.112000, rms=0.842 (0.225%), neg=0, invalid=762 0240: dt=0.175000, rms=0.840 (0.280%), neg=0, invalid=762 0241: dt=0.112000, rms=0.839 (0.124%), neg=0, invalid=762 0242: dt=0.096000, rms=0.838 (0.084%), neg=0, invalid=762 0243: dt=0.096000, rms=0.838 (0.069%), neg=0, invalid=762 0244: dt=0.096000, rms=0.837 (0.057%), neg=0, invalid=762 0245: dt=0.112000, rms=0.837 (0.054%), neg=0, invalid=762 0246: dt=0.112000, rms=0.836 (0.042%), neg=0, invalid=762 0247: dt=0.112000, rms=0.836 (0.034%), neg=0, invalid=762 0248: dt=0.112000, rms=0.836 (0.054%), neg=0, invalid=762 0249: dt=0.112000, rms=0.835 (0.058%), neg=0, invalid=762 0250: dt=0.112000, rms=0.835 (0.043%), neg=0, invalid=762 0251: dt=0.112000, rms=0.835 (0.016%), neg=0, invalid=762 0252: dt=0.112000, rms=0.835 (-0.023%), neg=0, invalid=762 0253: dt=0.000000, rms=0.835 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.830, neg=0, invalid=762 0254: dt=5.780000, rms=0.829 (0.133%), neg=0, invalid=762 0255: dt=1.445000, rms=0.829 (0.001%), neg=0, invalid=762 0256: dt=1.445000, rms=0.829 (0.000%), neg=0, invalid=762 0257: dt=1.445000, rms=0.829 (0.001%), neg=0, invalid=762 0258: dt=1.445000, rms=0.829 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.830, neg=0, invalid=762 0259: dt=27.744000, rms=0.828 (0.157%), neg=0, invalid=762 0260: dt=27.744000, rms=0.828 (0.005%), neg=0, invalid=762 0261: dt=27.744000, rms=0.828 (0.004%), neg=0, invalid=762 0262: dt=27.744000, rms=0.828 (0.005%), neg=0, invalid=762 0263: dt=27.744000, rms=0.828 (0.003%), neg=0, invalid=762 0264: dt=27.744000, rms=0.828 (0.007%), neg=0, invalid=762 0265: dt=27.744000, rms=0.828 (0.015%), neg=0, invalid=762 0266: dt=27.744000, rms=0.828 (0.018%), neg=0, invalid=762 0267: dt=27.744000, rms=0.828 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.829, neg=0, invalid=762 0268: dt=23.680000, rms=0.826 (0.306%), neg=0, invalid=762 0269: dt=31.104000, rms=0.826 (0.093%), neg=0, invalid=762 0270: dt=31.104000, rms=0.825 (0.029%), neg=0, invalid=762 0271: dt=31.104000, rms=0.825 (-0.038%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.827, neg=0, invalid=762 0272: dt=36.288000, rms=0.823 (0.463%), neg=0, invalid=762 0273: dt=36.288000, rms=0.821 (0.233%), neg=0, invalid=762 0274: dt=36.288000, rms=0.820 (0.107%), neg=0, invalid=762 0275: dt=36.288000, rms=0.818 (0.174%), neg=0, invalid=762 0276: dt=36.288000, rms=0.817 (0.233%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0277: dt=36.288000, rms=0.815 (0.189%), neg=0, invalid=762 0278: dt=36.288000, rms=0.814 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0279: dt=36.288000, rms=0.813 (0.112%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0280: dt=36.288000, rms=0.812 (0.156%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 3 iterations, nbhd size=0, neg = 0 0281: dt=36.288000, rms=0.810 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 14 iterations, nbhd size=1, neg = 0 0282: dt=36.288000, rms=0.809 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 9 iterations, nbhd size=1, neg = 0 0283: dt=36.288000, rms=0.809 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 11 iterations, nbhd size=1, neg = 0 0284: dt=145.152000, rms=0.808 (0.115%), neg=0, invalid=762 0285: dt=20.736000, rms=0.808 (0.009%), neg=0, invalid=762 0286: dt=20.736000, rms=0.807 (0.017%), neg=0, invalid=762 0287: dt=20.736000, rms=0.807 (0.009%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0288: dt=20.736000, rms=0.807 (0.024%), neg=0, invalid=762 0289: dt=20.736000, rms=0.807 (0.033%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0290: dt=20.736000, rms=0.807 (0.033%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 9 iterations, nbhd size=1, neg = 0 0291: dt=20.736000, rms=0.806 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.809, neg=0, invalid=762 iter 0, gcam->neg = 121 after 12 iterations, nbhd size=1, neg = 0 0292: dt=22.468085, rms=0.804 (0.602%), neg=0, invalid=762 iter 0, gcam->neg = 664 after 17 iterations, nbhd size=1, neg = 0 0293: dt=55.733333, rms=0.800 (0.554%), neg=0, invalid=762 iter 0, gcam->neg = 146 after 17 iterations, nbhd size=1, neg = 0 0294: dt=25.600000, rms=0.798 (0.290%), neg=0, invalid=762 iter 0, gcam->neg = 780 after 21 iterations, nbhd size=1, neg = 0 0295: dt=66.169492, rms=0.795 (0.341%), neg=0, invalid=762 iter 0, gcam->neg = 48 after 12 iterations, nbhd size=1, neg = 0 0296: dt=11.200000, rms=0.793 (0.249%), neg=0, invalid=762 iter 0, gcam->neg = 50 after 12 iterations, nbhd size=1, neg = 0 0297: dt=11.200000, rms=0.792 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 94 after 14 iterations, nbhd size=1, neg = 0 0298: dt=11.200000, rms=0.791 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 184 after 27 iterations, nbhd size=1, neg = 0 0299: dt=11.200000, rms=0.791 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 199 after 15 iterations, nbhd size=1, neg = 0 0300: dt=32.000000, rms=0.789 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 112 after 22 iterations, nbhd size=1, neg = 0 0301: dt=25.600000, rms=0.788 (0.165%), neg=0, invalid=762 iter 0, gcam->neg = 112 after 17 iterations, nbhd size=1, neg = 0 0302: dt=25.600000, rms=0.787 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 215 after 22 iterations, nbhd size=1, neg = 0 0303: dt=25.600000, rms=0.786 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 442 after 28 iterations, nbhd size=1, neg = 0 0304: dt=25.600000, rms=0.784 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 657 after 34 iterations, nbhd size=1, neg = 0 0305: dt=25.600000, rms=0.783 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 685 after 27 iterations, nbhd size=1, neg = 0 0306: dt=25.600000, rms=0.782 (0.092%), neg=0, invalid=762 iter 0, gcam->neg = 122 after 26 iterations, nbhd size=1, neg = 0 0307: dt=32.000000, rms=0.780 (0.268%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 22 iterations, nbhd size=1, neg = 0 0308: dt=11.200000, rms=0.780 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 16 iterations, nbhd size=1, neg = 0 0309: dt=11.200000, rms=0.779 (0.031%), neg=0, invalid=762 iter 0, gcam->neg = 55 after 18 iterations, nbhd size=1, neg = 0 0310: dt=11.200000, rms=0.779 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 97 after 21 iterations, nbhd size=1, neg = 0 0311: dt=11.200000, rms=0.779 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 128 after 20 iterations, nbhd size=1, neg = 0 0312: dt=11.200000, rms=0.778 (0.073%), neg=0, invalid=762 iter 0, gcam->neg = 164 after 28 iterations, nbhd size=1, neg = 0 0313: dt=11.200000, rms=0.778 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 177 after 29 iterations, nbhd size=1, neg = 0 0314: dt=11.200000, rms=0.777 (0.064%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 20 iterations, nbhd size=2, neg = 0 0315: dt=9.600000, rms=0.777 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.778, neg=0, invalid=762 iter 0, gcam->neg = 10 after 11 iterations, nbhd size=1, neg = 0 0316: dt=32.000000, rms=0.775 (0.433%), neg=0, invalid=762 iter 0, gcam->neg = 109 after 20 iterations, nbhd size=1, neg = 0 0317: dt=44.800000, rms=0.772 (0.359%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0318: dt=11.200000, rms=0.772 (0.052%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0319: dt=11.200000, rms=0.771 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0320: dt=11.200000, rms=0.771 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0321: dt=11.200000, rms=0.770 (0.072%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 13 iterations, nbhd size=1, neg = 0 0322: dt=11.200000, rms=0.770 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 16 iterations, nbhd size=1, neg = 0 0323: dt=11.200000, rms=0.770 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 14 iterations, nbhd size=1, neg = 0 0324: dt=44.800000, rms=0.769 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 85 after 16 iterations, nbhd size=0, neg = 0 0325: dt=44.800000, rms=0.768 (0.078%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.793, neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0326: dt=4.240000, rms=0.791 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 11 iterations, nbhd size=1, neg = 0 0327: dt=5.818182, rms=0.791 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 16 iterations, nbhd size=1, neg = 0 0328: dt=5.818182, rms=0.790 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 13 iterations, nbhd size=1, neg = 0 0329: dt=5.818182, rms=0.790 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 102 after 14 iterations, nbhd size=1, neg = 0 0330: dt=5.818182, rms=0.789 (0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.790, neg=0, invalid=762 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=1, neg = 0 0331: dt=2.880000, rms=0.789 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0332: dt=6.285714, rms=0.789 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 15 iterations, nbhd size=1, neg = 0 0333: dt=6.285714, rms=0.788 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=1, neg = 0 0334: dt=6.285714, rms=0.787 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 11 iterations, nbhd size=1, neg = 0 0335: dt=6.285714, rms=0.787 (-0.020%), neg=0, invalid=762 iter 0, gcam->neg = 259 after 18 iterations, nbhd size=1, neg = 0 0336: dt=24.592593, rms=0.785 (0.237%), neg=0, invalid=762 iter 0, gcam->neg = 135 after 23 iterations, nbhd size=1, neg = 0 0337: dt=11.520000, rms=0.784 (0.228%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.804, neg=0, invalid=762 0338: dt=0.000000, rms=0.803 (0.135%), neg=0, invalid=762 0339: dt=0.000000, rms=0.803 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.804, neg=0, invalid=762 0340: dt=0.000000, rms=0.803 (0.135%), neg=0, invalid=762 0341: dt=0.000000, rms=0.803 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.772, neg=0, invalid=762 iter 0, gcam->neg = 4805 after 20 iterations, nbhd size=1, neg = 0 0342: dt=1.693601, rms=0.736 (4.638%), neg=0, invalid=762 0343: dt=0.024000, rms=0.736 (-0.001%), neg=0, invalid=762 0344: dt=0.024000, rms=0.736 (0.003%), neg=0, invalid=762 0345: dt=0.024000, rms=0.736 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.737, neg=0, invalid=762 0346: dt=0.112000, rms=0.735 (0.287%), neg=0, invalid=762 0347: dt=0.112000, rms=0.735 (0.042%), neg=0, invalid=762 0348: dt=0.112000, rms=0.735 (-0.005%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.724, neg=0, invalid=762 0349: dt=0.000000, rms=0.724 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.724, neg=0, invalid=762 0350: dt=27.744000, rms=0.724 (0.011%), neg=0, invalid=762 0351: dt=8.092000, rms=0.724 (0.000%), neg=0, invalid=762 0352: dt=8.092000, rms=0.724 (0.000%), neg=0, invalid=762 0353: dt=8.092000, rms=0.724 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.724, neg=0, invalid=762 0354: dt=9.072000, rms=0.723 (0.059%), neg=0, invalid=762 0355: dt=9.072000, rms=0.723 (0.022%), neg=0, invalid=762 0356: dt=9.072000, rms=0.723 (0.011%), neg=0, invalid=762 0357: dt=9.072000, rms=0.723 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0358: dt=31.104000, rms=0.722 (0.173%), neg=0, invalid=762 0359: dt=82.944000, rms=0.721 (0.129%), neg=0, invalid=762 0360: dt=82.944000, rms=0.721 (-0.038%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.721, neg=0, invalid=762 iter 0, gcam->neg = 32 after 11 iterations, nbhd size=1, neg = 0 0361: dt=21.925926, rms=0.717 (0.654%), neg=0, invalid=762 iter 0, gcam->neg = 86 after 13 iterations, nbhd size=1, neg = 0 0362: dt=29.814634, rms=0.714 (0.317%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 10 iterations, nbhd size=1, neg = 0 0363: dt=8.000000, rms=0.714 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 16 iterations, nbhd size=1, neg = 0 0364: dt=8.000000, rms=0.714 (-0.080%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.714, neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0365: dt=32.000000, rms=0.710 (0.624%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 16 iterations, nbhd size=1, neg = 0 0366: dt=32.000000, rms=0.707 (0.391%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 0 iterations, nbhd size=0, neg = 0 0367: dt=19.200000, rms=0.706 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0368: dt=19.200000, rms=0.705 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 16 iterations, nbhd size=1, neg = 0 0369: dt=19.200000, rms=0.704 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 10 iterations, nbhd size=1, neg = 0 0370: dt=19.200000, rms=0.703 (0.203%), neg=0, invalid=762 iter 0, gcam->neg = 58 after 17 iterations, nbhd size=1, neg = 0 0371: dt=19.200000, rms=0.702 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 52 after 21 iterations, nbhd size=1, neg = 0 0372: dt=19.200000, rms=0.701 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 91 after 21 iterations, nbhd size=1, neg = 0 0373: dt=19.200000, rms=0.699 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 130 after 33 iterations, nbhd size=2, neg = 0 0374: dt=19.200000, rms=0.699 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 137 after 14 iterations, nbhd size=1, neg = 0 0375: dt=19.200000, rms=0.698 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 101 after 20 iterations, nbhd size=1, neg = 0 0376: dt=19.200000, rms=0.698 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 88 after 25 iterations, nbhd size=1, neg = 0 0377: dt=38.400000, rms=0.697 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 17 iterations, nbhd size=1, neg = 0 0378: dt=38.400000, rms=0.697 (0.031%), neg=0, invalid=762 iter 0, gcam->neg = 54 after 23 iterations, nbhd size=1, neg = 0 0379: dt=38.400000, rms=0.697 (0.045%), neg=0, invalid=762 iter 0, gcam->neg = 196 after 34 iterations, nbhd size=1, neg = 0 0380: dt=38.400000, rms=0.697 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 80 after 29 iterations, nbhd size=2, neg = 0 0381: dt=38.400000, rms=0.696 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.704, neg=0, invalid=762 iter 0, gcam->neg = 51 after 13 iterations, nbhd size=1, neg = 0 0382: dt=7.150000, rms=0.702 (0.273%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0383: dt=1.008000, rms=0.702 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 11 iterations, nbhd size=1, neg = 0 0384: dt=1.008000, rms=0.702 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0385: dt=2.880000, rms=0.702 (0.017%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0386: dt=4.032000, rms=0.701 (0.067%), neg=0, invalid=762 iter 0, gcam->neg = 69 after 12 iterations, nbhd size=1, neg = 0 0387: dt=10.520548, rms=0.700 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 301 after 30 iterations, nbhd size=1, neg = 0 0388: dt=18.382979, rms=0.699 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 202 after 18 iterations, nbhd size=1, neg = 0 0389: dt=10.725275, rms=0.698 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 148 after 24 iterations, nbhd size=1, neg = 0 0390: dt=10.725275, rms=0.697 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 196 after 24 iterations, nbhd size=1, neg = 0 0391: dt=10.725275, rms=0.696 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 443 after 24 iterations, nbhd size=1, neg = 0 0392: dt=10.725275, rms=0.695 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 458 after 31 iterations, nbhd size=1, neg = 0 0393: dt=10.725275, rms=0.694 (0.200%), neg=0, invalid=762 iter 0, gcam->neg = 578 after 25 iterations, nbhd size=1, neg = 0 0394: dt=10.725275, rms=0.693 (0.098%), neg=0, invalid=762 iter 0, gcam->neg = 628 after 21 iterations, nbhd size=1, neg = 0 0395: dt=10.725275, rms=0.692 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 812 after 29 iterations, nbhd size=1, neg = 0 0396: dt=10.725275, rms=0.691 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 862 after 33 iterations, nbhd size=1, neg = 0 0397: dt=10.725275, rms=0.691 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 1052 after 27 iterations, nbhd size=1, neg = 0 0398: dt=10.725275, rms=0.690 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 137 after 20 iterations, nbhd size=1, neg = 0 0399: dt=8.345679, rms=0.689 (0.135%), neg=0, invalid=762 iter 0, gcam->neg = 137 after 17 iterations, nbhd size=1, neg = 0 0400: dt=9.636364, rms=0.688 (0.090%), neg=0, invalid=762 iter 0, gcam->neg = 102 after 15 iterations, nbhd size=1, neg = 0 0401: dt=9.636364, rms=0.688 (-0.025%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.699, neg=0, invalid=762 0402: dt=0.000000, rms=0.699 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.699, neg=0, invalid=762 0403: dt=0.000040, rms=0.699 (0.000%), neg=0, invalid=762 0404: dt=0.000000, rms=0.699 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.681, neg=0, invalid=762 iter 0, gcam->neg = 2465 after 26 iterations, nbhd size=1, neg = 0 0405: dt=0.984758, rms=0.669 (1.743%), neg=0, invalid=762 0406: dt=0.096000, rms=0.669 (0.039%), neg=0, invalid=762 0407: dt=0.096000, rms=0.669 (0.019%), neg=0, invalid=762 0408: dt=0.096000, rms=0.669 (-0.038%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 iter 0, gcam->neg = 100 after 13 iterations, nbhd size=1, neg = 0 0409: dt=0.564748, rms=0.663 (0.946%), neg=0, invalid=762 iter 0, gcam->neg = 110 after 8 iterations, nbhd size=1, neg = 0 0410: dt=0.495098, rms=0.659 (0.568%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0411: dt=0.320000, rms=0.657 (0.236%), neg=0, invalid=762 0412: dt=0.320000, rms=0.656 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0413: dt=0.320000, rms=0.654 (0.247%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 8 iterations, nbhd size=1, neg = 0 0414: dt=0.320000, rms=0.653 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 48 after 12 iterations, nbhd size=1, neg = 0 0415: dt=0.320000, rms=0.653 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 81 after 5 iterations, nbhd size=0, neg = 0 0416: dt=0.320000, rms=0.653 (-0.008%), neg=0, invalid=762 0417: dt=0.112000, rms=0.653 (0.032%), neg=0, invalid=762 0418: dt=0.256000, rms=0.652 (0.037%), neg=0, invalid=762 0419: dt=0.096000, rms=0.652 (0.005%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 44 minutes and 44 seconds. mri_ca_register utimesec 6238.943148 mri_ca_register stimesec 36.105981 mri_ca_register ru_maxrss 1332368 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 7779985 mri_ca_register ru_majflt 6 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1072 mri_ca_register ru_oublock 65776 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1041 mri_ca_register ru_nivcsw 18484 FSRUNTIME@ mri_ca_register 1.7455 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri 15 Mar 2024 11:48:22 AM CET mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname ramones machine x86_64 setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS cd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 9.61 Atlas used for the 3D morph was /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.07001 (45) Left_Lateral_Ventricle (4): linear fit = 2.22 x + 0.0 (680 voxels, overlap=0.011) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (680 voxels, peak = 44), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.06322 (51) Right_Lateral_Ventricle (43): linear fit = 3.36 x + 0.0 (1427 voxels, overlap=0.011) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1427 voxels, peak = 44), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.06368 (97) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (954 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (954 voxels, peak = 97), gca=97.4 gca peak = 0.16930 (96) mri peak = 0.11885 (89) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (683 voxels, overlap=0.403) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (683 voxels, peak = 89), gca=88.8 gca peak = 0.24553 (55) mri peak = 0.05316 (74) Right_Hippocampus (53): linear fit = 1.46 x + 0.0 (450 voxels, overlap=0.260) Right_Hippocampus (53): linear fit = 1.46 x + 0.0 (450 voxels, peak = 80), gca=80.0 gca peak = 0.30264 (59) mri peak = 0.07928 (50) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1913 voxels, overlap=0.711) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (1913 voxels, peak = 52), gca=51.6 gca peak = 0.07580 (103) mri peak = 0.07202 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (48528 voxels, overlap=0.737) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (48528 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.09378 (92) Left_Cerebral_White_Matter (2): linear fit = 0.92 x + 0.0 (41575 voxels, overlap=0.428) Left_Cerebral_White_Matter (2): linear fit = 0.92 x + 0.0 (41575 voxels, peak = 95), gca=95.2 gca peak = 0.09712 (58) mri peak = 0.03621 (58) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (34790 voxels, overlap=0.982) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (34790 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.03882 (52) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (36663 voxels, overlap=0.452) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (36663 voxels, peak = 52), gca=51.9 gca peak = 0.30970 (66) mri peak = 0.08376 (52) Right_Caudate: unreasonable value (49.8/52.0), not in range [50, 100] - rejecting gca peak = 0.15280 (69) mri peak = 0.07143 (52) Left_Caudate (11): linear fit = 0.74 x + 0.0 (391 voxels, overlap=0.214) Left_Caudate (11): linear fit = 0.74 x + 0.0 (391 voxels, peak = 51), gca=50.7 gca peak = 0.13902 (56) mri peak = 0.03116 (57) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (30196 voxels, overlap=0.841) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (30196 voxels, peak = 54), gca=54.0 gca peak = 0.14777 (55) mri peak = 0.04201 (54) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (33526 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (33526 voxels, peak = 54), gca=54.2 gca peak = 0.16765 (84) mri peak = 0.03657 (39) Left_Cerebellum_White_Matter (7): linear fit = 0.47 x + 0.0 (10309 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 0.47 x + 0.0 (10309 voxels, peak = 40), gca=39.9 gca peak = 0.18739 (84) mri peak = 0.04598 (79) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (8327 voxels, overlap=0.861) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (8327 voxels, peak = 81), gca=81.1 gca peak = 0.29869 (57) mri peak = 0.05607 (79) Left_Amygdala (18): linear fit = 1.39 x + 0.0 (493 voxels, overlap=0.084) Left_Amygdala (18): linear fit = 1.39 x + 0.0 (493 voxels, peak = 80), gca=79.5 gca peak = 0.33601 (57) mri peak = 0.07733 (52) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (543 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (543 voxels, peak = 53), gca=52.7 gca peak = 0.11131 (90) mri peak = 0.06957 (92) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (1358 voxels, overlap=0.864) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (1358 voxels, peak = 93), gca=93.1 gca peak = 0.11793 (83) mri peak = 0.06996 (77) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2368 voxels, overlap=0.608) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (2368 voxels, peak = 78), gca=78.4 gca peak = 0.08324 (81) mri peak = 0.07577 (60) Left_Putamen (12): linear fit = 0.86 x + 0.0 (2236 voxels, overlap=0.492) Left_Putamen (12): linear fit = 0.86 x + 0.0 (2236 voxels, peak = 69), gca=69.3 gca peak = 0.10360 (77) mri peak = 0.05876 (104) Right_Putamen (51): linear fit = 1.29 x + 0.0 (3745 voxels, overlap=0.013) Right_Putamen (51): linear fit = 1.29 x + 0.0 (3745 voxels, peak = 100), gca=99.7 gca peak = 0.08424 (78) mri peak = 0.12719 (81) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12554 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12554 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.10393 (87) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (770 voxels, overlap=0.822) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (770 voxels, peak = 87), gca=86.8 gca peak = 0.14500 (87) mri peak = 0.13115 (80) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (894 voxels, overlap=0.915) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (894 voxels, peak = 81), gca=81.3 gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) mri peak = 0.06781 (44) Fourth_Ventricle (15): linear fit = 2.69 x + 0.0 (1171 voxels, overlap=0.031) Fourth_Ventricle (15): linear fit = 2.69 x + 0.0 (1171 voxels, peak = 38), gca=37.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_White_Matter = 0.16765 (84) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means setting label Right_Caudate based on Left_Caudate = 0.74 x + 0: 51 setting label Left_Cerebellum_White_Matter based on Right_Cerebellum_White_Matter = 0.96 x + 0: 81 estimating mean gm scale to be 1.10 x + 0.0 estimating mean wm scale to be 0.97 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Right_Putamen too bright - rescaling by 0.906 (from 1.295) to 90.3 (was 99.7) Right_Pallidum too bright - rescaling by 1.000 (from 1.025) to 97.4 (was 97.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.07001 (45) Left_Lateral_Ventricle (4): linear fit = 1.47 x + 0.0 (680 voxels, overlap=0.202) Left_Lateral_Ventricle (4): linear fit = 1.47 x + 0.0 (680 voxels, peak = 45), gca=45.4 gca peak = 0.13981 (19) mri peak = 0.06322 (51) Right_Lateral_Ventricle (43): linear fit = 2.21 x + 0.0 (1427 voxels, overlap=0.108) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1427 voxels, peak = 42), gca=28.5 gca peak = 0.28594 (98) mri peak = 0.06368 (97) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (954 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (954 voxels, peak = 99), gca=99.5 gca peak = 0.16970 (88) mri peak = 0.11885 (89) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (683 voxels, overlap=0.908) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (683 voxels, peak = 89), gca=89.3 gca peak = 0.23197 (81) mri peak = 0.05316 (74) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (450 voxels, overlap=0.884) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (450 voxels, peak = 80), gca=79.8 gca peak = 0.32337 (52) mri peak = 0.07928 (50) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1913 voxels, overlap=0.995) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1913 voxels, peak = 52), gca=52.0 gca peak = 0.07607 (105) mri peak = 0.07202 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48528 voxels, overlap=0.829) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (48528 voxels, peak = 104), gca=104.5 gca peak = 0.08604 (96) mri peak = 0.09378 (92) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41575 voxels, overlap=0.649) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41575 voxels, peak = 96), gca=96.5 gca peak = 0.09481 (59) mri peak = 0.03621 (58) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (34790 voxels, overlap=0.960) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (34790 voxels, peak = 57), gca=56.9 gca peak = 0.12825 (52) mri peak = 0.03882 (52) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (36663 voxels, overlap=0.965) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (36663 voxels, peak = 50), gca=50.2 gca peak = 0.29474 (49) mri peak = 0.08376 (52) Right_Caudate: unreasonable value (49.7/52.0), not in range [50, 100] - rejecting gca peak = 0.13975 (54) mri peak = 0.07143 (52) Left_Caudate (11): linear fit = 0.99 x + 0.0 (391 voxels, overlap=0.755) Left_Caudate (11): linear fit = 0.99 x + 0.0 (391 voxels, peak = 53), gca=53.2 gca peak = 0.14830 (54) mri peak = 0.03116 (57) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (30196 voxels, overlap=0.895) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (30196 voxels, peak = 56), gca=56.4 gca peak = 0.14616 (54) mri peak = 0.04201 (54) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (33526 voxels, overlap=0.982) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (33526 voxels, peak = 53), gca=53.2 gca peak = 0.17048 (81) mri peak = 0.03657 (39) Left_Cerebellum_White_Matter (7): linear fit = 0.47 x + 0.0 (10309 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 0.47 x + 0.0 (10309 voxels, peak = 38), gca=38.5 gca peak = 0.17712 (81) mri peak = 0.04598 (79) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8327 voxels, overlap=0.975) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8327 voxels, peak = 80), gca=79.8 gca peak = 0.22941 (79) mri peak = 0.05607 (79) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (493 voxels, overlap=0.954) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (493 voxels, peak = 80), gca=80.2 gca peak = 0.32498 (53) mri peak = 0.07733 (52) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (543 voxels, overlap=0.991) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (543 voxels, peak = 53), gca=53.0 gca peak = 0.10992 (93) mri peak = 0.06957 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (1358 voxels, overlap=0.951) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (1358 voxels, peak = 93), gca=92.5 gca peak = 0.10578 (76) mri peak = 0.06996 (77) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2368 voxels, overlap=0.752) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2368 voxels, peak = 77), gca=77.1 gca peak = 0.09591 (66) mri peak = 0.07577 (60) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2236 voxels, overlap=0.862) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2236 voxels, peak = 64), gca=64.3 gca peak = 0.08616 (89) mri peak = 0.05876 (104) Right_Putamen (51): linear fit = 1.10 x + 0.0 (3745 voxels, overlap=0.280) Right_Putamen (51): linear fit = 1.10 x + 0.0 (3745 voxels, peak = 97), gca=97.5 gca peak = 0.08004 (85) mri peak = 0.12719 (81) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12554 voxels, overlap=0.704) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12554 voxels, peak = 85), gca=85.0 gca peak = 0.12475 (87) mri peak = 0.10393 (87) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (770 voxels, overlap=0.790) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (770 voxels, peak = 87), gca=87.0 gca peak = 0.14936 (80) mri peak = 0.13115 (80) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (894 voxels, overlap=0.772) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (894 voxels, peak = 80), gca=80.0 gca peak = 0.12656 (38) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.16542 (24) mri peak = 0.06781 (44) Fourth_Ventricle (15): linear fit = 1.78 x + 0.0 (1171 voxels, overlap=0.195) Fourth_Ventricle (15): linear fit = 1.78 x + 0.0 (1171 voxels, peak = 43), gca=42.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17004 (24) gca peak Left_Cerebellum_White_Matter = 0.17048 (81) gca peak Left_Thalamus = 0.36646 (93) gca peak Third_Ventricle = 0.12656 (38) gca peak Fourth_Ventricle = 0.16542 (24) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.56536 (46) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.78636 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.17280 (34) gca peak Right_Caudate = 0.29474 (49) gca peak Right_Accumbens_area = 0.42479 (48) gca peak Right_vessel = 0.81794 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.07585 (74) gca peak non_WM_hypointensities = 0.09187 (42) gca peak Optic_Chiasm = 0.71087 (75) not using caudate to estimate GM means setting label Right_Caudate based on Left_Caudate = 0.99 x + 0: 53 setting label Left_Cerebellum_White_Matter based on Right_Cerebellum_White_Matter = 0.99 x + 0: 80 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.48 x + 0.0 Right_Putamen too bright - rescaling by 0.928 (from 1.095) to 90.4 (was 97.5) Right_Pallidum too bright - rescaling by 0.980 (from 1.015) to 97.5 (was 99.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 234949 voxels changed in iteration 0 of unlikely voxel relabeling 256 voxels changed in iteration 1 of unlikely voxel relabeling 47 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 138357 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 2072 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 171467 changed. image ll: -10.788, PF=0.500 pass 2: 54244 changed. image ll: -10.785, PF=0.500 pass 3: 21403 changed. pass 4: 9509 changed. pass 5: 4942 changed. 167668 voxels changed in iteration 0 of unlikely voxel relabeling 769 voxels changed in iteration 1 of unlikely voxel relabeling 72 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 17596 voxels changed in iteration 0 of unlikely voxel relabeling 254 voxels changed in iteration 1 of unlikely voxel relabeling 43 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 15561 voxels changed in iteration 0 of unlikely voxel relabeling 100 voxels changed in iteration 1 of unlikely voxel relabeling 14 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 14939 voxels changed in iteration 0 of unlikely voxel relabeling 64 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3515.213908 mri_ca_label stimesec 4.159675 mri_ca_label ru_maxrss 2414376 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 923495 mri_ca_label ru_majflt 2 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 184 mri_ca_label ru_oublock 600 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 55 mri_ca_label ru_nivcsw 22498 auto-labeling took 59 minutes and 14 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/cc_up.lta LS5K will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/cc_up.lta reading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.auto_noCCseg.mgz reading norm from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/norm.mgz 329701 voxels in left wm, 146741 in right wm, xrange [131, 176] searching rotation angles z=[10 24], y=[-19 -5] searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.7 searching scale 1 Z rot 10.9 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.4 searching scale 1 Z rot 11.7 searching scale 1 Z rot 11.9 searching scale 1 Z rot 12.2 searching scale 1 Z rot 12.4 searching scale 1 Z rot 12.7 searching scale 1 Z rot 12.9 searching scale 1 Z rot 13.2 searching scale 1 Z rot 13.4 searching scale 1 Z rot 13.7 searching scale 1 Z rot 13.9 searching scale 1 Z rot 14.2 searching scale 1 Z rot 14.4 searching scale 1 Z rot 14.7 searching scale 1 Z rot 14.9 searching scale 1 Z rot 15.2 searching scale 1 Z rot 15.4 searching scale 1 Z rot 15.7 searching scale 1 Z rot 15.9 searching scale 1 Z rot 16.2 searching scale 1 Z rot 16.4 searching scale 1 Z rot 16.7 searching scale 1 Z rot 16.9 searching scale 1 Z rot 17.2 searching scale 1 Z rot 17.4 searching scale 1 Z rot 17.7 searching scale 1 Z rot 17.9 searching scale 1 Z rot 18.2 searching scale 1 Z rot 18.4 searching scale 1 Z rot 18.7 searching scale 1 Z rot 18.9 searching scale 1 Z rot 19.2 searching scale 1 Z rot 19.4 searching scale 1 Z rot 19.7 searching scale 1 Z rot 19.9 searching scale 1 Z rot 20.2 searching scale 1 Z rot 20.4 searching scale 1 Z rot 20.7 searching scale 1 Z rot 20.9 searching scale 1 Z rot 21.2 searching scale 1 Z rot 21.4 searching scale 1 Z rot 21.7 searching scale 1 Z rot 21.9 searching scale 1 Z rot 22.2 searching scale 1 Z rot 22.4 searching scale 1 Z rot 22.7 searching scale 1 Z rot 22.9 searching scale 1 Z rot 23.2 global minimum found at slice 145.0, rotations (-12.67, 16.43) final transformation (x=145.0, yr=-12.671, zr=16.434): 0.93579 -0.28290 -0.21039 49.96777; 0.27601 0.95915 -0.06205 8.02322; 0.21935 0.00000 0.97565 -49.17659; 0.00000 0.00000 0.00000 1.00000; updating x range to be [116, 138] in xformed coordinates best xformed slice 129 cc center is found at 129 93 149 eigenvectors: 0.00650 -0.00634 0.99996; 0.90198 -0.43170 -0.00860; 0.43173 0.90200 0.00291; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.auto.mgz... corpus callosum segmentation took 7.7 minutes #-------------------------------------- #@# Merge ASeg Fri 15 Mar 2024 12:55:19 PM CET cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri 15 Mar 2024 12:55:19 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_normalize -f /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 11 control points... only using 11 control points from file, mean 94.4, scaling by 1.17... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... processing with aseg removing outliers in the aseg WM... 13161 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 68 (68), valley at 0 (-1) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 71 (71), valley at 0 (-1) csf peak at 35, setting threshold to 59 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 2 seconds. #-------------------------------------------- #@# Mask BFS Fri 15 Mar 2024 12:58:22 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 3963790 voxels in mask (pct= 23.63) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri 15 Mar 2024 12:58:23 PM CET mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 108.0 +- 7.2 [79.0 --> 125.0] GM (69.0) : 66.9 +- 10.1 [30.0 --> 95.0] setting bottom of white matter range to 77.0 setting top of gray matter range to 87.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 76105 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1259 filled 44286 bright non-wm voxels segmented. 41125 diagonally connected voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.86 minutes reading wm segmentation from wm.seg.mgz... 5100 voxels added to wm to prevent paths from MTL structures to cortex 39636 additional wm voxels added 0 additional wm voxels added SEG EDIT: 134580 voxels turned on, 671958 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 98 new 98 115,126,128 old 98 new 98 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 418 found - 418 modified | TOTAL: 418 pass 2 (xy+): 0 found - 418 modified | TOTAL: 418 pass 1 (xy-): 432 found - 432 modified | TOTAL: 850 pass 2 (xy-): 0 found - 432 modified | TOTAL: 850 pass 1 (yz+): 311 found - 311 modified | TOTAL: 1161 pass 2 (yz+): 0 found - 311 modified | TOTAL: 1161 pass 1 (yz-): 422 found - 422 modified | TOTAL: 1583 pass 2 (yz-): 0 found - 422 modified | TOTAL: 1583 pass 1 (xz+): 366 found - 366 modified | TOTAL: 1949 pass 2 (xz+): 0 found - 366 modified | TOTAL: 1949 pass 1 (xz-): 414 found - 414 modified | TOTAL: 2363 pass 2 (xz-): 0 found - 414 modified | TOTAL: 2363 Iteration Number : 1 pass 1 (+++): 357 found - 357 modified | TOTAL: 357 pass 2 (+++): 0 found - 357 modified | TOTAL: 357 pass 1 (+++): 437 found - 437 modified | TOTAL: 794 pass 2 (+++): 0 found - 437 modified | TOTAL: 794 pass 1 (+++): 493 found - 493 modified | TOTAL: 1287 pass 2 (+++): 0 found - 493 modified | TOTAL: 1287 pass 1 (+++): 417 found - 417 modified | TOTAL: 1704 pass 2 (+++): 0 found - 417 modified | TOTAL: 1704 Iteration Number : 1 pass 1 (++): 644 found - 644 modified | TOTAL: 644 pass 2 (++): 0 found - 644 modified | TOTAL: 644 pass 1 (+-): 598 found - 598 modified | TOTAL: 1242 pass 2 (+-): 6 found - 604 modified | TOTAL: 1248 pass 3 (+-): 0 found - 604 modified | TOTAL: 1248 pass 1 (--): 665 found - 665 modified | TOTAL: 1913 pass 2 (--): 10 found - 675 modified | TOTAL: 1923 pass 3 (--): 0 found - 675 modified | TOTAL: 1923 pass 1 (-+): 534 found - 534 modified | TOTAL: 2457 pass 2 (-+): 0 found - 534 modified | TOTAL: 2457 Iteration Number : 2 pass 1 (xy+): 153 found - 153 modified | TOTAL: 153 pass 2 (xy+): 0 found - 153 modified | TOTAL: 153 pass 1 (xy-): 156 found - 156 modified | TOTAL: 309 pass 2 (xy-): 0 found - 156 modified | TOTAL: 309 pass 1 (yz+): 141 found - 141 modified | TOTAL: 450 pass 2 (yz+): 0 found - 141 modified | TOTAL: 450 pass 1 (yz-): 144 found - 144 modified | TOTAL: 594 pass 2 (yz-): 0 found - 144 modified | TOTAL: 594 pass 1 (xz+): 121 found - 121 modified | TOTAL: 715 pass 2 (xz+): 0 found - 121 modified | TOTAL: 715 pass 1 (xz-): 167 found - 167 modified | TOTAL: 882 pass 2 (xz-): 0 found - 167 modified | TOTAL: 882 Iteration Number : 2 pass 1 (+++): 39 found - 39 modified | TOTAL: 39 pass 2 (+++): 0 found - 39 modified | TOTAL: 39 pass 1 (+++): 42 found - 42 modified | TOTAL: 81 pass 2 (+++): 0 found - 42 modified | TOTAL: 81 pass 1 (+++): 79 found - 79 modified | TOTAL: 160 pass 2 (+++): 0 found - 79 modified | TOTAL: 160 pass 1 (+++): 31 found - 31 modified | TOTAL: 191 pass 2 (+++): 0 found - 31 modified | TOTAL: 191 Iteration Number : 2 pass 1 (++): 81 found - 81 modified | TOTAL: 81 pass 2 (++): 0 found - 81 modified | TOTAL: 81 pass 1 (+-): 68 found - 68 modified | TOTAL: 149 pass 2 (+-): 0 found - 68 modified | TOTAL: 149 pass 1 (--): 71 found - 71 modified | TOTAL: 220 pass 2 (--): 0 found - 71 modified | TOTAL: 220 pass 1 (-+): 80 found - 80 modified | TOTAL: 300 pass 2 (-+): 0 found - 80 modified | TOTAL: 300 Iteration Number : 3 pass 1 (xy+): 20 found - 20 modified | TOTAL: 20 pass 2 (xy+): 0 found - 20 modified | TOTAL: 20 pass 1 (xy-): 17 found - 17 modified | TOTAL: 37 pass 2 (xy-): 0 found - 17 modified | TOTAL: 37 pass 1 (yz+): 23 found - 23 modified | TOTAL: 60 pass 2 (yz+): 0 found - 23 modified | TOTAL: 60 pass 1 (yz-): 18 found - 18 modified | TOTAL: 78 pass 2 (yz-): 0 found - 18 modified | TOTAL: 78 pass 1 (xz+): 7 found - 7 modified | TOTAL: 85 pass 2 (xz+): 0 found - 7 modified | TOTAL: 85 pass 1 (xz-): 20 found - 20 modified | TOTAL: 105 pass 2 (xz-): 0 found - 20 modified | TOTAL: 105 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 7 found - 7 modified | TOTAL: 7 pass 2 (+++): 0 found - 7 modified | TOTAL: 7 pass 1 (+++): 0 found - 0 modified | TOTAL: 7 pass 1 (+++): 7 found - 7 modified | TOTAL: 14 pass 2 (+++): 0 found - 7 modified | TOTAL: 14 Iteration Number : 3 pass 1 (++): 9 found - 9 modified | TOTAL: 9 pass 2 (++): 0 found - 9 modified | TOTAL: 9 pass 1 (+-): 10 found - 10 modified | TOTAL: 19 pass 2 (+-): 0 found - 10 modified | TOTAL: 19 pass 1 (--): 6 found - 6 modified | TOTAL: 25 pass 2 (--): 0 found - 6 modified | TOTAL: 25 pass 1 (-+): 9 found - 9 modified | TOTAL: 34 pass 2 (-+): 0 found - 9 modified | TOTAL: 34 Iteration Number : 4 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 4 found - 4 modified | TOTAL: 11 pass 2 (xy-): 0 found - 4 modified | TOTAL: 11 pass 1 (yz+): 2 found - 2 modified | TOTAL: 13 pass 2 (yz+): 0 found - 2 modified | TOTAL: 13 pass 1 (yz-): 2 found - 2 modified | TOTAL: 15 pass 2 (yz-): 0 found - 2 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 1 found - 1 modified | TOTAL: 18 pass 2 (xz-): 0 found - 1 modified | TOTAL: 18 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 3 found - 3 modified | TOTAL: 3 pass 2 (+++): 0 found - 3 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 4 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 4 found - 4 modified | TOTAL: 5 pass 2 (--): 0 found - 4 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 6 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8079 (out of 669965: 1.205884) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri 15 Mar 2024 01:01:44 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.88813 -0.33003 -0.13063 45.20975; 0.20850 1.13371 0.10005 -45.77451; 0.05463 0.03065 0.77168 -4.12897; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.88813 -0.33003 -0.13063 45.20975; 0.20850 1.13371 0.10005 -45.77451; 0.05463 0.03065 0.77168 -4.12897; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 4985 (min = 350, max = 1400), aspect = 0.81 (min = 0.10, max = 0.75) need search nearby using seed (110, 125, 92), TAL = (18.0, -36.0, 3.0) talairach voxel to voxel transform 1.04680 0.30099 0.13817 -32.97726; -0.18663 0.83150 -0.13940 45.92337; -0.06670 -0.05433 1.29163 5.86156; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (110, 125, 92) --> (18.0, -36.0, 3.0) done. writing output to filled.mgz... filling took 0.4 minutes badRH = 77492/355959, badLH=64/291035 Please check filled volume. Cerebellum may be included. talairach cc position changed to (18.00, -36.00, 3.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(36.00, -36.00, 3.00) SRC: (113.66, 119.87, 111.76) search lh wm seed point around talairach space (0.00, -36.00, 3.00), SRC: (151.35, 113.15, 109.36) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri 15 Mar 2024 01:02:08 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 64 found - 64 modified | TOTAL: 64 pass 2 (xy+): 0 found - 64 modified | TOTAL: 64 pass 1 (xy-): 31 found - 31 modified | TOTAL: 95 pass 2 (xy-): 0 found - 31 modified | TOTAL: 95 pass 1 (yz+): 15 found - 15 modified | TOTAL: 110 pass 2 (yz+): 0 found - 15 modified | TOTAL: 110 pass 1 (yz-): 45 found - 45 modified | TOTAL: 155 pass 2 (yz-): 0 found - 45 modified | TOTAL: 155 pass 1 (xz+): 25 found - 25 modified | TOTAL: 180 pass 2 (xz+): 0 found - 25 modified | TOTAL: 180 pass 1 (xz-): 22 found - 22 modified | TOTAL: 202 pass 2 (xz-): 0 found - 22 modified | TOTAL: 202 Iteration Number : 1 pass 1 (+++): 10 found - 10 modified | TOTAL: 10 pass 2 (+++): 0 found - 10 modified | TOTAL: 10 pass 1 (+++): 6 found - 6 modified | TOTAL: 16 pass 2 (+++): 0 found - 6 modified | TOTAL: 16 pass 1 (+++): 2 found - 2 modified | TOTAL: 18 pass 2 (+++): 0 found - 2 modified | TOTAL: 18 pass 1 (+++): 2 found - 2 modified | TOTAL: 20 pass 2 (+++): 0 found - 2 modified | TOTAL: 20 Iteration Number : 1 pass 1 (++): 17 found - 17 modified | TOTAL: 17 pass 2 (++): 0 found - 17 modified | TOTAL: 17 pass 1 (+-): 14 found - 14 modified | TOTAL: 31 pass 2 (+-): 0 found - 14 modified | TOTAL: 31 pass 1 (--): 28 found - 28 modified | TOTAL: 59 pass 2 (--): 0 found - 28 modified | TOTAL: 59 pass 1 (-+): 13 found - 13 modified | TOTAL: 72 pass 2 (-+): 0 found - 13 modified | TOTAL: 72 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 0 found - 0 modified | TOTAL: 8 pass 1 (xz+): 0 found - 0 modified | TOTAL: 8 pass 1 (xz-): 2 found - 2 modified | TOTAL: 10 pass 2 (xz-): 0 found - 2 modified | TOTAL: 10 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 3 found - 3 modified | TOTAL: 5 pass 2 (-+): 0 found - 3 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 311 (out of 291346: 0.106746) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1206 vertices, 1412 faces slice 50: 11817 vertices, 12357 faces slice 60: 24653 vertices, 25368 faces slice 70: 38406 vertices, 39277 faces slice 80: 51253 vertices, 52079 faces slice 90: 60259 vertices, 61061 faces slice 100: 69705 vertices, 70568 faces slice 110: 80272 vertices, 81179 faces slice 120: 91543 vertices, 92539 faces slice 130: 104271 vertices, 105331 faces slice 140: 118850 vertices, 120164 faces slice 150: 133875 vertices, 135113 faces slice 160: 148324 vertices, 149798 faces slice 170: 165184 vertices, 166999 faces slice 180: 185694 vertices, 188059 faces slice 190: 207827 vertices, 210803 faces slice 200: 230756 vertices, 234459 faces slice 210: 253133 vertices, 257390 faces slice 220: 270199 vertices, 274723 faces slice 230: 275778 vertices, 279894 faces slice 240: 275778 vertices, 279894 faces slice 250: 275778 vertices, 279894 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 275778 voxel in cpt #1: X=-4116 [v=275778,e=839682,f=559788] located at (-46.890129, 14.489735, 27.117083) For the whole surface: X=-4116 [v=275778,e=839682,f=559788] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri 15 Mar 2024 01:02:13 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 38 found - 38 modified | TOTAL: 38 pass 2 (xy+): 0 found - 38 modified | TOTAL: 38 pass 1 (xy-): 25 found - 25 modified | TOTAL: 63 pass 2 (xy-): 0 found - 25 modified | TOTAL: 63 pass 1 (yz+): 17 found - 17 modified | TOTAL: 80 pass 2 (yz+): 0 found - 17 modified | TOTAL: 80 pass 1 (yz-): 21 found - 21 modified | TOTAL: 101 pass 2 (yz-): 0 found - 21 modified | TOTAL: 101 pass 1 (xz+): 30 found - 30 modified | TOTAL: 131 pass 2 (xz+): 0 found - 30 modified | TOTAL: 131 pass 1 (xz-): 9 found - 9 modified | TOTAL: 140 pass 2 (xz-): 0 found - 9 modified | TOTAL: 140 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 2 pass 2 (+++): 0 found - 1 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 15 found - 15 modified | TOTAL: 23 pass 2 (+-): 0 found - 15 modified | TOTAL: 23 pass 1 (--): 17 found - 17 modified | TOTAL: 40 pass 2 (--): 0 found - 17 modified | TOTAL: 40 pass 1 (-+): 12 found - 12 modified | TOTAL: 52 pass 2 (-+): 0 found - 12 modified | TOTAL: 52 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 198 (out of 356157: 0.055593) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 336 vertices, 376 faces slice 60: 4428 vertices, 4663 faces slice 70: 13008 vertices, 13329 faces slice 80: 23699 vertices, 24085 faces slice 90: 34748 vertices, 35158 faces slice 100: 45880 vertices, 46317 faces slice 110: 60669 vertices, 61325 faces slice 120: 76065 vertices, 76717 faces slice 130: 89884 vertices, 90501 faces slice 140: 101893 vertices, 102594 faces slice 150: 118565 vertices, 119473 faces slice 160: 133871 vertices, 134758 faces slice 170: 148862 vertices, 149851 faces slice 180: 164677 vertices, 165821 faces slice 190: 180828 vertices, 182133 faces slice 200: 202411 vertices, 204321 faces slice 210: 228793 vertices, 231516 faces slice 220: 253533 vertices, 257050 faces slice 230: 262862 vertices, 265724 faces slice 240: 262862 vertices, 265724 faces slice 250: 262862 vertices, 265724 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 262854 voxel in cpt #1: X=-2864 [v=262854,e=797154,f=531436] located at (12.561627, 24.371103, 23.479053) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (-35.000000, 92.000000, 19.000000) For the whole surface: X=-2862 [v=262862,e=797172,f=531448] 2 components have been found keeping component #1 with 262854 vertices done #-------------------------------------------- #@# Smooth1 lh Fri 15 Mar 2024 01:02:19 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Fri 15 Mar 2024 01:02:26 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri 15 Mar 2024 01:02:33 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 60.8 mm, total surface area = 128130 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.9 minutes step 000: RMS=0.262 (target=0.015) step 005: RMS=0.230 (target=0.015) step 010: RMS=0.209 (target=0.015) step 015: RMS=0.201 (target=0.015) step 020: RMS=0.199 (target=0.015) step 025: RMS=0.197 (target=0.015) step 030: RMS=0.196 (target=0.015) step 035: RMS=0.195 (target=0.015) step 040: RMS=0.194 (target=0.015) step 045: RMS=0.193 (target=0.015) step 050: RMS=0.193 (target=0.015) step 055: RMS=0.193 (target=0.015) step 060: RMS=0.193 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 52.736998 mris_inflate stimesec 0.140002 mris_inflate ru_maxrss 368196 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 46917 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 128 mris_inflate ru_oublock 19592 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 371 mris_inflate ru_nivcsw 86 #-------------------------------------------- #@# Inflation1 rh Fri 15 Mar 2024 01:03:26 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 58.5 mm, total surface area = 127228 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.237 (target=0.015) step 005: RMS=0.203 (target=0.015) step 010: RMS=0.182 (target=0.015) step 015: RMS=0.172 (target=0.015) step 020: RMS=0.169 (target=0.015) step 025: RMS=0.168 (target=0.015) step 030: RMS=0.166 (target=0.015) step 035: RMS=0.165 (target=0.015) step 040: RMS=0.165 (target=0.015) step 045: RMS=0.164 (target=0.015) step 050: RMS=0.164 (target=0.015) step 055: RMS=0.164 (target=0.015) step 060: RMS=0.164 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 50.141286 mris_inflate stimesec 0.340008 mris_inflate ru_maxrss 348044 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 72921 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 18624 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 428 mris_inflate ru_nivcsw 99 #-------------------------------------------- #@# QSphere lh Fri 15 Mar 2024 01:04:17 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.78 +- 0.94 (0.00-->27.08) (max @ vno 118188 --> 118196) face area 0.02 +- 0.21 (-16.76-->8.51) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.554, avgs=0 005/300: dt: 0.9000, rms radial error=174.304, avgs=0 010/300: dt: 0.9000, rms radial error=173.769, avgs=0 015/300: dt: 0.9000, rms radial error=173.065, avgs=0 020/300: dt: 0.9000, rms radial error=172.264, avgs=0 025/300: dt: 0.9000, rms radial error=171.412, avgs=0 030/300: dt: 0.9000, rms radial error=170.527, avgs=0 035/300: dt: 0.9000, rms radial error=169.628, avgs=0 040/300: dt: 0.9000, rms radial error=168.722, avgs=0 045/300: dt: 0.9000, rms radial error=167.815, avgs=0 050/300: dt: 0.9000, rms radial error=166.910, avgs=0 055/300: dt: 0.9000, rms radial error=166.009, avgs=0 060/300: dt: 0.9000, rms radial error=165.115, avgs=0 065/300: dt: 0.9000, rms radial error=164.226, avgs=0 070/300: dt: 0.9000, rms radial error=163.343, avgs=0 075/300: dt: 0.9000, rms radial error=162.465, avgs=0 080/300: dt: 0.9000, rms radial error=161.592, avgs=0 085/300: dt: 0.9000, rms radial error=160.722, avgs=0 090/300: dt: 0.9000, rms radial error=159.858, avgs=0 095/300: dt: 0.9000, rms radial error=158.999, avgs=0 100/300: dt: 0.9000, rms radial error=158.144, avgs=0 105/300: dt: 0.9000, rms radial error=157.294, avgs=0 110/300: dt: 0.9000, rms radial error=156.448, avgs=0 115/300: dt: 0.9000, rms radial error=155.607, avgs=0 120/300: dt: 0.9000, rms radial error=154.770, avgs=0 125/300: dt: 0.9000, rms radial error=153.937, avgs=0 130/300: dt: 0.9000, rms radial error=153.109, avgs=0 135/300: dt: 0.9000, rms radial error=152.285, avgs=0 140/300: dt: 0.9000, rms radial error=151.465, avgs=0 145/300: dt: 0.9000, rms radial error=150.650, avgs=0 150/300: dt: 0.9000, rms radial error=149.838, avgs=0 155/300: dt: 0.9000, rms radial error=149.030, avgs=0 160/300: dt: 0.9000, rms radial error=148.225, avgs=0 165/300: dt: 0.9000, rms radial error=147.419, avgs=0 170/300: dt: 0.9000, rms radial error=146.603, avgs=0 175/300: dt: 0.9000, rms radial error=145.793, avgs=0 180/300: dt: 0.9000, rms radial error=144.986, avgs=0 185/300: dt: 0.9000, rms radial error=144.184, avgs=0 190/300: dt: 0.9000, rms radial error=143.388, avgs=0 195/300: dt: 0.9000, rms radial error=142.596, avgs=0 200/300: dt: 0.9000, rms radial error=141.808, avgs=0 205/300: dt: 0.9000, rms radial error=141.024, avgs=0 210/300: dt: 0.9000, rms radial error=140.245, avgs=0 215/300: dt: 0.9000, rms radial error=139.470, avgs=0 220/300: dt: 0.9000, rms radial error=138.699, avgs=0 225/300: dt: 0.9000, rms radial error=137.932, avgs=0 230/300: dt: 0.9000, rms radial error=137.170, avgs=0 235/300: dt: 0.9000, rms radial error=136.411, avgs=0 240/300: dt: 0.9000, rms radial error=135.657, avgs=0 245/300: dt: 0.9000, rms radial error=134.907, avgs=0 250/300: dt: 0.9000, rms radial error=134.161, avgs=0 255/300: dt: 0.9000, rms radial error=133.419, avgs=0 260/300: dt: 0.9000, rms radial error=132.682, avgs=0 265/300: dt: 0.9000, rms radial error=131.954, avgs=0 270/300: dt: 0.9000, rms radial error=131.229, avgs=0 275/300: dt: 0.9000, rms radial error=130.509, avgs=0 280/300: dt: 0.9000, rms radial error=129.792, avgs=0 285/300: dt: 0.9000, rms radial error=129.079, avgs=0 290/300: dt: 0.9000, rms radial error=128.370, avgs=0 295/300: dt: 0.9000, rms radial error=127.665, avgs=0 300/300: dt: 0.9000, rms radial error=126.963, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 38517.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00145 epoch 2 (K=40.0), pass 1, starting sse = 11415.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00607 epoch 3 (K=160.0), pass 1, starting sse = 5121.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/12 = 0.01231 epoch 4 (K=640.0), pass 1, starting sse = 3324.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/10 = 0.00848 final distance error %55.66 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours mris_sphere utimesec 292.115913 mris_sphere stimesec 0.123993 mris_sphere ru_maxrss 368836 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 48197 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 16 mris_sphere ru_oublock 19592 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 543 mris_sphere ru_nivcsw 710 FSRUNTIME@ mris_sphere 0.0812 hours 1 threads #-------------------------------------------- #@# QSphere rh Fri 15 Mar 2024 01:09:09 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.80 +- 0.71 (0.00-->15.55) (max @ vno 113827 --> 115680) face area 0.02 +- 0.07 (-1.10-->1.94) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.243, avgs=0 005/300: dt: 0.9000, rms radial error=173.998, avgs=0 010/300: dt: 0.9000, rms radial error=173.470, avgs=0 015/300: dt: 0.9000, rms radial error=172.776, avgs=0 020/300: dt: 0.9000, rms radial error=171.985, avgs=0 025/300: dt: 0.9000, rms radial error=171.137, avgs=0 030/300: dt: 0.9000, rms radial error=170.262, avgs=0 035/300: dt: 0.9000, rms radial error=169.371, avgs=0 040/300: dt: 0.9000, rms radial error=168.471, avgs=0 045/300: dt: 0.9000, rms radial error=167.570, avgs=0 050/300: dt: 0.9000, rms radial error=166.669, avgs=0 055/300: dt: 0.9000, rms radial error=165.770, avgs=0 060/300: dt: 0.9000, rms radial error=164.874, avgs=0 065/300: dt: 0.9000, rms radial error=163.982, avgs=0 070/300: dt: 0.9000, rms radial error=163.095, avgs=0 075/300: dt: 0.9000, rms radial error=162.207, avgs=0 080/300: dt: 0.9000, rms radial error=161.327, avgs=0 085/300: dt: 0.9000, rms radial error=160.457, avgs=0 090/300: dt: 0.9000, rms radial error=159.578, avgs=0 095/300: dt: 0.9000, rms radial error=158.704, avgs=0 100/300: dt: 0.9000, rms radial error=157.838, avgs=0 105/300: dt: 0.9000, rms radial error=156.981, avgs=0 110/300: dt: 0.9000, rms radial error=156.127, avgs=0 115/300: dt: 0.9000, rms radial error=155.278, avgs=0 120/300: dt: 0.9000, rms radial error=154.433, avgs=0 125/300: dt: 0.9000, rms radial error=153.592, avgs=0 130/300: dt: 0.9000, rms radial error=152.754, avgs=0 135/300: dt: 0.9000, rms radial error=151.921, avgs=0 140/300: dt: 0.9000, rms radial error=151.091, avgs=0 145/300: dt: 0.9000, rms radial error=150.263, avgs=0 150/300: dt: 0.9000, rms radial error=149.439, avgs=0 155/300: dt: 0.9000, rms radial error=148.620, avgs=0 160/300: dt: 0.9000, rms radial error=147.805, avgs=0 165/300: dt: 0.9000, rms radial error=146.995, avgs=0 170/300: dt: 0.9000, rms radial error=146.189, avgs=0 175/300: dt: 0.9000, rms radial error=145.387, avgs=0 180/300: dt: 0.9000, rms radial error=144.590, avgs=0 185/300: dt: 0.9000, rms radial error=143.798, avgs=0 190/300: dt: 0.9000, rms radial error=143.011, avgs=0 195/300: dt: 0.9000, rms radial error=142.227, avgs=0 200/300: dt: 0.9000, rms radial error=141.448, avgs=0 205/300: dt: 0.9000, rms radial error=140.673, avgs=0 210/300: dt: 0.9000, rms radial error=139.898, avgs=0 215/300: dt: 0.9000, rms radial error=139.125, avgs=0 220/300: dt: 0.9000, rms radial error=138.355, avgs=0 225/300: dt: 0.9000, rms radial error=137.590, avgs=0 230/300: dt: 0.9000, rms radial error=136.829, avgs=0 235/300: dt: 0.9000, rms radial error=136.072, avgs=0 240/300: dt: 0.9000, rms radial error=135.319, avgs=0 245/300: dt: 0.9000, rms radial error=134.570, avgs=0 250/300: dt: 0.9000, rms radial error=133.825, avgs=0 255/300: dt: 0.9000, rms radial error=133.084, avgs=0 260/300: dt: 0.9000, rms radial error=132.348, avgs=0 265/300: dt: 0.9000, rms radial error=131.616, avgs=0 270/300: dt: 0.9000, rms radial error=130.887, avgs=0 275/300: dt: 0.9000, rms radial error=130.163, avgs=0 280/300: dt: 0.9000, rms radial error=129.442, avgs=0 285/300: dt: 0.9000, rms radial error=128.726, avgs=0 290/300: dt: 0.9000, rms radial error=128.013, avgs=0 295/300: dt: 0.9000, rms radial error=127.305, avgs=0 300/300: dt: 0.9000, rms radial error=126.600, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 33696.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00061 epoch 2 (K=40.0), pass 1, starting sse = 8465.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00310 epoch 3 (K=160.0), pass 1, starting sse = 3200.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.01013 epoch 4 (K=640.0), pass 1, starting sse = 1920.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00956 final distance error %43.99 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 310.372314 mris_sphere stimesec 0.135980 mris_sphere ru_maxrss 348480 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 45458 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 18624 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 331 mris_sphere ru_nivcsw 571 FSRUNTIME@ mris_sphere 0.0866 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Fri 15 Mar 2024 01:14:21 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri 15 Mar 2024 01:14:21 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri 15 Mar 2024 01:14:21 PM CET mris_fix_topology -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 LS5K lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-4116 (nv=275778, nf=559788, ne=839682, g=2059) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 25 iterations marking ambiguous vertices... 453067 ambiguous faces found in tessellation segmenting defects... 60 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 0 -merging segment 22 into 0 -merging segment 33 into 0 -merging segment 36 into 0 -merging segment 37 into 0 -merging segment 47 into 0 -merging segment 50 into 0 -merging segment 53 into 0 -merging segment 56 into 0 -merging segment 17 into 16 -merging segment 27 into 24 -merging segment 42 into 46 -merging segment 0 into 51 -merging segment 55 into 51 46 defects to be corrected 0 vertices coincident reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2316 (-4.6158) -vertex loglikelihood: -7.5133 (-3.7567) -normal dot loglikelihood: -3.4697 (-3.4697) -quad curv loglikelihood: -6.2972 (-3.1486) Total Loglikelihood : -26.5117 CORRECTING DEFECT 0 (vertices=117, convex hull=117, v0=4614) After retessellation of defect 0 (v0=4614), euler #=115 (47017,133115,86213) : difference with theory (-43) = -158 CORRECTING DEFECT 1 (vertices=79, convex hull=44, v0=6886) After retessellation of defect 1 (v0=6886), euler #=116 (47024,133153,86245) : difference with theory (-42) = -158 CORRECTING DEFECT 2 (vertices=215, convex hull=69, v0=10559) After retessellation of defect 2 (v0=10559), euler #=117 (47063,133299,86353) : difference with theory (-41) = -158 CORRECTING DEFECT 3 (vertices=50, convex hull=72, v0=17717) After retessellation of defect 3 (v0=17717), euler #=118 (47091,133408,86435) : difference with theory (-40) = -158 CORRECTING DEFECT 4 (vertices=2613, convex hull=415, v0=18208) XL defect detected... After retessellation of defect 4 (v0=18208), euler #=119 (47899,136043,88263) : difference with theory (-39) = -158 CORRECTING DEFECT 5 (vertices=9, convex hull=37, v0=21932) After retessellation of defect 5 (v0=21932), euler #=120 (47902,136063,88281) : difference with theory (-38) = -158 CORRECTING DEFECT 6 (vertices=119, convex hull=114, v0=31871) After retessellation of defect 6 (v0=31871), euler #=121 (47961,136286,88446) : difference with theory (-37) = -158 CORRECTING DEFECT 7 (vertices=92, convex hull=112, v0=33949) After retessellation of defect 7 (v0=33949), euler #=122 (48006,136465,88581) : difference with theory (-36) = -158 CORRECTING DEFECT 8 (vertices=31, convex hull=84, v0=34826) After retessellation of defect 8 (v0=34826), euler #=123 (48026,136556,88653) : difference with theory (-35) = -158 CORRECTING DEFECT 9 (vertices=5, convex hull=30, v0=42519) After retessellation of defect 9 (v0=42519), euler #=124 (48026,136567,88665) : difference with theory (-34) = -158 CORRECTING DEFECT 10 (vertices=10, convex hull=26, v0=43813) After retessellation of defect 10 (v0=43813), euler #=125 (48027,136580,88678) : difference with theory (-33) = -158 CORRECTING DEFECT 11 (vertices=29, convex hull=37, v0=45300) After retessellation of defect 11 (v0=45300), euler #=126 (48033,136610,88703) : difference with theory (-32) = -158 CORRECTING DEFECT 12 (vertices=18, convex hull=55, v0=61013) After retessellation of defect 12 (v0=61013), euler #=127 (48042,136658,88743) : difference with theory (-31) = -158 CORRECTING DEFECT 13 (vertices=53, convex hull=106, v0=63162) After retessellation of defect 13 (v0=63162), euler #=128 (48073,136799,88854) : difference with theory (-30) = -158 CORRECTING DEFECT 14 (vertices=463, convex hull=194, v0=63737) After retessellation of defect 14 (v0=63737), euler #=129 (48156,137152,89125) : difference with theory (-29) = -158 CORRECTING DEFECT 15 (vertices=22, convex hull=58, v0=80993) After retessellation of defect 15 (v0=80993), euler #=130 (48168,137211,89173) : difference with theory (-28) = -158 CORRECTING DEFECT 16 (vertices=46, convex hull=33, v0=82067) After retessellation of defect 16 (v0=82067), euler #=131 (48176,137241,89196) : difference with theory (-27) = -158 CORRECTING DEFECT 17 (vertices=1210, convex hull=77, v0=83294) After retessellation of defect 17 (v0=83294), euler #=132 (48194,137324,89262) : difference with theory (-26) = -158 CORRECTING DEFECT 18 (vertices=35, convex hull=42, v0=88853) After retessellation of defect 18 (v0=88853), euler #=133 (48207,137379,89305) : difference with theory (-25) = -158 CORRECTING DEFECT 19 (vertices=401, convex hull=105, v0=100126) After retessellation of defect 19 (v0=100126), euler #=134 (48231,137494,89397) : difference with theory (-24) = -158 CORRECTING DEFECT 20 (vertices=98, convex hull=90, v0=101274) After retessellation of defect 20 (v0=101274), euler #=136 (48272,137659,89523) : difference with theory (-23) = -159 CORRECTING DEFECT 21 (vertices=6, convex hull=27, v0=101333) After retessellation of defect 21 (v0=101333), euler #=137 (48273,137669,89533) : difference with theory (-22) = -159 CORRECTING DEFECT 22 (vertices=34, convex hull=48, v0=103957) After retessellation of defect 22 (v0=103957), euler #=138 (48290,137735,89583) : difference with theory (-21) = -159 CORRECTING DEFECT 23 (vertices=42, convex hull=74, v0=105345) After retessellation of defect 23 (v0=105345), euler #=139 (48317,137843,89665) : difference with theory (-20) = -159 CORRECTING DEFECT 24 (vertices=177, convex hull=90, v0=107732) After retessellation of defect 24 (v0=107732), euler #=140 (48377,138068,89831) : difference with theory (-19) = -159 CORRECTING DEFECT 25 (vertices=6, convex hull=17, v0=108788) After retessellation of defect 25 (v0=108788), euler #=141 (48378,138075,89838) : difference with theory (-18) = -159 CORRECTING DEFECT 26 (vertices=13, convex hull=17, v0=110422) After retessellation of defect 26 (v0=110422), euler #=142 (48380,138087,89849) : difference with theory (-17) = -159 CORRECTING DEFECT 27 (vertices=25, convex hull=67, v0=110508) After retessellation of defect 27 (v0=110508), euler #=143 (48389,138143,89897) : difference with theory (-16) = -159 CORRECTING DEFECT 28 (vertices=231, convex hull=76, v0=114929) After retessellation of defect 28 (v0=114929), euler #=144 (48404,138215,89955) : difference with theory (-15) = -159 CORRECTING DEFECT 29 (vertices=26, convex hull=24, v0=119889) After retessellation of defect 29 (v0=119889), euler #=145 (48408,138234,89971) : difference with theory (-14) = -159 CORRECTING DEFECT 30 (vertices=8, convex hull=13, v0=128228) After retessellation of defect 30 (v0=128228), euler #=146 (48410,138241,89977) : difference with theory (-13) = -159 CORRECTING DEFECT 31 (vertices=117, convex hull=56, v0=129619) After retessellation of defect 31 (v0=129619), euler #=147 (48424,138310,90033) : difference with theory (-12) = -159 CORRECTING DEFECT 32 (vertices=19, convex hull=38, v0=132568) After retessellation of defect 32 (v0=132568), euler #=148 (48430,138338,90056) : difference with theory (-11) = -159 CORRECTING DEFECT 33 (vertices=30, convex hull=18, v0=136725) After retessellation of defect 33 (v0=136725), euler #=149 (48433,138351,90067) : difference with theory (-10) = -159 CORRECTING DEFECT 34 (vertices=14, convex hull=12, v0=144711) After retessellation of defect 34 (v0=144711), euler #=150 (48433,138353,90070) : difference with theory (-9) = -159 CORRECTING DEFECT 35 (vertices=38, convex hull=32, v0=146516) After retessellation of defect 35 (v0=146516), euler #=151 (48437,138379,90093) : difference with theory (-8) = -159 CORRECTING DEFECT 36 (vertices=5, convex hull=11, v0=147821) After retessellation of defect 36 (v0=147821), euler #=152 (48437,138382,90097) : difference with theory (-7) = -159 CORRECTING DEFECT 37 (vertices=179, convex hull=68, v0=148541) After retessellation of defect 37 (v0=148541), euler #=153 (48455,138468,90166) : difference with theory (-6) = -159 CORRECTING DEFECT 38 (vertices=10, convex hull=17, v0=153010) After retessellation of defect 38 (v0=153010), euler #=154 (48456,138473,90171) : difference with theory (-5) = -159 CORRECTING DEFECT 39 (vertices=35, convex hull=59, v0=155446) After retessellation of defect 39 (v0=155446), euler #=155 (48462,138513,90206) : difference with theory (-4) = -159 CORRECTING DEFECT 40 (vertices=221814, convex hull=10151, v0=160447) Segmentation fault Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux recon-all -s LS5K exited with ERRORS at Fri 15 Mar 2024 03:12:49 PM CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Fri 15 Mar 2024 05:18:24 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -motioncor subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 71859976 177094728 109036 145900536 320214684 Swap: 9765884 9765800 84 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:24-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri 15 Mar 2024 05:18:24 PM CET Found 1 runs /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig/001.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_convert /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform mri_convert.bin /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz... TR=5000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996779, 0, 0.080199) j_ras = (0, 1, 0) k_ras = (-0.080199, 0, 0.996779) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz... mri_add_xform_to_header -c /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/talairach.xfm /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz INFO: extension is mgz Started at Fri 15 Mar 2024 05:18:24 PM CET Ended at Fri 15 Mar 2024 05:18:34 PM CET #@#%# recon-all-run-time-hours 0.003 recon-all -s LS5K finished without error at Fri 15 Mar 2024 05:18:34 PM CET New invocation of recon-all Fri 15 Mar 2024 05:18:35 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -s LS5K -normalization -skullstrip subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 71856820 176892172 109036 146106248 320217204 Swap: 9765884 9765800 84 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:18:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization Fri 15 Mar 2024 05:18:35 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_normalize -g 1 -f /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat -mprage nu.mgz T1.mgz using max gradient = 1.000 using control points from file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... Reading 8 control points... only using 8 control points from file, mean 177.6, scaling by 0.62... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... talairach transform 1.17259 -0.15608 0.06831 0.88898; 0.16758 1.14045 -0.10487 -9.39799; -0.03649 0.10201 1.09959 -51.21169; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 10 Starting OpenSpline(): npoints = 10 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 65 (65), valley at 0 (-1) csf peak at 32, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 89 gm peak at 64 (64), valley at 0 (-1) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 48 seconds. #-------------------------------------------- #@# Skull Stripping Fri 15 Mar 2024 05:21:24 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_watershed -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=138 y=104 z=122 r=92 first estimation of the main basin volume: 3270519 voxels Looking for seedpoints 2 found in the cerebellum 10 found in the rest of the brain global maximum in x=113, y=102, z=132, Imax=255 CSF=14, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=1292146766 voxels, voxel volume =1.000 = 1292146766 mmm3 = 1292146.816 cm3 done. PostAnalyze...Basin Prior 153 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=137,y=146, z=144, r=10468 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 33473 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1031250777 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1104838473 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1054297977 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1084217100 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1082405278 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 5, 32, 44 after analyzing : 3, 23, 32, 28 RIGHT_CER before analyzing : 3, 5, 32, 44 after analyzing : 3, 23, 32, 28 LEFT_CER before analyzing : 3, 5, 32, 44 after analyzing : 3, 23, 32, 28 RIGHT_BRAIN before analyzing : 3, 4, 28, 48 after analyzing : 3, 20, 28, 27 LEFT_BRAIN before analyzing : 3, 6, 35, 44 after analyzing : 3, 25, 35, 29 OTHER before analyzing : 3, 4, 28, 45 after analyzing : 3, 20, 28, 26 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.009, std = 0.008 curvature mean = 96.273, std = 9.515 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 34.58, sigma = 90.69 after rotation: sse = 34.58, sigma = 90.69 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 41.89, its var is 66.51 before Erosion-Dilatation 43.14% of inacurate vertices after Erosion-Dilatation 62.40% of inacurate vertices 51.84% of 'positive' inacurate vertices 48.16% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...50 iterations mri_strip_skull: done peeling brain Brain Size = 4037080 voxels, voxel volume = 1.000 mm3 = 4037080 mmm3 = 4037.080 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done mri_watershed utimesec 20.063020 mri_watershed stimesec 0.717968 mri_watershed ru_maxrss 874384 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 242691 mri_watershed ru_majflt 10 mri_watershed ru_nswap 0 mri_watershed ru_inblock 124640 mri_watershed ru_oublock 12816 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 740 mri_watershed ru_nivcsw 2942 mri_watershed done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. Started at Fri 15 Mar 2024 05:18:35 PM CET Ended at Fri 15 Mar 2024 05:21:46 PM CET #@#%# recon-all-run-time-hours 0.053 recon-all -s LS5K finished without error at Fri 15 Mar 2024 05:21:46 PM CET New invocation of recon-all Fri 15 Mar 2024 05:21:46 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/recon-all -autorecon2 -autorecon3 -s LS5K subjid LS5K setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/ubuntu-xenial-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 1500000 kbytes maxproc 1542210 maxlocks unlimited maxsignal 1542210 maxmessage 819200 maxnice 0 maxrtprio 95 maxrttime unlimited total used free shared buff/cache available Mem: 394855240 65738016 182334176 109536 146783048 326335644 Swap: 9765884 9765800 84 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2024/03/15-16:21:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: yangc Machine: ramones Platform: Linux PlatformVersion: 5.10.0-28-amd64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Fri 15 Mar 2024 05:21:46 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_em_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (37, 51, 51) --> (217, 228, 225) using (97, 110, 138) as brain centroid... mean wm in atlas = 107, using box (75,88,117) --> (119, 131,159) to find MRI wm before smoothing, mri peak at 178 robust fit to distribution - 176 +- 11.0 after smoothing, mri peak at 177, scaling input intensities by 0.605 scaling channel 0 by 0.60452 initial log_p = -5.041 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.592059 @ (-9.091, 9.091, -9.091) max log p = -4.553317 @ (4.545, -4.545, 4.545) max log p = -4.524586 @ (-2.273, -2.273, 2.273) max log p = -4.509941 @ (1.136, 1.136, -1.136) max log p = -4.498222 @ (0.568, -0.568, -0.568) max log p = -4.498222 @ (0.000, 0.000, 0.000) Found translation: (-5.1, 2.8, -4.0): log p = -4.498 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.178, old_max_log_p =-4.498 (thresh=-4.5) 1.22567 0.01831 0.15998 -54.50720; 0.00000 1.06580 -0.16136 5.33478; -0.15011 0.12941 1.13041 -13.52482; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.096, old_max_log_p =-4.178 (thresh=-4.2) 1.22567 0.01831 0.15998 -54.50720; -0.01959 1.23208 -0.03643 -26.16597; -0.14882 -0.03168 1.14496 4.59824; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.096, old_max_log_p =-4.096 (thresh=-4.1) 1.22567 0.01831 0.15998 -54.50720; -0.01959 1.23208 -0.03643 -26.16597; -0.14882 -0.03168 1.14496 4.59824; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.989, old_max_log_p =-4.096 (thresh=-4.1) 1.22887 0.05571 0.12026 -55.10811; -0.04483 1.22790 -0.15485 -9.33281; -0.11257 0.09230 1.13992 -16.79955; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.989, old_max_log_p =-3.989 (thresh=-4.0) 1.22887 0.05571 0.12026 -55.10811; -0.04483 1.22790 -0.15485 -9.33281; -0.11257 0.09230 1.13992 -16.79955; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.964, old_max_log_p =-3.989 (thresh=-4.0) 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.964, old_max_log_p =-3.964 (thresh=-4.0) 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.964 (old=-5.041) transform before final EM align: 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 594.483650 mri_em_register stimesec 2.175910 mri_em_register ru_maxrss 605976 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 247362 mri_em_register ru_majflt 8 mri_em_register ru_nswap 0 mri_em_register ru_inblock 66720 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 389 mri_em_register ru_nivcsw 4109 registration took 10 minutes and 7 seconds. #-------------------------------------- #@# CA Normalize Fri 15 Mar 2024 05:31:54 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (37, 51, 51) --> (217, 228, 225) using (97, 110, 138) as brain centroid... mean wm in atlas = 107, using box (75,88,117) --> (119, 131,159) to find MRI wm before smoothing, mri peak at 178 robust fit to distribution - 176 +- 11.0 after smoothing, mri peak at 177, scaling input intensities by 0.605 scaling channel 0 by 0.60452 using 246344 sample points... INFO: compute sample coordinates transform 1.23065 0.04570 0.12151 -54.24540; -0.03665 1.23110 -0.13539 -12.48039; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 68, 41) --> (185, 169, 188) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 0 of 348 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (79, 67, 40) --> (135, 167, 186) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 567 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 135, 59) --> (173, 170, 107) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 135, 55) --> (134, 169, 106) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 18 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 131, 87) --> (145, 187, 117) Brain_Stem: limiting intensities to 95.0 --> 132.0 2 of 21 (9.5%) samples deleted using 970 total control points for intensity normalization... bias field = 0.989 +- 0.065 1 of 968 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 68, 41) --> (185, 169, 188) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 450 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (79, 67, 40) --> (135, 167, 186) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 755 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 135, 59) --> (173, 170, 107) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 76 (32.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 135, 55) --> (134, 169, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 26 of 70 (37.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 131, 87) --> (145, 187, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 64 of 113 (56.6%) samples deleted using 1464 total control points for intensity normalization... bias field = 1.030 +- 0.060 2 of 1303 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 68, 41) --> (185, 169, 188) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 573 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (79, 67, 40) --> (135, 167, 186) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 794 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (134, 135, 59) --> (173, 170, 107) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 96 (42.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 135, 55) --> (134, 169, 106) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 50 of 96 (52.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 131, 87) --> (145, 187, 117) Brain_Stem: limiting intensities to 88.0 --> 132.0 95 of 146 (65.1%) samples deleted using 1705 total control points for intensity normalization... bias field = 1.020 +- 0.052 2 of 1495 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 17 seconds. #-------------------------------------- #@# CA Reg Fri 15 Mar 2024 05:34:11 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_register -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.76 (predicted orig area = 4.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.898, neg=0, invalid=762 0001: dt=265.096252, rms=0.788 (12.336%), neg=0, invalid=762 0002: dt=181.502646, rms=0.764 (2.927%), neg=0, invalid=762 0003: dt=145.113553, rms=0.753 (1.526%), neg=0, invalid=762 0004: dt=183.351351, rms=0.745 (1.038%), neg=0, invalid=762 0005: dt=149.120000, rms=0.740 (0.649%), neg=0, invalid=762 0006: dt=221.952000, rms=0.736 (0.597%), neg=0, invalid=762 0007: dt=129.472000, rms=0.733 (0.403%), neg=0, invalid=762 0008: dt=295.936000, rms=0.730 (0.392%), neg=0, invalid=762 0009: dt=110.976000, rms=0.728 (0.319%), neg=0, invalid=762 0010: dt=369.920000, rms=0.725 (0.322%), neg=0, invalid=762 0011: dt=92.480000, rms=0.724 (0.216%), neg=0, invalid=762 0012: dt=92.480000, rms=0.723 (0.076%), neg=0, invalid=762 0013: dt=92.480000, rms=0.722 (0.140%), neg=0, invalid=762 0014: dt=92.480000, rms=0.721 (0.181%), neg=0, invalid=762 0015: dt=92.480000, rms=0.719 (0.187%), neg=0, invalid=762 0016: dt=92.480000, rms=0.718 (0.188%), neg=0, invalid=762 0017: dt=92.480000, rms=0.717 (0.182%), neg=0, invalid=762 0018: dt=92.480000, rms=0.716 (0.164%), neg=0, invalid=762 0019: dt=92.480000, rms=0.715 (0.149%), neg=0, invalid=762 0020: dt=92.480000, rms=0.714 (0.133%), neg=0, invalid=762 0021: dt=92.480000, rms=0.713 (0.121%), neg=0, invalid=762 0022: dt=92.480000, rms=0.712 (0.119%), neg=0, invalid=762 0023: dt=1775.616000, rms=0.709 (0.394%), neg=0, invalid=762 0024: dt=92.480000, rms=0.708 (0.139%), neg=0, invalid=762 0025: dt=92.480000, rms=0.708 (0.036%), neg=0, invalid=762 0026: dt=92.480000, rms=0.707 (0.051%), neg=0, invalid=762 0027: dt=92.480000, rms=0.707 (0.055%), neg=0, invalid=762 0028: dt=92.480000, rms=0.707 (0.052%), neg=0, invalid=762 0029: dt=92.480000, rms=0.706 (0.054%), neg=0, invalid=762 0030: dt=92.480000, rms=0.706 (0.061%), neg=0, invalid=762 0031: dt=92.480000, rms=0.705 (0.071%), neg=0, invalid=762 0032: dt=92.480000, rms=0.705 (0.082%), neg=0, invalid=762 0033: dt=92.480000, rms=0.704 (0.096%), neg=0, invalid=762 0034: dt=92.480000, rms=0.703 (0.103%), neg=0, invalid=762 0035: dt=92.480000, rms=0.703 (0.104%), neg=0, invalid=762 0036: dt=92.480000, rms=0.702 (0.096%), neg=0, invalid=762 0037: dt=129.472000, rms=0.702 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=762 0038: dt=161.185185, rms=0.696 (0.927%), neg=0, invalid=762 0039: dt=129.472000, rms=0.695 (0.163%), neg=0, invalid=762 0040: dt=129.472000, rms=0.695 (0.039%), neg=0, invalid=762 0041: dt=129.472000, rms=0.695 (-0.117%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0042: dt=41.600000, rms=0.695 (0.602%), neg=0, invalid=762 0043: dt=36.288000, rms=0.694 (0.148%), neg=0, invalid=762 0044: dt=36.288000, rms=0.693 (0.209%), neg=0, invalid=762 0045: dt=36.288000, rms=0.690 (0.393%), neg=0, invalid=762 0046: dt=36.288000, rms=0.686 (0.604%), neg=0, invalid=762 0047: dt=36.288000, rms=0.680 (0.890%), neg=0, invalid=762 0048: dt=36.288000, rms=0.672 (1.110%), neg=0, invalid=762 0049: dt=36.288000, rms=0.665 (1.124%), neg=0, invalid=762 0050: dt=36.288000, rms=0.659 (0.942%), neg=0, invalid=762 0051: dt=36.288000, rms=0.654 (0.669%), neg=0, invalid=762 0052: dt=36.288000, rms=0.652 (0.356%), neg=0, invalid=762 0053: dt=36.288000, rms=0.651 (0.151%), neg=0, invalid=762 0054: dt=36.288000, rms=0.650 (0.111%), neg=0, invalid=762 0055: dt=36.288000, rms=0.649 (0.201%), neg=0, invalid=762 0056: dt=36.288000, rms=0.647 (0.289%), neg=0, invalid=762 0057: dt=36.288000, rms=0.645 (0.306%), neg=0, invalid=762 0058: dt=36.288000, rms=0.643 (0.250%), neg=0, invalid=762 0059: dt=36.288000, rms=0.642 (0.146%), neg=0, invalid=762 0060: dt=36.288000, rms=0.642 (0.071%), neg=0, invalid=762 0061: dt=36.288000, rms=0.642 (0.073%), neg=0, invalid=762 0062: dt=36.288000, rms=0.641 (0.122%), neg=0, invalid=762 0063: dt=36.288000, rms=0.640 (0.164%), neg=0, invalid=762 0064: dt=36.288000, rms=0.639 (0.147%), neg=0, invalid=762 0065: dt=36.288000, rms=0.638 (0.095%), neg=0, invalid=762 0066: dt=36.288000, rms=0.638 (0.039%), neg=0, invalid=762 0067: dt=103.680000, rms=0.638 (0.037%), neg=0, invalid=762 0068: dt=103.680000, rms=0.637 (0.164%), neg=0, invalid=762 0069: dt=103.680000, rms=0.636 (0.110%), neg=0, invalid=762 0070: dt=103.680000, rms=0.636 (0.021%), neg=0, invalid=762 0071: dt=497.664000, rms=0.634 (0.293%), neg=0, invalid=762 0072: dt=9.072000, rms=0.634 (-0.006%), neg=0, invalid=762 0073: dt=9.072000, rms=0.634 (0.007%), neg=0, invalid=762 0074: dt=9.072000, rms=0.634 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=762 0075: dt=83.143219, rms=0.623 (1.857%), neg=0, invalid=762 0076: dt=87.771429, rms=0.620 (0.543%), neg=0, invalid=762 0077: dt=36.288000, rms=0.619 (0.075%), neg=0, invalid=762 0078: dt=36.288000, rms=0.619 (0.043%), neg=0, invalid=762 0079: dt=36.288000, rms=0.619 (0.054%), neg=0, invalid=762 0080: dt=36.288000, rms=0.618 (0.038%), neg=0, invalid=762 0081: dt=36.288000, rms=0.618 (0.020%), neg=0, invalid=762 0082: dt=331.776000, rms=0.617 (0.152%), neg=0, invalid=762 0083: dt=25.920000, rms=0.617 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.642, neg=0, invalid=762 0084: dt=1.200000, rms=0.641 (0.137%), neg=0, invalid=762 0085: dt=0.175000, rms=0.641 (0.000%), neg=0, invalid=762 0086: dt=0.175000, rms=0.641 (0.000%), neg=0, invalid=762 0087: dt=0.175000, rms=0.641 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.642, neg=0, invalid=762 0088: dt=0.000000, rms=0.641 (0.126%), neg=0, invalid=762 0089: dt=0.000000, rms=0.641 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.711, neg=0, invalid=762 0090: dt=4.390476, rms=0.695 (2.300%), neg=0, invalid=762 0091: dt=1.880000, rms=0.694 (0.099%), neg=0, invalid=762 0092: dt=1.880000, rms=0.694 (-0.045%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.695, neg=0, invalid=762 0093: dt=2.602410, rms=0.693 (0.256%), neg=0, invalid=762 0094: dt=0.216000, rms=0.693 (0.003%), neg=0, invalid=762 0095: dt=0.216000, rms=0.693 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.758, neg=0, invalid=762 0096: dt=0.448000, rms=0.756 (0.200%), neg=0, invalid=762 0097: dt=0.768000, rms=0.755 (0.136%), neg=0, invalid=762 0098: dt=0.768000, rms=0.754 (0.145%), neg=0, invalid=762 0099: dt=0.768000, rms=0.754 (0.006%), neg=0, invalid=762 0100: dt=0.768000, rms=0.754 (-0.366%), neg=0, invalid=762 0101: dt=1.536000, rms=0.753 (0.075%), neg=0, invalid=762 0102: dt=0.000000, rms=0.753 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.754, neg=0, invalid=762 0103: dt=1.792000, rms=0.751 (0.442%), neg=0, invalid=762 0104: dt=0.000000, rms=0.751 (0.003%), neg=0, invalid=762 0105: dt=0.100000, rms=0.751 (-0.007%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.701, neg=0, invalid=762 0106: dt=0.691748, rms=0.687 (2.002%), neg=0, invalid=762 0107: dt=0.064000, rms=0.686 (0.100%), neg=0, invalid=762 0108: dt=0.064000, rms=0.686 (-0.031%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.687, neg=0, invalid=762 0109: dt=0.048000, rms=0.686 (0.135%), neg=0, invalid=762 0110: dt=0.007000, rms=0.686 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.04863 (55) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (351 voxels, overlap=0.331) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (351 voxels, peak = 13), gca=13.3 gca peak = 0.15565 (16) mri peak = 0.05914 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (239 voxels, overlap=0.110) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (239 voxels, peak = 6), gca=6.4 gca peak = 0.26829 (96) mri peak = 0.06591 (81) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (560 voxels, overlap=0.245) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (560 voxels, peak = 85), gca=85.0 gca peak = 0.20183 (93) mri peak = 0.06625 (87) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (493 voxels, overlap=0.843) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (493 voxels, peak = 86), gca=86.0 gca peak = 0.21683 (55) mri peak = 0.10269 (50) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, overlap=0.986) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (593 voxels, peak = 50), gca=50.3 gca peak = 0.30730 (58) mri peak = 0.09907 (53) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (483 voxels, overlap=0.990) Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (483 voxels, peak = 52), gca=51.9 gca peak = 0.11430 (101) mri peak = 0.08567 (106) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (34044 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.07 x + 0.0 (34044 voxels, peak = 108), gca=107.6 gca peak = 0.12076 (102) mri peak = 0.07573 (108) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (34382 voxels, overlap=0.510) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (34382 voxels, peak = 110), gca=109.7 gca peak = 0.14995 (59) mri peak = 0.04422 (50) Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (17056 voxels, overlap=0.715) Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (17056 voxels, peak = 53), gca=52.8 gca peak = 0.15082 (58) mri peak = 0.04573 (48) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (15933 voxels, overlap=0.755) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (15933 voxels, peak = 52), gca=51.9 gca peak = 0.14161 (67) mri peak = 0.08780 (67) Right_Caudate (50): linear fit = 0.95 x + 0.0 (566 voxels, overlap=0.850) Right_Caudate (50): linear fit = 0.95 x + 0.0 (566 voxels, peak = 64), gca=64.0 gca peak = 0.15243 (71) mri peak = 0.07284 (69) Left_Caudate (11): linear fit = 0.93 x + 0.0 (510 voxels, overlap=0.749) Left_Caudate (11): linear fit = 0.93 x + 0.0 (510 voxels, peak = 66), gca=65.7 gca peak = 0.13336 (57) mri peak = 0.05524 (52) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22351 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (22351 voxels, peak = 54), gca=53.9 gca peak = 0.13252 (56) mri peak = 0.05922 (50) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (12581 voxels, overlap=0.903) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (12581 voxels, peak = 53), gca=52.9 gca peak = 0.18181 (84) mri peak = 0.04860 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6167 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6167 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.06162 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5167 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (5167 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.13115 (57) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (235 voxels, overlap=0.996) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (235 voxels, peak = 53), gca=53.3 gca peak = 0.39313 (56) mri peak = 0.18182 (50) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (305 voxels, overlap=0.465) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (305 voxels, peak = 52), gca=51.8 gca peak = 0.14181 (85) mri peak = 0.06147 (80) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3362 voxels, overlap=0.993) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (3362 voxels, peak = 82), gca=82.0 gca peak = 0.11978 (83) mri peak = 0.06877 (81) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2920 voxels, overlap=0.928) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2920 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.06730 (71) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1432 voxels, overlap=0.752) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1432 voxels, peak = 72), gca=72.3 gca peak = 0.14159 (79) mri peak = 0.08028 (70) Right_Putamen (51): linear fit = 0.93 x + 0.0 (1525 voxels, overlap=0.813) Right_Putamen (51): linear fit = 0.93 x + 0.0 (1525 voxels, peak = 73), gca=73.1 gca peak = 0.10025 (80) mri peak = 0.08922 (83) Brain_Stem (16): linear fit = 1.10 x + 0.0 (7893 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (7893 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06908 (93) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (934 voxels, overlap=0.725) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (934 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.06190 (84) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1037 voxels, overlap=0.850) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1037 voxels, peak = 93), gca=93.0 gca peak = 0.20494 (23) mri peak = 0.04851 (35) gca peak = 0.15061 (21) mri peak = 0.12834 ( 6) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (248 voxels, overlap=0.653) Fourth_Ventricle (15): linear fit = 0.38 x + 0.0 (248 voxels, peak = 8), gca=7.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 0.53 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.741, neg=0, invalid=762 0111: dt=110.976000, rms=0.736 (0.706%), neg=0, invalid=762 0112: dt=221.952000, rms=0.733 (0.411%), neg=0, invalid=762 0113: dt=92.480000, rms=0.732 (0.142%), neg=0, invalid=762 0114: dt=295.936000, rms=0.731 (0.228%), neg=0, invalid=762 0115: dt=73.984000, rms=0.730 (0.100%), neg=0, invalid=762 0116: dt=517.888000, rms=0.728 (0.247%), neg=0, invalid=762 0117: dt=73.984000, rms=0.728 (0.056%), neg=0, invalid=762 0118: dt=1183.744000, rms=0.725 (0.320%), neg=0, invalid=762 0119: dt=32.368000, rms=0.725 (0.090%), neg=0, invalid=762 0120: dt=32.368000, rms=0.724 (0.020%), neg=0, invalid=762 0121: dt=32.368000, rms=0.724 (0.005%), neg=0, invalid=762 0122: dt=32.368000, rms=0.724 (0.000%), neg=0, invalid=762 0123: dt=32.368000, rms=0.724 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=762 0124: dt=129.641026, rms=0.719 (0.851%), neg=0, invalid=762 0125: dt=129.472000, rms=0.717 (0.327%), neg=0, invalid=762 0126: dt=129.472000, rms=0.716 (0.164%), neg=0, invalid=762 0127: dt=129.472000, rms=0.715 (0.089%), neg=0, invalid=762 0128: dt=295.936000, rms=0.715 (0.067%), neg=0, invalid=762 0129: dt=129.472000, rms=0.714 (0.038%), neg=0, invalid=762 0130: dt=129.472000, rms=0.714 (0.037%), neg=0, invalid=762 0131: dt=129.472000, rms=0.714 (0.048%), neg=0, invalid=762 0132: dt=129.472000, rms=0.713 (0.049%), neg=0, invalid=762 0133: dt=129.472000, rms=0.713 (0.047%), neg=0, invalid=762 0134: dt=129.472000, rms=0.713 (0.055%), neg=0, invalid=762 0135: dt=129.472000, rms=0.712 (0.055%), neg=0, invalid=762 0136: dt=129.472000, rms=0.712 (0.064%), neg=0, invalid=762 0137: dt=129.472000, rms=0.711 (0.077%), neg=0, invalid=762 0138: dt=129.472000, rms=0.711 (0.096%), neg=0, invalid=762 0139: dt=129.472000, rms=0.710 (0.093%), neg=0, invalid=762 0140: dt=129.472000, rms=0.709 (0.095%), neg=0, invalid=762 0141: dt=129.472000, rms=0.709 (0.088%), neg=0, invalid=762 0142: dt=129.472000, rms=0.708 (0.084%), neg=0, invalid=762 0143: dt=129.472000, rms=0.707 (0.076%), neg=0, invalid=762 0144: dt=129.472000, rms=0.707 (0.081%), neg=0, invalid=762 0145: dt=129.472000, rms=0.706 (0.085%), neg=0, invalid=762 0146: dt=129.472000, rms=0.706 (0.090%), neg=0, invalid=762 0147: dt=129.472000, rms=0.705 (0.076%), neg=0, invalid=762 0148: dt=129.472000, rms=0.705 (0.071%), neg=0, invalid=762 0149: dt=129.472000, rms=0.704 (0.072%), neg=0, invalid=762 0150: dt=129.472000, rms=0.704 (0.075%), neg=0, invalid=762 0151: dt=129.472000, rms=0.703 (0.072%), neg=0, invalid=762 0152: dt=129.472000, rms=0.703 (0.071%), neg=0, invalid=762 0153: dt=129.472000, rms=0.702 (0.070%), neg=0, invalid=762 0154: dt=129.472000, rms=0.702 (0.074%), neg=0, invalid=762 0155: dt=129.472000, rms=0.701 (0.075%), neg=0, invalid=762 0156: dt=129.472000, rms=0.700 (0.071%), neg=0, invalid=762 0157: dt=129.472000, rms=0.700 (0.068%), neg=0, invalid=762 0158: dt=129.472000, rms=0.700 (0.061%), neg=0, invalid=762 0159: dt=129.472000, rms=0.699 (0.053%), neg=0, invalid=762 0160: dt=129.472000, rms=0.699 (0.050%), neg=0, invalid=762 0161: dt=129.472000, rms=0.698 (0.053%), neg=0, invalid=762 0162: dt=129.472000, rms=0.698 (0.054%), neg=0, invalid=762 0163: dt=129.472000, rms=0.698 (0.050%), neg=0, invalid=762 0164: dt=129.472000, rms=0.697 (0.043%), neg=0, invalid=762 0165: dt=129.472000, rms=0.697 (0.042%), neg=0, invalid=762 0166: dt=129.472000, rms=0.697 (0.047%), neg=0, invalid=762 0167: dt=129.472000, rms=0.697 (0.047%), neg=0, invalid=762 0168: dt=129.472000, rms=0.696 (0.043%), neg=0, invalid=762 0169: dt=129.472000, rms=0.696 (0.035%), neg=0, invalid=762 0170: dt=129.472000, rms=0.696 (0.032%), neg=0, invalid=762 0171: dt=129.472000, rms=0.696 (0.034%), neg=0, invalid=762 0172: dt=129.472000, rms=0.695 (0.035%), neg=0, invalid=762 0173: dt=129.472000, rms=0.695 (0.035%), neg=0, invalid=762 0174: dt=129.472000, rms=0.695 (0.031%), neg=0, invalid=762 0175: dt=129.472000, rms=0.695 (0.030%), neg=0, invalid=762 0176: dt=129.472000, rms=0.694 (0.029%), neg=0, invalid=762 0177: dt=129.472000, rms=0.694 (0.032%), neg=0, invalid=762 0178: dt=129.472000, rms=0.694 (0.034%), neg=0, invalid=762 0179: dt=129.472000, rms=0.694 (0.033%), neg=0, invalid=762 0180: dt=129.472000, rms=0.693 (0.033%), neg=0, invalid=762 0181: dt=129.472000, rms=0.693 (0.031%), neg=0, invalid=762 0182: dt=129.472000, rms=0.693 (0.031%), neg=0, invalid=762 0183: dt=129.472000, rms=0.693 (0.032%), neg=0, invalid=762 0184: dt=129.472000, rms=0.693 (0.029%), neg=0, invalid=762 0185: dt=129.472000, rms=0.692 (0.027%), neg=0, invalid=762 0186: dt=129.472000, rms=0.692 (0.026%), neg=0, invalid=762 0187: dt=129.472000, rms=0.692 (0.028%), neg=0, invalid=762 0188: dt=129.472000, rms=0.692 (0.031%), neg=0, invalid=762 0189: dt=129.472000, rms=0.692 (0.027%), neg=0, invalid=762 0190: dt=129.472000, rms=0.692 (0.024%), neg=0, invalid=762 0191: dt=129.472000, rms=0.691 (0.022%), neg=0, invalid=762 0192: dt=7102.464000, rms=0.690 (0.147%), neg=0, invalid=762 0193: dt=32.368000, rms=0.690 (0.020%), neg=0, invalid=762 0194: dt=32.368000, rms=0.690 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.692, neg=0, invalid=762 0195: dt=24.366972, rms=0.689 (0.498%), neg=0, invalid=762 0196: dt=3.888000, rms=0.689 (0.001%), neg=0, invalid=762 0197: dt=3.888000, rms=0.689 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.690, neg=0, invalid=762 0198: dt=36.288000, rms=0.686 (0.531%), neg=0, invalid=762 0199: dt=94.753247, rms=0.684 (0.348%), neg=0, invalid=762 0200: dt=414.720000, rms=0.670 (1.975%), neg=0, invalid=762 0201: dt=50.253521, rms=0.665 (0.755%), neg=0, invalid=762 0202: dt=36.288000, rms=0.664 (0.128%), neg=0, invalid=762 0203: dt=36.288000, rms=0.664 (0.109%), neg=0, invalid=762 0204: dt=36.288000, rms=0.663 (0.117%), neg=0, invalid=762 0205: dt=9.072000, rms=0.663 (0.029%), neg=0, invalid=762 0206: dt=1.134000, rms=0.663 (0.004%), neg=0, invalid=762 0207: dt=0.141750, rms=0.663 (0.000%), neg=0, invalid=762 0208: dt=0.035437, rms=0.663 (0.000%), neg=0, invalid=762 0209: dt=0.008859, rms=0.663 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.668, neg=0, invalid=762 0210: dt=2.800000, rms=0.664 (0.541%), neg=0, invalid=762 0211: dt=0.150000, rms=0.664 (0.019%), neg=0, invalid=762 0212: dt=0.018750, rms=0.664 (0.002%), neg=0, invalid=762 0213: dt=0.002344, rms=0.664 (0.000%), neg=0, invalid=762 0214: dt=0.000293, rms=0.664 (0.000%), neg=0, invalid=762 0215: dt=0.000000, rms=0.664 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0216: dt=0.000000, rms=0.664 (0.176%), neg=0, invalid=762 0217: dt=0.000000, rms=0.664 (0.000%), neg=0, invalid=762 0218: dt=0.000122, rms=0.664 (0.000%), neg=0, invalid=762 0219: dt=0.000061, rms=0.664 (0.000%), neg=0, invalid=762 0220: dt=0.000001, rms=0.664 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0221: dt=4.032000, rms=0.660 (2.489%), neg=0, invalid=762 0222: dt=4.032000, rms=0.650 (1.524%), neg=0, invalid=762 0223: dt=1.008000, rms=0.648 (0.276%), neg=0, invalid=762 0224: dt=0.252000, rms=0.648 (0.065%), neg=0, invalid=762 0225: dt=0.252000, rms=0.647 (0.063%), neg=0, invalid=762 0226: dt=0.216000, rms=0.647 (0.054%), neg=0, invalid=762 0227: dt=0.023438, rms=0.647 (0.007%), neg=0, invalid=762 0228: dt=0.002930, rms=0.647 (0.001%), neg=0, invalid=762 0229: dt=0.000366, rms=0.647 (0.000%), neg=0, invalid=762 0230: dt=0.000183, rms=0.647 (0.000%), neg=0, invalid=762 0231: dt=0.000000, rms=0.647 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0232: dt=0.000984, rms=0.647 (0.183%), neg=0, invalid=762 0233: dt=0.000246, rms=0.647 (-0.000%), neg=0, invalid=762 0234: dt=0.000246, rms=0.647 (0.000%), neg=0, invalid=762 0235: dt=0.000015, rms=0.647 (0.000%), neg=0, invalid=762 0236: dt=0.000008, rms=0.647 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.674, neg=0, invalid=762 0237: dt=1.792000, rms=0.668 (0.889%), neg=0, invalid=762 0238: dt=1.792000, rms=0.666 (0.359%), neg=0, invalid=762 0239: dt=1.792000, rms=0.665 (0.200%), neg=0, invalid=762 0240: dt=1.792000, rms=0.664 (0.127%), neg=0, invalid=762 0241: dt=1.792000, rms=0.663 (0.089%), neg=0, invalid=762 0242: dt=1.792000, rms=0.663 (0.065%), neg=0, invalid=762 0243: dt=1.792000, rms=0.662 (0.058%), neg=0, invalid=762 0244: dt=1.792000, rms=0.662 (0.042%), neg=0, invalid=762 0245: dt=1.792000, rms=0.662 (0.041%), neg=0, invalid=762 0246: dt=1.792000, rms=0.661 (0.062%), neg=0, invalid=762 0247: dt=1.792000, rms=0.661 (0.052%), neg=0, invalid=762 0248: dt=1.792000, rms=0.661 (0.026%), neg=0, invalid=762 0249: dt=1.792000, rms=0.661 (0.035%), neg=0, invalid=762 0250: dt=1.792000, rms=0.660 (0.038%), neg=0, invalid=762 0251: dt=1.792000, rms=0.660 (0.044%), neg=0, invalid=762 0252: dt=1.792000, rms=0.660 (0.018%), neg=0, invalid=762 0253: dt=1.792000, rms=0.660 (0.030%), neg=0, invalid=762 0254: dt=1.792000, rms=0.659 (0.042%), neg=0, invalid=762 0255: dt=1.792000, rms=0.659 (0.014%), neg=0, invalid=762 0256: dt=1.792000, rms=0.659 (0.021%), neg=0, invalid=762 0257: dt=1.792000, rms=0.659 (0.019%), neg=0, invalid=762 0258: dt=1.792000, rms=0.659 (0.012%), neg=0, invalid=762 0259: dt=1.792000, rms=0.659 (0.009%), neg=0, invalid=762 0260: dt=1.792000, rms=0.659 (0.023%), neg=0, invalid=762 0261: dt=1.792000, rms=0.659 (0.028%), neg=0, invalid=762 0262: dt=1.792000, rms=0.658 (0.023%), neg=0, invalid=762 0263: dt=1.792000, rms=0.658 (0.026%), neg=0, invalid=762 0264: dt=1.792000, rms=0.658 (0.017%), neg=0, invalid=762 0265: dt=1.792000, rms=0.658 (0.014%), neg=0, invalid=762 0266: dt=1.536000, rms=0.658 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.659, neg=0, invalid=762 0267: dt=1.792000, rms=0.653 (0.982%), neg=0, invalid=762 0268: dt=1.792000, rms=0.649 (0.524%), neg=0, invalid=762 0269: dt=1.792000, rms=0.647 (0.350%), neg=0, invalid=762 0270: dt=1.792000, rms=0.645 (0.258%), neg=0, invalid=762 0271: dt=1.792000, rms=0.644 (0.189%), neg=0, invalid=762 0272: dt=2.428571, rms=0.643 (0.212%), neg=0, invalid=762 0273: dt=1.792000, rms=0.642 (0.103%), neg=0, invalid=762 0274: dt=1.792000, rms=0.641 (0.110%), neg=0, invalid=762 0275: dt=1.792000, rms=0.641 (0.074%), neg=0, invalid=762 0276: dt=1.792000, rms=0.640 (0.083%), neg=0, invalid=762 0277: dt=1.792000, rms=0.640 (0.058%), neg=0, invalid=762 0278: dt=1.792000, rms=0.640 (0.071%), neg=0, invalid=762 0279: dt=1.792000, rms=0.639 (0.047%), neg=0, invalid=762 0280: dt=1.792000, rms=0.639 (0.059%), neg=0, invalid=762 0281: dt=1.792000, rms=0.638 (0.092%), neg=0, invalid=762 0282: dt=1.792000, rms=0.638 (0.113%), neg=0, invalid=762 0283: dt=1.792000, rms=0.637 (0.138%), neg=0, invalid=762 0284: dt=1.792000, rms=0.636 (0.145%), neg=0, invalid=762 0285: dt=1.792000, rms=0.635 (0.122%), neg=0, invalid=762 0286: dt=1.792000, rms=0.634 (0.102%), neg=0, invalid=762 0287: dt=1.792000, rms=0.634 (0.003%), neg=0, invalid=762 0288: dt=1.792000, rms=0.634 (-0.004%), neg=0, invalid=762 0289: dt=0.000024, rms=0.634 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0290: dt=0.320000, rms=0.612 (1.754%), neg=0, invalid=762 0291: dt=0.448000, rms=0.605 (1.122%), neg=0, invalid=762 0292: dt=0.320000, rms=0.603 (0.349%), neg=0, invalid=762 0293: dt=0.384000, rms=0.601 (0.298%), neg=0, invalid=762 0294: dt=0.320000, rms=0.600 (0.187%), neg=0, invalid=762 0295: dt=0.384000, rms=0.599 (0.164%), neg=0, invalid=762 0296: dt=0.320000, rms=0.598 (0.117%), neg=0, invalid=762 0297: dt=0.320000, rms=0.597 (0.086%), neg=0, invalid=762 0298: dt=0.320000, rms=0.597 (0.079%), neg=0, invalid=762 0299: dt=0.320000, rms=0.597 (0.055%), neg=0, invalid=762 0300: dt=0.320000, rms=0.596 (0.061%), neg=0, invalid=762 0301: dt=0.320000, rms=0.596 (0.037%), neg=0, invalid=762 0302: dt=0.320000, rms=0.596 (0.045%), neg=0, invalid=762 0303: dt=0.320000, rms=0.595 (0.066%), neg=0, invalid=762 0304: dt=0.320000, rms=0.595 (0.071%), neg=0, invalid=762 0305: dt=0.320000, rms=0.595 (0.078%), neg=0, invalid=762 0306: dt=0.320000, rms=0.594 (0.060%), neg=0, invalid=762 0307: dt=0.320000, rms=0.594 (0.035%), neg=0, invalid=762 0308: dt=0.320000, rms=0.594 (-0.016%), neg=0, invalid=762 0309: dt=0.000000, rms=0.594 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.595, neg=0, invalid=762 0310: dt=0.320000, rms=0.589 (1.048%), neg=0, invalid=762 0311: dt=0.384000, rms=0.586 (0.524%), neg=0, invalid=762 0312: dt=0.320000, rms=0.585 (0.214%), neg=0, invalid=762 0313: dt=0.320000, rms=0.584 (0.145%), neg=0, invalid=762 0314: dt=0.384000, rms=0.583 (0.112%), neg=0, invalid=762 0315: dt=0.384000, rms=0.583 (0.081%), neg=0, invalid=762 0316: dt=0.384000, rms=0.582 (0.055%), neg=0, invalid=762 0317: dt=0.384000, rms=0.582 (0.054%), neg=0, invalid=762 0318: dt=0.384000, rms=0.582 (0.037%), neg=0, invalid=762 0319: dt=0.384000, rms=0.582 (0.038%), neg=0, invalid=762 0320: dt=0.384000, rms=0.581 (0.061%), neg=0, invalid=762 0321: dt=0.192000, rms=0.581 (0.015%), neg=0, invalid=762 0322: dt=0.192000, rms=0.581 (0.031%), neg=0, invalid=762 0323: dt=0.192000, rms=0.581 (0.041%), neg=0, invalid=762 0324: dt=0.192000, rms=0.581 (0.008%), neg=0, invalid=762 0325: dt=0.192000, rms=0.581 (0.014%), neg=0, invalid=762 0326: dt=0.192000, rms=0.580 (0.025%), neg=0, invalid=762 0327: dt=0.192000, rms=0.580 (0.037%), neg=0, invalid=762 0328: dt=0.192000, rms=0.580 (0.039%), neg=0, invalid=762 0329: dt=0.192000, rms=0.580 (0.034%), neg=0, invalid=762 0330: dt=0.192000, rms=0.580 (0.032%), neg=0, invalid=762 0331: dt=0.192000, rms=0.579 (0.034%), neg=0, invalid=762 0332: dt=0.192000, rms=0.579 (0.034%), neg=0, invalid=762 0333: dt=0.192000, rms=0.579 (0.032%), neg=0, invalid=762 0334: dt=0.192000, rms=0.579 (0.029%), neg=0, invalid=762 0335: dt=0.192000, rms=0.579 (0.025%), neg=0, invalid=762 0336: dt=0.192000, rms=0.579 (0.026%), neg=0, invalid=762 0337: dt=0.192000, rms=0.578 (0.025%), neg=0, invalid=762 0338: dt=0.192000, rms=0.578 (0.022%), neg=0, invalid=762 0339: dt=0.192000, rms=0.578 (0.002%), neg=0, invalid=762 0340: dt=0.112000, rms=0.578 (0.000%), neg=0, invalid=762 0341: dt=0.112000, rms=0.578 (0.000%), neg=0, invalid=762 0342: dt=0.112000, rms=0.578 (0.002%), neg=0, invalid=762 0343: dt=0.112000, rms=0.578 (0.000%), neg=0, invalid=762 0344: dt=0.112000, rms=0.578 (0.002%), neg=0, invalid=762 0345: dt=0.112000, rms=0.578 (0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=762 0346: dt=0.000000, rms=0.575 (0.208%), neg=0, invalid=762 0347: dt=0.000000, rms=0.575 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.576, neg=0, invalid=762 0348: dt=110.976000, rms=0.574 (0.330%), neg=0, invalid=762 0349: dt=73.984000, rms=0.574 (0.036%), neg=0, invalid=762 0350: dt=73.984000, rms=0.574 (0.023%), neg=0, invalid=762 0351: dt=73.984000, rms=0.573 (0.039%), neg=0, invalid=762 0352: dt=73.984000, rms=0.573 (0.040%), neg=0, invalid=762 0353: dt=73.984000, rms=0.573 (0.030%), neg=0, invalid=762 0354: dt=73.984000, rms=0.573 (0.031%), neg=0, invalid=762 0355: dt=73.984000, rms=0.573 (0.028%), neg=0, invalid=762 0356: dt=73.984000, rms=0.573 (0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.574, neg=0, invalid=762 0357: dt=0.000000, rms=0.573 (0.208%), neg=0, invalid=762 0358: dt=0.000000, rms=0.573 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.574, neg=0, invalid=762 0359: dt=145.152000, rms=0.569 (0.906%), neg=0, invalid=762 0360: dt=36.288000, rms=0.568 (0.140%), neg=0, invalid=762 0361: dt=36.288000, rms=0.567 (0.097%), neg=0, invalid=762 0362: dt=36.288000, rms=0.567 (0.142%), neg=0, invalid=762 0363: dt=36.288000, rms=0.566 (0.172%), neg=0, invalid=762 0364: dt=36.288000, rms=0.565 (0.178%), neg=0, invalid=762 0365: dt=36.288000, rms=0.564 (0.177%), neg=0, invalid=762 0366: dt=36.288000, rms=0.563 (0.156%), neg=0, invalid=762 0367: dt=36.288000, rms=0.562 (0.122%), neg=0, invalid=762 0368: dt=36.288000, rms=0.561 (0.103%), neg=0, invalid=762 0369: dt=248.832000, rms=0.561 (0.120%), neg=0, invalid=762 0370: dt=25.920000, rms=0.561 (0.038%), neg=0, invalid=762 0371: dt=25.920000, rms=0.560 (0.015%), neg=0, invalid=762 0372: dt=25.920000, rms=0.560 (0.023%), neg=0, invalid=762 0373: dt=25.920000, rms=0.560 (0.029%), neg=0, invalid=762 0374: dt=25.920000, rms=0.560 (0.036%), neg=0, invalid=762 0375: dt=25.920000, rms=0.560 (0.043%), neg=0, invalid=762 0376: dt=25.920000, rms=0.559 (0.047%), neg=0, invalid=762 0377: dt=25.920000, rms=0.559 (0.047%), neg=0, invalid=762 0378: dt=25.920000, rms=0.559 (0.047%), neg=0, invalid=762 0379: dt=25.920000, rms=0.559 (0.047%), neg=0, invalid=762 0380: dt=25.920000, rms=0.558 (0.047%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.561, neg=0, invalid=762 0381: dt=0.000000, rms=0.559 (0.231%), neg=0, invalid=762 0382: dt=0.000000, rms=0.559 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=762 iter 0, gcam->neg = 42 after 12 iterations, nbhd size=1, neg = 0 0383: dt=168.879581, rms=0.544 (2.875%), neg=0, invalid=762 0384: dt=32.000000, rms=0.540 (0.804%), neg=0, invalid=762 0385: dt=25.600000, rms=0.539 (0.200%), neg=0, invalid=762 0386: dt=25.600000, rms=0.539 (0.070%), neg=0, invalid=762 0387: dt=25.600000, rms=0.537 (0.217%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0388: dt=25.600000, rms=0.536 (0.331%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0389: dt=25.600000, rms=0.534 (0.311%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0390: dt=25.600000, rms=0.533 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0391: dt=25.600000, rms=0.530 (0.474%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0392: dt=25.600000, rms=0.528 (0.329%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0393: dt=25.600000, rms=0.526 (0.375%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 1 iterations, nbhd size=0, neg = 0 0394: dt=25.600000, rms=0.526 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0395: dt=25.600000, rms=0.524 (0.366%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0396: dt=25.600000, rms=0.523 (0.212%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0397: dt=25.600000, rms=0.522 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 4 iterations, nbhd size=0, neg = 0 0398: dt=25.600000, rms=0.522 (0.090%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=22.765101, rms=0.521 (0.125%), neg=0, invalid=762 0400: dt=11.200000, rms=0.521 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0401: dt=11.200000, rms=0.521 (0.003%), neg=0, invalid=762 0402: dt=11.200000, rms=0.521 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0403: dt=11.200000, rms=0.521 (0.001%), neg=0, invalid=762 0404: dt=11.200000, rms=0.521 (-0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0405: dt=0.000000, rms=0.531 (0.244%), neg=0, invalid=762 0406: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0407: dt=0.252000, rms=0.531 (0.245%), neg=0, invalid=762 0408: dt=0.252000, rms=0.531 (0.000%), neg=0, invalid=762 0409: dt=0.252000, rms=0.531 (0.000%), neg=0, invalid=762 0410: dt=0.252000, rms=0.531 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=762 0411: dt=0.448000, rms=0.551 (0.353%), neg=0, invalid=762 0412: dt=0.448000, rms=0.551 (0.040%), neg=0, invalid=762 0413: dt=0.448000, rms=0.551 (-0.031%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0414: dt=1.792000, rms=0.548 (0.721%), neg=0, invalid=762 0415: dt=1.024000, rms=0.548 (0.052%), neg=0, invalid=762 0416: dt=1.024000, rms=0.548 (-0.030%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 iter 0, gcam->neg = 435 after 14 iterations, nbhd size=1, neg = 0 0417: dt=1.536000, rms=0.515 (3.134%), neg=0, invalid=762 0418: dt=0.012000, rms=0.515 (0.006%), neg=0, invalid=762 0419: dt=0.012000, rms=0.515 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0420: dt=0.256000, rms=0.514 (0.510%), neg=0, invalid=762 0421: dt=0.112000, rms=0.514 (0.041%), neg=0, invalid=762 0422: dt=0.112000, rms=0.514 (0.023%), neg=0, invalid=762 0423: dt=0.112000, rms=0.514 (0.003%), neg=0, invalid=762 0424: dt=0.112000, rms=0.514 (-0.079%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 0425: dt=0.000000, rms=0.512 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=762 0426: dt=92.480000, rms=0.511 (0.222%), neg=0, invalid=762 0427: dt=32.368000, rms=0.511 (0.027%), neg=0, invalid=762 0428: dt=32.368000, rms=0.511 (0.009%), neg=0, invalid=762 0429: dt=32.368000, rms=0.511 (0.009%), neg=0, invalid=762 0430: dt=32.368000, rms=0.511 (0.010%), neg=0, invalid=762 0431: dt=32.368000, rms=0.511 (0.022%), neg=0, invalid=762 0432: dt=32.368000, rms=0.511 (0.031%), neg=0, invalid=762 0433: dt=32.368000, rms=0.510 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0434: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=762 0435: dt=145.152000, rms=0.510 (0.136%), neg=0, invalid=762 0436: dt=82.944000, rms=0.509 (0.146%), neg=0, invalid=762 0437: dt=15.552000, rms=0.509 (0.012%), neg=0, invalid=762 0438: dt=15.552000, rms=0.509 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 0439: dt=0.000000, rms=0.509 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=762 0440: dt=80.516129, rms=0.504 (1.031%), neg=0, invalid=762 0441: dt=20.455988, rms=0.501 (0.521%), neg=0, invalid=762 0442: dt=11.200000, rms=0.501 (0.065%), neg=0, invalid=762 0443: dt=11.200000, rms=0.501 (0.067%), neg=0, invalid=762 0444: dt=11.200000, rms=0.500 (0.114%), neg=0, invalid=762 0445: dt=11.200000, rms=0.499 (0.147%), neg=0, invalid=762 0446: dt=11.200000, rms=0.498 (0.169%), neg=0, invalid=762 0447: dt=11.200000, rms=0.497 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0448: dt=11.200000, rms=0.496 (0.195%), neg=0, invalid=762 0449: dt=11.200000, rms=0.495 (0.200%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0450: dt=11.200000, rms=0.495 (0.187%), neg=0, invalid=762 0451: dt=11.200000, rms=0.494 (0.162%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0452: dt=11.200000, rms=0.493 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=0, neg = 0 0453: dt=11.200000, rms=0.493 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0454: dt=11.200000, rms=0.492 (0.111%), neg=0, invalid=762 0455: dt=44.800000, rms=0.492 (0.036%), neg=0, invalid=762 0456: dt=44.800000, rms=0.492 (-0.225%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0457: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0458: dt=4.032000, rms=0.495 (0.076%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 13 iterations, nbhd size=1, neg = 0 0459: dt=11.870968, rms=0.494 (0.222%), neg=0, invalid=762 0460: dt=4.941176, rms=0.493 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0461: dt=4.941176, rms=0.492 (0.172%), neg=0, invalid=762 0462: dt=4.941176, rms=0.492 (0.189%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0463: dt=4.941176, rms=0.491 (0.153%), neg=0, invalid=762 0464: dt=4.941176, rms=0.490 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 11 iterations, nbhd size=1, neg = 0 0465: dt=4.941176, rms=0.489 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0466: dt=4.941176, rms=0.488 (0.225%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0467: dt=4.941176, rms=0.487 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0468: dt=4.941176, rms=0.486 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0469: dt=4.941176, rms=0.485 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0470: dt=4.941176, rms=0.484 (0.151%), neg=0, invalid=762 0471: dt=4.941176, rms=0.484 (0.057%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0472: dt=4.941176, rms=0.484 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0473: dt=6.666667, rms=0.484 (0.016%), neg=0, invalid=762 0474: dt=0.000176, rms=0.484 (0.000%), neg=0, invalid=762 0475: dt=0.000176, rms=0.484 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0476: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0477: dt=0.000050, rms=0.490 (0.000%), neg=0, invalid=762 0478: dt=0.000000, rms=0.490 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 iter 0, gcam->neg = 275 after 18 iterations, nbhd size=1, neg = 0 0479: dt=0.849630, rms=0.475 (1.054%), neg=0, invalid=762 0480: dt=0.000040, rms=0.475 (0.000%), neg=0, invalid=762 0481: dt=0.000040, rms=0.475 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0482: dt=0.448000, rms=0.472 (0.620%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 8 iterations, nbhd size=1, neg = 0 0483: dt=0.461538, rms=0.471 (0.375%), neg=0, invalid=762 0484: dt=0.320000, rms=0.470 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0485: dt=0.320000, rms=0.469 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0486: dt=0.320000, rms=0.469 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 8 iterations, nbhd size=1, neg = 0 0487: dt=0.320000, rms=0.469 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 32 after 3 iterations, nbhd size=0, neg = 0 0488: dt=0.320000, rms=0.468 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 46 after 12 iterations, nbhd size=1, neg = 0 0489: dt=0.320000, rms=0.468 (0.004%), neg=0, invalid=762 0490: dt=0.112000, rms=0.468 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0491: dt=0.320000, rms=0.468 (0.043%), neg=0, invalid=762 0492: dt=0.064000, rms=0.468 (0.002%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 3 minutes and 42 seconds. mri_ca_register utimesec 7282.847199 mri_ca_register stimesec 29.124989 mri_ca_register ru_maxrss 1333852 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 8862271 mri_ca_register ru_majflt 11 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 8352 mri_ca_register ru_oublock 65320 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1050 mri_ca_register ru_nivcsw 64871 FSRUNTIME@ mri_ca_register 2.0618 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri 15 Mar 2024 07:37:53 PM CET mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname ramones machine x86_64 user yangc Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname ramones machine x86_64 setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS cd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 4.56 Atlas used for the 3D morph was /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.05974 (24) Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (146 voxels, overlap=0.704) Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (146 voxels, peak = 22), gca=21.7 gca peak = 0.17677 (13) mri peak = 0.08660 ( 7) Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (106 voxels, overlap=0.423) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (106 voxels, peak = 4), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.07634 (86) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (532 voxels, overlap=0.486) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (532 voxels, peak = 87), gca=86.9 gca peak = 0.16930 (96) mri peak = 0.06667 (86) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (522 voxels, overlap=0.820) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (522 voxels, peak = 89), gca=88.8 gca peak = 0.24553 (55) mri peak = 0.09773 (51) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (862 voxels, overlap=0.962) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (862 voxels, peak = 50), gca=50.3 gca peak = 0.30264 (59) mri peak = 0.11674 (53) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (764 voxels, overlap=0.892) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (764 voxels, peak = 54), gca=54.0 gca peak = 0.07580 (103) mri peak = 0.09288 (106) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (19261 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (19261 voxels, peak = 108), gca=107.6 gca peak = 0.07714 (104) mri peak = 0.07952 (108) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (18776 voxels, overlap=0.567) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (18776 voxels, peak = 110), gca=109.7 gca peak = 0.09712 (58) mri peak = 0.04253 (51) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (22129 voxels, overlap=0.801) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (22129 voxels, peak = 53), gca=53.1 gca peak = 0.11620 (58) mri peak = 0.04740 (51) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (22333 voxels, overlap=0.777) Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (22333 voxels, peak = 52), gca=51.9 gca peak = 0.30970 (66) mri peak = 0.10599 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, peak = 66), gca=66.0 gca peak = 0.15280 (69) mri peak = 0.09170 (69) Left_Caudate (11): linear fit = 0.93 x + 0.0 (576 voxels, overlap=0.710) Left_Caudate (11): linear fit = 0.93 x + 0.0 (576 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.06039 (53) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (22467 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (22467 voxels, peak = 54), gca=54.0 gca peak = 0.14777 (55) mri peak = 0.06497 (54) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10261 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (10261 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.08859 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3734 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (3734 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.09557 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (2684 voxels, overlap=0.910) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (2684 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.10015 (57) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (411 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (411 voxels, peak = 52), gca=52.2 gca peak = 0.33601 (57) mri peak = 0.12662 (55) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (421 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 0.89 x + 0.0 (421 voxels, peak = 51), gca=51.0 gca peak = 0.11131 (90) mri peak = 0.07332 (80) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2864 voxels, overlap=0.976) Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (2864 voxels, peak = 87), gca=86.8 gca peak = 0.11793 (83) mri peak = 0.07143 (81) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3058 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3058 voxels, peak = 82), gca=81.8 gca peak = 0.08324 (81) mri peak = 0.07642 (70) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1439 voxels, overlap=0.653) Left_Putamen (12): linear fit = 0.92 x + 0.0 (1439 voxels, peak = 74), gca=74.1 gca peak = 0.10360 (77) mri peak = 0.07798 (70) Right_Putamen (51): linear fit = 0.90 x + 0.0 (1526 voxels, overlap=0.622) Right_Putamen (51): linear fit = 0.90 x + 0.0 (1526 voxels, peak = 70), gca=69.7 gca peak = 0.08424 (78) mri peak = 0.09139 (83) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7704 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7704 voxels, peak = 82), gca=82.3 gca peak = 0.12631 (89) mri peak = 0.07046 (93) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1026 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1026 voxels, peak = 95), gca=94.8 gca peak = 0.14500 (87) mri peak = 0.06369 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1009 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1009 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) mri peak = 0.11372 ( 6) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (395 voxels, overlap=0.651) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (395 voxels, peak = 3), gca=3.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.91 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.74 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17226 (22) mri peak = 0.05974 (24) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (146 voxels, overlap=0.703) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (146 voxels, peak = 23), gca=22.5 gca peak = 0.30173 ( 5) mri peak = 0.08660 ( 7) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (106 voxels, overlap=0.961) Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (106 voxels, peak = 6), gca=6.5 gca peak = 0.28259 (87) mri peak = 0.07634 (86) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (532 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (532 voxels, peak = 87), gca=86.6 gca peak = 0.18393 (89) mri peak = 0.06667 (86) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (522 voxels, overlap=1.015) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (522 voxels, peak = 89), gca=88.6 gca peak = 0.33036 (51) mri peak = 0.09773 (51) Right_Hippocampus: unreasonable value (49.7/51.0), not in range [50, 90] - rejecting gca peak = 0.31579 (54) mri peak = 0.11674 (53) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (764 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (764 voxels, peak = 54), gca=54.0 gca peak = 0.07599 (108) mri peak = 0.09288 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (19261 voxels, overlap=0.783) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (19261 voxels, peak = 107), gca=107.5 gca peak = 0.07551 (110) mri peak = 0.07952 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (18776 voxels, overlap=0.798) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (18776 voxels, peak = 110), gca=110.0 gca peak = 0.10689 (53) mri peak = 0.04253 (51) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22129 voxels, overlap=0.998) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22129 voxels, peak = 51), gca=51.1 gca peak = 0.12870 (52) mri peak = 0.04740 (51) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22333 voxels, overlap=0.978) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22333 voxels, peak = 52), gca=52.0 gca peak = 0.30267 (66) mri peak = 0.10599 (67) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (650 voxels, peak = 66), gca=66.0 gca peak = 0.14924 (72) mri peak = 0.09170 (69) Left_Caudate (11): linear fit = 1.00 x + 0.0 (576 voxels, overlap=1.003) Left_Caudate (11): linear fit = 1.00 x + 0.0 (576 voxels, peak = 72), gca=72.0 gca peak = 0.14721 (54) mri peak = 0.06039 (53) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, overlap=0.996) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (22467 voxels, peak = 54), gca=54.0 gca peak = 0.15601 (53) mri peak = 0.06497 (54) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (10261 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (10261 voxels, peak = 53), gca=53.0 gca peak = 0.15873 (90) mri peak = 0.08859 (88) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (3734 voxels, overlap=0.974) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (3734 voxels, peak = 89), gca=88.7 gca peak = 0.18253 (87) mri peak = 0.09557 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2684 voxels, overlap=0.979) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (2684 voxels, peak = 87), gca=87.0 gca peak = 0.30120 (52) mri peak = 0.10015 (57) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (411 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (411 voxels, peak = 56), gca=56.4 gca peak = 0.35318 (51) mri peak = 0.12662 (55) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (421 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (421 voxels, peak = 51), gca=51.0 gca peak = 0.10679 (87) mri peak = 0.07332 (80) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2864 voxels, overlap=0.972) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2864 voxels, peak = 87), gca=86.6 gca peak = 0.11340 (82) mri peak = 0.07143 (81) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3058 voxels, overlap=0.943) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (3058 voxels, peak = 83), gca=83.2 gca peak = 0.08998 (74) mri peak = 0.07642 (70) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1439 voxels, overlap=0.984) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1439 voxels, peak = 73), gca=72.9 gca peak = 0.10238 (72) mri peak = 0.07798 (70) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1526 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1526 voxels, peak = 72), gca=72.0 gca peak = 0.07681 (83) mri peak = 0.09139 (83) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7704 voxels, overlap=0.714) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7704 voxels, peak = 83), gca=82.6 gca peak = 0.11572 (95) mri peak = 0.07046 (93) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1026 voxels, overlap=0.900) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1026 voxels, peak = 94), gca=93.6 gca peak = 0.16524 (91) mri peak = 0.06369 (94) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1009 voxels, overlap=0.891) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1009 voxels, peak = 90), gca=89.6 gca peak = 0.21373 (19) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.23191 (11) mri peak = 0.11372 ( 6) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (395 voxels, overlap=0.852) Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (395 voxels, peak = 3), gca=2.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18969 (25) gca peak Left_Thalamus = 0.64095 (85) gca peak Third_Ventricle = 0.21373 (19) gca peak Fourth_Ventricle = 0.23191 (11) gca peak CSF = 0.29747 (27) gca peak Left_Accumbens_area = 0.54646 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.74527 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.23494 (21) gca peak Right_Hippocampus = 0.33036 (51) gca peak Right_Accumbens_area = 0.42978 (65) gca peak Right_vessel = 0.82808 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.54304 (24) gca peak WM_hypointensities = 0.07070 (80) gca peak non_WM_hypointensities = 0.11462 (57) gca peak Optic_Chiasm = 0.70629 (75) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.00 x + 0: 54 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.16 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 59095 voxels changed in iteration 0 of unlikely voxel relabeling 105 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 23381 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels) 365 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 60940 changed. image ll: -17.371, PF=0.500 pass 2: 17913 changed. image ll: -17.370, PF=0.500 pass 3: 5948 changed. pass 4: 2281 changed. 35699 voxels changed in iteration 0 of unlikely voxel relabeling 351 voxels changed in iteration 1 of unlikely voxel relabeling 28 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5619 voxels changed in iteration 0 of unlikely voxel relabeling 64 voxels changed in iteration 1 of unlikely voxel relabeling 18 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5072 voxels changed in iteration 0 of unlikely voxel relabeling 44 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4225 voxels changed in iteration 0 of unlikely voxel relabeling 22 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1695.662027 mri_ca_label stimesec 2.311915 mri_ca_label ru_maxrss 2109464 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 552350 mri_ca_label ru_majflt 9 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 66200 mri_ca_label ru_oublock 368 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 47 mri_ca_label ru_nivcsw 14413 auto-labeling took 28 minutes and 31 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/cc_up.lta LS5K will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/transforms/cc_up.lta reading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.auto_noCCseg.mgz reading norm from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/norm.mgz 52827 voxels in left wm, 78281 in right wm, xrange [121, 138] searching rotation angles z=[-10 4], y=[-1 13] searching scale 1 Z rot -10.2 searching scale 1 Z rot -10.0 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.5 searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 global minimum found at slice 132.0, rotations (7.44, -1.97) final transformation (x=132.0, yr=7.439, zr=-1.969): 0.99100 0.03436 0.12940 -21.47216; -0.03407 0.99941 -0.00445 23.07417; -0.12947 -0.00000 0.99158 31.05854; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 110 115 eigenvectors: 0.00090 0.00271 1.00000; 0.17100 -0.98527 0.00252; 0.98527 0.17099 -0.00135; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.auto.mgz... corpus callosum segmentation took 1.2 minutes #-------------------------------------- #@# Merge ASeg Fri 15 Mar 2024 08:07:36 PM CET cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri 15 Mar 2024 08:07:36 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_normalize -f /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 8 control points... only using 8 control points from file, mean 105.1, scaling by 1.05... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... processing with aseg removing outliers in the aseg WM... 1539 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 67 (67), valley at 20 (20) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 90 gm peak at 72 (72), valley at 0 (-1) csf peak at 36, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 55 seconds. #-------------------------------------------- #@# Mask BFS Fri 15 Mar 2024 08:10:31 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 3929088 voxels in mask (pct= 23.42) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri 15 Mar 2024 08:10:33 PM CET mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri cmdline mri_binarize.bin --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname ramones machine x86_64 user yangc input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri cmdline mri_binarize.bin --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname ramones machine x86_64 user yangc input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep -mprage brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 108.4 +- 7.5 [79.0 --> 125.0] GM (69.0) : 67.0 +- 10.1 [30.0 --> 95.0] setting bottom of white matter range to 77.1 setting top of gray matter range to 87.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 65658 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5392 filled 103342 bright non-wm voxels segmented. 63751 diagonally connected voxels added... white matter segmentation took 2.6 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.38 minutes reading wm segmentation from wm.seg.mgz... 1130 voxels added to wm to prevent paths from MTL structures to cortex 4076 additional wm voxels added 0 additional wm voxels added SEG EDIT: 43707 voxels turned on, 1004967 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 97 new 97 115,126,128 old 97 new 97 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 451 found - 451 modified | TOTAL: 451 pass 2 (xy+): 0 found - 451 modified | TOTAL: 451 pass 1 (xy-): 411 found - 411 modified | TOTAL: 862 pass 2 (xy-): 0 found - 411 modified | TOTAL: 862 pass 1 (yz+): 320 found - 320 modified | TOTAL: 1182 pass 2 (yz+): 0 found - 320 modified | TOTAL: 1182 pass 1 (yz-): 178 found - 178 modified | TOTAL: 1360 pass 2 (yz-): 0 found - 178 modified | TOTAL: 1360 pass 1 (xz+): 305 found - 305 modified | TOTAL: 1665 pass 2 (xz+): 0 found - 305 modified | TOTAL: 1665 pass 1 (xz-): 253 found - 253 modified | TOTAL: 1918 pass 2 (xz-): 0 found - 253 modified | TOTAL: 1918 Iteration Number : 1 pass 1 (+++): 104 found - 104 modified | TOTAL: 104 pass 2 (+++): 0 found - 104 modified | TOTAL: 104 pass 1 (+++): 110 found - 110 modified | TOTAL: 214 pass 2 (+++): 0 found - 110 modified | TOTAL: 214 pass 1 (+++): 162 found - 162 modified | TOTAL: 376 pass 2 (+++): 0 found - 162 modified | TOTAL: 376 pass 1 (+++): 107 found - 107 modified | TOTAL: 483 pass 2 (+++): 0 found - 107 modified | TOTAL: 483 Iteration Number : 1 pass 1 (++): 138 found - 138 modified | TOTAL: 138 pass 2 (++): 0 found - 138 modified | TOTAL: 138 pass 1 (+-): 402 found - 402 modified | TOTAL: 540 pass 2 (+-): 4 found - 406 modified | TOTAL: 544 pass 3 (+-): 0 found - 406 modified | TOTAL: 544 pass 1 (--): 248 found - 248 modified | TOTAL: 792 pass 2 (--): 4 found - 252 modified | TOTAL: 796 pass 3 (--): 0 found - 252 modified | TOTAL: 796 pass 1 (-+): 283 found - 283 modified | TOTAL: 1079 pass 2 (-+): 0 found - 283 modified | TOTAL: 1079 Iteration Number : 2 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 30 found - 30 modified | TOTAL: 42 pass 2 (xy-): 0 found - 30 modified | TOTAL: 42 pass 1 (yz+): 30 found - 30 modified | TOTAL: 72 pass 2 (yz+): 0 found - 30 modified | TOTAL: 72 pass 1 (yz-): 15 found - 15 modified | TOTAL: 87 pass 2 (yz-): 0 found - 15 modified | TOTAL: 87 pass 1 (xz+): 16 found - 16 modified | TOTAL: 103 pass 2 (xz+): 0 found - 16 modified | TOTAL: 103 pass 1 (xz-): 22 found - 22 modified | TOTAL: 125 pass 2 (xz-): 0 found - 22 modified | TOTAL: 125 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 pass 1 (+++): 0 found - 0 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 10 found - 10 modified | TOTAL: 10 pass 2 (++): 0 found - 10 modified | TOTAL: 10 pass 1 (+-): 18 found - 18 modified | TOTAL: 28 pass 2 (+-): 0 found - 18 modified | TOTAL: 28 pass 1 (--): 14 found - 14 modified | TOTAL: 42 pass 2 (--): 0 found - 14 modified | TOTAL: 42 pass 1 (-+): 24 found - 24 modified | TOTAL: 66 pass 2 (-+): 0 found - 24 modified | TOTAL: 66 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3685 (out of 342093: 1.077192) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Fri 15 Mar 2024 08:13:39 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.23065 0.04570 0.12151 -54.24541; -0.03665 1.23110 -0.13539 -12.48038; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.23065 0.04570 0.12151 -54.24541; -0.03665 1.23110 -0.13539 -12.48038; -0.11143 0.07189 1.13829 -14.25179; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 955 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (127, 121, 149), TAL = (1.0, 21.0, 7.0) talairach voxel to voxel transform 0.80381 -0.02466 -0.08874 42.03045; 0.03236 0.80569 0.09238 13.12696; 0.07664 -0.05330 0.86399 15.80556; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 121, 149) --> (1.0, 21.0, 7.0) done. writing output to filled.mgz... filling took 0.4 minutes talairach cc position changed to (1.00, 21.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 21.00, 7.00) SRC: (113.44, 127.91, 146.44) search lh wm seed point around talairach space (-17.00, 21.00, 7.00), SRC: (142.38, 129.07, 149.20) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri 15 Mar 2024 08:14:01 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2 (out of 159164: 0.001257) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1897 vertices, 2026 faces slice 60: 6836 vertices, 7037 faces slice 70: 13448 vertices, 13745 faces slice 80: 20305 vertices, 20566 faces slice 90: 27242 vertices, 27509 faces slice 100: 35098 vertices, 35437 faces slice 110: 44722 vertices, 45148 faces slice 120: 54838 vertices, 55258 faces slice 130: 64419 vertices, 64817 faces slice 140: 72141 vertices, 72483 faces slice 150: 77674 vertices, 77964 faces slice 160: 83265 vertices, 83576 faces slice 170: 88800 vertices, 89090 faces slice 180: 93326 vertices, 93611 faces slice 190: 95186 vertices, 95330 faces slice 200: 95186 vertices, 95330 faces slice 210: 95186 vertices, 95330 faces slice 220: 95186 vertices, 95330 faces slice 230: 95186 vertices, 95330 faces slice 240: 95186 vertices, 95330 faces slice 250: 95186 vertices, 95330 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 95186 voxel in cpt #1: X=-144 [v=95186,e=285990,f=190660] located at (-28.130913, -15.869067, 9.166516) For the whole surface: X=-144 [v=95186,e=285990,f=190660] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri 15 Mar 2024 08:14:04 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1 (out of 159213: 0.000628) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 60: 3031 vertices, 3216 faces slice 70: 9421 vertices, 9674 faces slice 80: 18063 vertices, 18390 faces slice 90: 26880 vertices, 27194 faces slice 100: 36042 vertices, 36368 faces slice 110: 46755 vertices, 47134 faces slice 120: 56877 vertices, 57264 faces slice 130: 65641 vertices, 65977 faces slice 140: 71568 vertices, 71823 faces slice 150: 77179 vertices, 77466 faces slice 160: 82594 vertices, 82823 faces slice 170: 87285 vertices, 87503 faces slice 180: 90357 vertices, 90512 faces slice 190: 91476 vertices, 91568 faces slice 200: 91476 vertices, 91568 faces slice 210: 91476 vertices, 91568 faces slice 220: 91476 vertices, 91568 faces slice 230: 91476 vertices, 91568 faces slice 240: 91476 vertices, 91568 faces slice 250: 91476 vertices, 91568 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 91476 voxel in cpt #1: X=-92 [v=91476,e=274704,f=183136] located at (21.175707, -17.361023, 11.782468) For the whole surface: X=-92 [v=91476,e=274704,f=183136] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri 15 Mar 2024 08:14:07 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Fri 15 Mar 2024 08:14:10 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri 15 Mar 2024 08:14:12 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 41.5 mm, total surface area = 48974 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.173 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.111 (target=0.015) step 015: RMS=0.102 (target=0.015) step 020: RMS=0.094 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.082 (target=0.015) step 035: RMS=0.079 (target=0.015) step 040: RMS=0.077 (target=0.015) step 045: RMS=0.073 (target=0.015) step 050: RMS=0.072 (target=0.015) step 055: RMS=0.072 (target=0.015) step 060: RMS=0.072 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 15.775986 mris_inflate stimesec 0.048024 mris_inflate ru_maxrss 128404 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 15833 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 7464 mris_inflate ru_oublock 6704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 270 mris_inflate ru_nivcsw 59 #-------------------------------------------- #@# Inflation1 rh Fri 15 Mar 2024 08:14:28 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 40.3 mm, total surface area = 48135 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.165 (target=0.015) step 005: RMS=0.130 (target=0.015) step 010: RMS=0.102 (target=0.015) step 015: RMS=0.091 (target=0.015) step 020: RMS=0.083 (target=0.015) step 025: RMS=0.075 (target=0.015) step 030: RMS=0.071 (target=0.015) step 035: RMS=0.065 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.061 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.059 (target=0.015) step 060: RMS=0.058 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 14.809859 mris_inflate stimesec 0.071970 mris_inflate ru_maxrss 123728 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 15638 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 6440 mris_inflate ru_oublock 6440 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 217 mris_inflate ru_nivcsw 33 #-------------------------------------------- #@# QSphere lh Fri 15 Mar 2024 08:14:43 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.15 +- 0.73 (0.00-->9.53) (max @ vno 29065 --> 29757) face area 0.03 +- 0.04 (-0.20-->1.19) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.354... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.537, avgs=0 005/300: dt: 0.9000, rms radial error=177.278, avgs=0 010/300: dt: 0.9000, rms radial error=176.720, avgs=0 015/300: dt: 0.9000, rms radial error=175.986, avgs=0 020/300: dt: 0.9000, rms radial error=175.149, avgs=0 025/300: dt: 0.9000, rms radial error=174.251, avgs=0 030/300: dt: 0.9000, rms radial error=173.320, avgs=0 035/300: dt: 0.9000, rms radial error=172.370, avgs=0 040/300: dt: 0.9000, rms radial error=171.420, avgs=0 045/300: dt: 0.9000, rms radial error=170.473, avgs=0 050/300: dt: 0.9000, rms radial error=169.527, avgs=0 055/300: dt: 0.9000, rms radial error=168.582, avgs=0 060/300: dt: 0.9000, rms radial error=167.641, avgs=0 065/300: dt: 0.9000, rms radial error=166.704, avgs=0 070/300: dt: 0.9000, rms radial error=165.771, avgs=0 075/300: dt: 0.9000, rms radial error=164.843, avgs=0 080/300: dt: 0.9000, rms radial error=163.919, avgs=0 085/300: dt: 0.9000, rms radial error=163.000, avgs=0 090/300: dt: 0.9000, rms radial error=162.086, avgs=0 095/300: dt: 0.9000, rms radial error=161.177, avgs=0 100/300: dt: 0.9000, rms radial error=160.272, avgs=0 105/300: dt: 0.9000, rms radial error=159.372, avgs=0 110/300: dt: 0.9000, rms radial error=158.477, avgs=0 115/300: dt: 0.9000, rms radial error=157.587, avgs=0 120/300: dt: 0.9000, rms radial error=156.701, avgs=0 125/300: dt: 0.9000, rms radial error=155.820, avgs=0 130/300: dt: 0.9000, rms radial error=154.944, avgs=0 135/300: dt: 0.9000, rms radial error=154.073, avgs=0 140/300: dt: 0.9000, rms radial error=153.205, avgs=0 145/300: dt: 0.9000, rms radial error=152.343, avgs=0 150/300: dt: 0.9000, rms radial error=151.485, avgs=0 155/300: dt: 0.9000, rms radial error=150.631, avgs=0 160/300: dt: 0.9000, rms radial error=149.783, avgs=0 165/300: dt: 0.9000, rms radial error=148.938, avgs=0 170/300: dt: 0.9000, rms radial error=148.099, avgs=0 175/300: dt: 0.9000, rms radial error=147.264, avgs=0 180/300: dt: 0.9000, rms radial error=146.434, avgs=0 185/300: dt: 0.9000, rms radial error=145.608, avgs=0 190/300: dt: 0.9000, rms radial error=144.787, avgs=0 195/300: dt: 0.9000, rms radial error=143.970, avgs=0 200/300: dt: 0.9000, rms radial error=143.158, avgs=0 205/300: dt: 0.9000, rms radial error=142.350, avgs=0 210/300: dt: 0.9000, rms radial error=141.546, avgs=0 215/300: dt: 0.9000, rms radial error=140.747, avgs=0 220/300: dt: 0.9000, rms radial error=139.953, avgs=0 225/300: dt: 0.9000, rms radial error=139.163, avgs=0 230/300: dt: 0.9000, rms radial error=138.377, avgs=0 235/300: dt: 0.9000, rms radial error=137.597, avgs=0 240/300: dt: 0.9000, rms radial error=136.820, avgs=0 245/300: dt: 0.9000, rms radial error=136.048, avgs=0 250/300: dt: 0.9000, rms radial error=135.280, avgs=0 255/300: dt: 0.9000, rms radial error=134.517, avgs=0 260/300: dt: 0.9000, rms radial error=133.757, avgs=0 265/300: dt: 0.9000, rms radial error=133.002, avgs=0 270/300: dt: 0.9000, rms radial error=132.252, avgs=0 275/300: dt: 0.9000, rms radial error=131.505, avgs=0 280/300: dt: 0.9000, rms radial error=130.763, avgs=0 285/300: dt: 0.9000, rms radial error=130.025, avgs=0 290/300: dt: 0.9000, rms radial error=129.291, avgs=0 295/300: dt: 0.9000, rms radial error=128.561, avgs=0 300/300: dt: 0.9000, rms radial error=127.835, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 10738.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 2 (K=40.0), pass 1, starting sse = 1732.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 202.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00478 epoch 4 (K=640.0), pass 1, starting sse = 24.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00448 final distance error %27.63 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 112.706658 mris_sphere stimesec 0.063981 mris_sphere ru_maxrss 128884 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 16521 mris_sphere ru_majflt 6 mris_sphere ru_nswap 0 mris_sphere ru_inblock 7112 mris_sphere ru_oublock 6704 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 156 mris_sphere ru_nivcsw 611 FSRUNTIME@ mris_sphere 0.0315 hours 1 threads #-------------------------------------------- #@# QSphere rh Fri 15 Mar 2024 08:16:36 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.19 +- 0.70 (0.00-->7.55) (max @ vno 60465 --> 60488) face area 0.04 +- 0.05 (-0.22-->0.74) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.393... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.676, avgs=0 005/300: dt: 0.9000, rms radial error=175.421, avgs=0 010/300: dt: 0.9000, rms radial error=174.872, avgs=0 015/300: dt: 0.9000, rms radial error=174.149, avgs=0 020/300: dt: 0.9000, rms radial error=173.321, avgs=0 025/300: dt: 0.9000, rms radial error=172.435, avgs=0 030/300: dt: 0.9000, rms radial error=171.519, avgs=0 035/300: dt: 0.9000, rms radial error=170.589, avgs=0 040/300: dt: 0.9000, rms radial error=169.653, avgs=0 045/300: dt: 0.9000, rms radial error=168.714, avgs=0 050/300: dt: 0.9000, rms radial error=167.777, avgs=0 055/300: dt: 0.9000, rms radial error=166.842, avgs=0 060/300: dt: 0.9000, rms radial error=165.911, avgs=0 065/300: dt: 0.9000, rms radial error=164.983, avgs=0 070/300: dt: 0.9000, rms radial error=164.060, avgs=0 075/300: dt: 0.9000, rms radial error=163.144, avgs=0 080/300: dt: 0.9000, rms radial error=162.234, avgs=0 085/300: dt: 0.9000, rms radial error=161.329, avgs=0 090/300: dt: 0.9000, rms radial error=160.428, avgs=0 095/300: dt: 0.9000, rms radial error=159.533, avgs=0 100/300: dt: 0.9000, rms radial error=158.643, avgs=0 105/300: dt: 0.9000, rms radial error=157.758, avgs=0 110/300: dt: 0.9000, rms radial error=156.877, avgs=0 115/300: dt: 0.9000, rms radial error=156.001, avgs=0 120/300: dt: 0.9000, rms radial error=155.130, avgs=0 125/300: dt: 0.9000, rms radial error=154.263, avgs=0 130/300: dt: 0.9000, rms radial error=153.401, avgs=0 135/300: dt: 0.9000, rms radial error=152.543, avgs=0 140/300: dt: 0.9000, rms radial error=151.690, avgs=0 145/300: dt: 0.9000, rms radial error=150.842, avgs=0 150/300: dt: 0.9000, rms radial error=149.998, avgs=0 155/300: dt: 0.9000, rms radial error=149.159, avgs=0 160/300: dt: 0.9000, rms radial error=148.324, avgs=0 165/300: dt: 0.9000, rms radial error=147.493, avgs=0 170/300: dt: 0.9000, rms radial error=146.667, avgs=0 175/300: dt: 0.9000, rms radial error=145.846, avgs=0 180/300: dt: 0.9000, rms radial error=145.029, avgs=0 185/300: dt: 0.9000, rms radial error=144.216, avgs=0 190/300: dt: 0.9000, rms radial error=143.408, avgs=0 195/300: dt: 0.9000, rms radial error=142.605, avgs=0 200/300: dt: 0.9000, rms radial error=141.805, avgs=0 205/300: dt: 0.9000, rms radial error=141.010, avgs=0 210/300: dt: 0.9000, rms radial error=140.220, avgs=0 215/300: dt: 0.9000, rms radial error=139.434, avgs=0 220/300: dt: 0.9000, rms radial error=138.652, avgs=0 225/300: dt: 0.9000, rms radial error=137.874, avgs=0 230/300: dt: 0.9000, rms radial error=137.101, avgs=0 235/300: dt: 0.9000, rms radial error=136.332, avgs=0 240/300: dt: 0.9000, rms radial error=135.567, avgs=0 245/300: dt: 0.9000, rms radial error=134.806, avgs=0 250/300: dt: 0.9000, rms radial error=134.049, avgs=0 255/300: dt: 0.9000, rms radial error=133.297, avgs=0 260/300: dt: 0.9000, rms radial error=132.548, avgs=0 265/300: dt: 0.9000, rms radial error=131.803, avgs=0 270/300: dt: 0.9000, rms radial error=131.063, avgs=0 275/300: dt: 0.9000, rms radial error=130.326, avgs=0 280/300: dt: 0.9000, rms radial error=129.594, avgs=0 285/300: dt: 0.9000, rms radial error=128.866, avgs=0 290/300: dt: 0.9000, rms radial error=128.142, avgs=0 295/300: dt: 0.9000, rms radial error=127.422, avgs=0 300/300: dt: 0.9000, rms radial error=126.706, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 9799.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 1442.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00131 epoch 3 (K=160.0), pass 1, starting sse = 139.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01006 epoch 4 (K=640.0), pass 1, starting sse = 13.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00951 final distance error %23.45 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 122.845283 mris_sphere stimesec 0.051992 mris_sphere ru_maxrss 124056 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 15830 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 6440 mris_sphere ru_oublock 6440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 83 mris_sphere ru_nivcsw 1015 FSRUNTIME@ mris_sphere 0.0344 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Fri 15 Mar 2024 08:18:40 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fri 15 Mar 2024 08:18:40 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fri 15 Mar 2024 08:18:40 PM CET mris_fix_topology -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 LS5K lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-144 (nv=95186, nf=190660, ne=285990, g=73) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 12546 ambiguous faces found in tessellation segmenting defects... 82 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 55 into 54 -merging segment 59 into 56 80 defects to be corrected 0 vertices coincident reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2804 (-4.6402) -vertex loglikelihood: -6.4504 (-3.2252) -normal dot loglikelihood: -3.5779 (-3.5779) -quad curv loglikelihood: -6.2032 (-3.1016) Total Loglikelihood : -25.5119 CORRECTING DEFECT 0 (vertices=2879, convex hull=785, v0=0) XL defect detected... After retessellation of defect 0 (v0=0), euler #=-77 (88189,262236,173970) : difference with theory (-77) = 0 CORRECTING DEFECT 1 (vertices=65, convex hull=89, v0=1484) After retessellation of defect 1 (v0=1484), euler #=-76 (88222,262376,174078) : difference with theory (-76) = 0 CORRECTING DEFECT 2 (vertices=5, convex hull=29, v0=2187) After retessellation of defect 2 (v0=2187), euler #=-75 (88222,262385,174088) : difference with theory (-75) = 0 CORRECTING DEFECT 3 (vertices=42, convex hull=80, v0=3777) After retessellation of defect 3 (v0=3777), euler #=-74 (88245,262486,174167) : difference with theory (-74) = 0 CORRECTING DEFECT 4 (vertices=134, convex hull=107, v0=6851) After retessellation of defect 4 (v0=6851), euler #=-73 (88264,262598,174261) : difference with theory (-73) = 0 CORRECTING DEFECT 5 (vertices=68, convex hull=85, v0=6958) After retessellation of defect 5 (v0=6958), euler #=-72 (88286,262700,174342) : difference with theory (-72) = 0 CORRECTING DEFECT 6 (vertices=19, convex hull=29, v0=7052) After retessellation of defect 6 (v0=7052), euler #=-71 (88288,262715,174356) : difference with theory (-71) = 0 CORRECTING DEFECT 7 (vertices=91, convex hull=58, v0=7109) After retessellation of defect 7 (v0=7109), euler #=-70 (88295,262761,174396) : difference with theory (-70) = 0 CORRECTING DEFECT 8 (vertices=60, convex hull=43, v0=7709) After retessellation of defect 8 (v0=7709), euler #=-69 (88299,262792,174424) : difference with theory (-69) = 0 CORRECTING DEFECT 9 (vertices=45, convex hull=72, v0=10531) After retessellation of defect 9 (v0=10531), euler #=-68 (88328,262906,174510) : difference with theory (-68) = 0 CORRECTING DEFECT 10 (vertices=39, convex hull=84, v0=10613) After retessellation of defect 10 (v0=10613), euler #=-67 (88347,262999,174585) : difference with theory (-67) = 0 CORRECTING DEFECT 11 (vertices=38, convex hull=86, v0=12206) After retessellation of defect 11 (v0=12206), euler #=-66 (88363,263079,174650) : difference with theory (-66) = 0 CORRECTING DEFECT 12 (vertices=54, convex hull=90, v0=12410) After retessellation of defect 12 (v0=12410), euler #=-65 (88391,263199,174743) : difference with theory (-65) = 0 CORRECTING DEFECT 13 (vertices=116, convex hull=135, v0=12722) After retessellation of defect 13 (v0=12722), euler #=-64 (88451,263437,174922) : difference with theory (-64) = 0 CORRECTING DEFECT 14 (vertices=54, convex hull=29, v0=13183) After retessellation of defect 14 (v0=13183), euler #=-63 (88455,263459,174941) : difference with theory (-63) = 0 CORRECTING DEFECT 15 (vertices=91, convex hull=45, v0=13767) After retessellation of defect 15 (v0=13767), euler #=-62 (88470,263520,174988) : difference with theory (-62) = 0 CORRECTING DEFECT 16 (vertices=82, convex hull=131, v0=14766) After retessellation of defect 16 (v0=14766), euler #=-61 (88527,263760,175172) : difference with theory (-61) = 0 CORRECTING DEFECT 17 (vertices=65, convex hull=45, v0=15379) After retessellation of defect 17 (v0=15379), euler #=-60 (88542,263825,175223) : difference with theory (-60) = 0 CORRECTING DEFECT 18 (vertices=18, convex hull=23, v0=15974) After retessellation of defect 18 (v0=15974), euler #=-59 (88543,263836,175234) : difference with theory (-59) = 0 CORRECTING DEFECT 19 (vertices=37, convex hull=65, v0=16654) After retessellation of defect 19 (v0=16654), euler #=-58 (88562,263916,175296) : difference with theory (-58) = 0 CORRECTING DEFECT 20 (vertices=38, convex hull=49, v0=17572) After retessellation of defect 20 (v0=17572), euler #=-57 (88575,263977,175345) : difference with theory (-57) = 0 CORRECTING DEFECT 21 (vertices=52, convex hull=99, v0=21712) After retessellation of defect 21 (v0=21712), euler #=-56 (88608,264120,175456) : difference with theory (-56) = 0 CORRECTING DEFECT 22 (vertices=18, convex hull=29, v0=23591) After retessellation of defect 22 (v0=23591), euler #=-55 (88610,264132,175467) : difference with theory (-55) = 0 CORRECTING DEFECT 23 (vertices=88, convex hull=95, v0=25136) After retessellation of defect 23 (v0=25136), euler #=-54 (88651,264301,175596) : difference with theory (-54) = 0 CORRECTING DEFECT 24 (vertices=56, convex hull=51, v0=26014) After retessellation of defect 24 (v0=26014), euler #=-53 (88664,264359,175642) : difference with theory (-53) = 0 CORRECTING DEFECT 25 (vertices=37, convex hull=64, v0=27854) After retessellation of defect 25 (v0=27854), euler #=-52 (88684,264446,175710) : difference with theory (-52) = 0 CORRECTING DEFECT 26 (vertices=84, convex hull=110, v0=33829) After retessellation of defect 26 (v0=33829), euler #=-51 (88722,264606,175833) : difference with theory (-51) = 0 CORRECTING DEFECT 27 (vertices=48, convex hull=78, v0=34251) After retessellation of defect 27 (v0=34251), euler #=-50 (88754,264727,175923) : difference with theory (-50) = 0 CORRECTING DEFECT 28 (vertices=67, convex hull=120, v0=35922) After retessellation of defect 28 (v0=35922), euler #=-49 (88793,264901,176059) : difference with theory (-49) = 0 CORRECTING DEFECT 29 (vertices=111, convex hull=86, v0=37033) After retessellation of defect 29 (v0=37033), euler #=-48 (88822,265026,176156) : difference with theory (-48) = 0 CORRECTING DEFECT 30 (vertices=81, convex hull=127, v0=40680) After retessellation of defect 30 (v0=40680), euler #=-47 (88865,265208,176296) : difference with theory (-47) = 0 CORRECTING DEFECT 31 (vertices=168, convex hull=130, v0=40843) After retessellation of defect 31 (v0=40843), euler #=-46 (88920,265436,176470) : difference with theory (-46) = 0 CORRECTING DEFECT 32 (vertices=29, convex hull=34, v0=41495) After retessellation of defect 32 (v0=41495), euler #=-45 (88925,265463,176493) : difference with theory (-45) = 0 CORRECTING DEFECT 33 (vertices=181, convex hull=146, v0=41886) After retessellation of defect 33 (v0=41886), euler #=-44 (88979,265690,176667) : difference with theory (-44) = 0 CORRECTING DEFECT 34 (vertices=15, convex hull=16, v0=42175) After retessellation of defect 34 (v0=42175), euler #=-43 (88980,265697,176674) : difference with theory (-43) = 0 CORRECTING DEFECT 35 (vertices=5, convex hull=23, v0=42347) After retessellation of defect 35 (v0=42347), euler #=-42 (88981,265707,176684) : difference with theory (-42) = 0 CORRECTING DEFECT 36 (vertices=28, convex hull=53, v0=56687) After retessellation of defect 36 (v0=56687), euler #=-41 (88996,265771,176734) : difference with theory (-41) = 0 CORRECTING DEFECT 37 (vertices=123, convex hull=119, v0=57445) After retessellation of defect 37 (v0=57445), euler #=-40 (89023,265902,176839) : difference with theory (-40) = 0 CORRECTING DEFECT 38 (vertices=74, convex hull=129, v0=59510) After retessellation of defect 38 (v0=59510), euler #=-39 (89053,266049,176957) : difference with theory (-39) = 0 CORRECTING DEFECT 39 (vertices=166, convex hull=38, v0=60505) After retessellation of defect 39 (v0=60505), euler #=-38 (89071,266116,177007) : difference with theory (-38) = 0 CORRECTING DEFECT 40 (vertices=17, convex hull=46, v0=63052) After retessellation of defect 40 (v0=63052), euler #=-37 (89080,266159,177042) : difference with theory (-37) = 0 CORRECTING DEFECT 41 (vertices=38, convex hull=82, v0=64292) After retessellation of defect 41 (v0=64292), euler #=-36 (89103,266260,177121) : difference with theory (-36) = 0 CORRECTING DEFECT 42 (vertices=45, convex hull=55, v0=64640) After retessellation of defect 42 (v0=64640), euler #=-35 (89118,266325,177172) : difference with theory (-35) = 0 CORRECTING DEFECT 43 (vertices=62, convex hull=103, v0=65461) After retessellation of defect 43 (v0=65461), euler #=-34 (89143,266441,177264) : difference with theory (-34) = 0 CORRECTING DEFECT 44 (vertices=42, convex hull=88, v0=69462) After retessellation of defect 44 (v0=69462), euler #=-33 (89163,266534,177338) : difference with theory (-33) = 0 CORRECTING DEFECT 45 (vertices=59, convex hull=39, v0=70002) After retessellation of defect 45 (v0=70002), euler #=-32 (89175,266582,177375) : difference with theory (-32) = 0 CORRECTING DEFECT 46 (vertices=38, convex hull=45, v0=70739) After retessellation of defect 46 (v0=70739), euler #=-31 (89184,266629,177414) : difference with theory (-31) = 0 CORRECTING DEFECT 47 (vertices=30, convex hull=79, v0=71249) After retessellation of defect 47 (v0=71249), euler #=-30 (89195,266694,177469) : difference with theory (-30) = 0 CORRECTING DEFECT 48 (vertices=22, convex hull=36, v0=72114) After retessellation of defect 48 (v0=72114), euler #=-29 (89199,266718,177490) : difference with theory (-29) = 0 CORRECTING DEFECT 49 (vertices=21, convex hull=33, v0=72788) After retessellation of defect 49 (v0=72788), euler #=-28 (89201,266734,177505) : difference with theory (-28) = 0 CORRECTING DEFECT 50 (vertices=40, convex hull=71, v0=72983) After retessellation of defect 50 (v0=72983), euler #=-27 (89216,266809,177566) : difference with theory (-27) = 0 CORRECTING DEFECT 51 (vertices=61, convex hull=139, v0=73947) After retessellation of defect 51 (v0=73947), euler #=-26 (89261,267002,177715) : difference with theory (-26) = 0 CORRECTING DEFECT 52 (vertices=93, convex hull=97, v0=74652) After retessellation of defect 52 (v0=74652), euler #=-25 (89296,267153,177832) : difference with theory (-25) = 0 CORRECTING DEFECT 53 (vertices=50, convex hull=81, v0=76513) After retessellation of defect 53 (v0=76513), euler #=-24 (89329,267285,177932) : difference with theory (-24) = 0 CORRECTING DEFECT 54 (vertices=143, convex hull=124, v0=76602) After retessellation of defect 54 (v0=76602), euler #=-22 (89379,267494,178093) : difference with theory (-23) = -1 CORRECTING DEFECT 55 (vertices=66, convex hull=102, v0=80887) After retessellation of defect 55 (v0=80887), euler #=-20 (89405,267624,178199) : difference with theory (-22) = -2 CORRECTING DEFECT 56 (vertices=77, convex hull=75, v0=80966) After retessellation of defect 56 (v0=80966), euler #=-19 (89439,267758,178300) : difference with theory (-21) = -2 CORRECTING DEFECT 57 (vertices=101, convex hull=129, v0=81128) After retessellation of defect 57 (v0=81128), euler #=-18 (89477,267926,178431) : difference with theory (-20) = -2 CORRECTING DEFECT 58 (vertices=72, convex hull=86, v0=83430) After retessellation of defect 58 (v0=83430), euler #=-17 (89508,268056,178531) : difference with theory (-19) = -2 CORRECTING DEFECT 59 (vertices=27, convex hull=43, v0=83583) After retessellation of defect 59 (v0=83583), euler #=-16 (89524,268121,178581) : difference with theory (-18) = -2 CORRECTING DEFECT 60 (vertices=40, convex hull=74, v0=83870) After retessellation of defect 60 (v0=83870), euler #=-15 (89544,268211,178652) : difference with theory (-17) = -2 CORRECTING DEFECT 61 (vertices=20, convex hull=55, v0=87895) After retessellation of defect 61 (v0=87895), euler #=-14 (89551,268254,178689) : difference with theory (-16) = -2 CORRECTING DEFECT 62 (vertices=18, convex hull=25, v0=88343) After retessellation of defect 62 (v0=88343), euler #=-13 (89553,268271,178705) : difference with theory (-15) = -2 CORRECTING DEFECT 63 (vertices=51, convex hull=69, v0=88605) After retessellation of defect 63 (v0=88605), euler #=-12 (89579,268382,178791) : difference with theory (-14) = -2 CORRECTING DEFECT 64 (vertices=80, convex hull=59, v0=88611) After retessellation of defect 64 (v0=88611), euler #=-12 (89588,268434,178834) : difference with theory (-13) = -1 CORRECTING DEFECT 65 (vertices=46, convex hull=57, v0=88851) After retessellation of defect 65 (v0=88851), euler #=-12 (89598,268491,178881) : difference with theory (-12) = 0 CORRECTING DEFECT 66 (vertices=80, convex hull=67, v0=90415) After retessellation of defect 66 (v0=90415), euler #=-11 (89619,268581,178951) : difference with theory (-11) = 0 CORRECTING DEFECT 67 (vertices=28, convex hull=38, v0=90779) After retessellation of defect 67 (v0=90779), euler #=-10 (89629,268626,178987) : difference with theory (-10) = 0 CORRECTING DEFECT 68 (vertices=146, convex hull=117, v0=91148) After retessellation of defect 68 (v0=91148), euler #=-9 (89675,268817,179133) : difference with theory (-9) = 0 CORRECTING DEFECT 69 (vertices=28, convex hull=67, v0=91493) After retessellation of defect 69 (v0=91493), euler #=-8 (89693,268894,179193) : difference with theory (-8) = 0 CORRECTING DEFECT 70 (vertices=29, convex hull=32, v0=92553) After retessellation of defect 70 (v0=92553), euler #=-7 (89698,268923,179218) : difference with theory (-7) = 0 CORRECTING DEFECT 71 (vertices=41, convex hull=75, v0=92595) After retessellation of defect 71 (v0=92595), euler #=-6 (89722,269023,179295) : difference with theory (-6) = 0 CORRECTING DEFECT 72 (vertices=44, convex hull=73, v0=92618) After retessellation of defect 72 (v0=92618), euler #=-5 (89746,269120,179369) : difference with theory (-5) = 0 CORRECTING DEFECT 73 (vertices=47, convex hull=35, v0=93469) After retessellation of defect 73 (v0=93469), euler #=-4 (89751,269148,179393) : difference with theory (-4) = 0 CORRECTING DEFECT 74 (vertices=26, convex hull=45, v0=94191) After retessellation of defect 74 (v0=94191), euler #=-3 (89755,269176,179418) : difference with theory (-3) = 0 CORRECTING DEFECT 75 (vertices=33, convex hull=42, v0=94213) After retessellation of defect 75 (v0=94213), euler #=-2 (89761,269210,179447) : difference with theory (-2) = 0 CORRECTING DEFECT 76 (vertices=14, convex hull=21, v0=94361) After retessellation of defect 76 (v0=94361), euler #=-1 (89762,269221,179458) : difference with theory (-1) = 0 CORRECTING DEFECT 77 (vertices=114, convex hull=95, v0=94496) After retessellation of defect 77 (v0=94496), euler #=0 (89796,269364,179568) : difference with theory (0) = 0 CORRECTING DEFECT 78 (vertices=15, convex hull=22, v0=94608) After retessellation of defect 78 (v0=94608), euler #=1 (89798,269381,179584) : difference with theory (1) = 0 CORRECTING DEFECT 79 (vertices=11, convex hull=23, v0=95070) After retessellation of defect 79 (v0=95070), euler #=2 (89800,269394,179596) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.05-->14.67) (max @ vno 3914 --> 90217) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.05-->14.67) (max @ vno 3914 --> 90217) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 240 mutations (35.2%), 442 crossovers (64.8%), 131 vertices were eliminated building final representation... 5386 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=89800, nf=179596, ne=269394, g=0) writing corrected surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.8 minutes 0 defective edges removing intersecting faces 000: 677 intersecting 001: 39 intersecting 002: 7 intersecting mris_fix_topology utimesec 1581.023372 mris_fix_topology stimesec 0.219963 mris_fix_topology ru_maxrss 331624 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 57446 mris_fix_topology ru_majflt 11 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 12824 mris_fix_topology ru_oublock 8552 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 132 mris_fix_topology ru_nivcsw 10670 FSRUNTIME@ mris_fix_topology lh 0.4473 hours 1 threads #@# Fix Topology rh Fri 15 Mar 2024 08:45:31 PM CET mris_fix_topology -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 LS5K rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-92 (nv=91476, nf=183136, ne=274704, g=47) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 6221 ambiguous faces found in tessellation segmenting defects... 59 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 39 into 36 58 defects to be corrected 0 vertices coincident reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2112 (-4.6056) -vertex loglikelihood: -6.4812 (-3.2406) -normal dot loglikelihood: -3.6283 (-3.6283) -quad curv loglikelihood: -6.0860 (-3.0430) Total Loglikelihood : -25.4067 CORRECTING DEFECT 0 (vertices=40, convex hull=51, v0=26) After retessellation of defect 0 (v0=26), euler #=-56 (87610,261073,173407) : difference with theory (-55) = 1 CORRECTING DEFECT 1 (vertices=33, convex hull=67, v0=245) After retessellation of defect 1 (v0=245), euler #=-55 (87629,261160,173476) : difference with theory (-54) = 1 CORRECTING DEFECT 2 (vertices=219, convex hull=102, v0=422) After retessellation of defect 2 (v0=422), euler #=-54 (87659,261302,173589) : difference with theory (-53) = 1 CORRECTING DEFECT 3 (vertices=20, convex hull=20, v0=3031) After retessellation of defect 3 (v0=3031), euler #=-53 (87660,261312,173599) : difference with theory (-52) = 1 CORRECTING DEFECT 4 (vertices=222, convex hull=126, v0=5071) After retessellation of defect 4 (v0=5071), euler #=-52 (87714,261528,173762) : difference with theory (-51) = 1 CORRECTING DEFECT 5 (vertices=97, convex hull=46, v0=7028) After retessellation of defect 5 (v0=7028), euler #=-51 (87727,261586,173808) : difference with theory (-50) = 1 CORRECTING DEFECT 6 (vertices=48, convex hull=71, v0=7633) After retessellation of defect 6 (v0=7633), euler #=-50 (87738,261644,173856) : difference with theory (-49) = 1 CORRECTING DEFECT 7 (vertices=121, convex hull=110, v0=13053) After retessellation of defect 7 (v0=13053), euler #=-49 (87754,261744,173941) : difference with theory (-48) = 1 CORRECTING DEFECT 8 (vertices=22, convex hull=62, v0=13412) After retessellation of defect 8 (v0=13412), euler #=-48 (87766,261803,173989) : difference with theory (-47) = 1 CORRECTING DEFECT 9 (vertices=26, convex hull=71, v0=15413) After retessellation of defect 9 (v0=15413), euler #=-47 (87781,261878,174050) : difference with theory (-46) = 1 CORRECTING DEFECT 10 (vertices=150, convex hull=133, v0=18065) After retessellation of defect 10 (v0=18065), euler #=-46 (87813,262032,174173) : difference with theory (-45) = 1 CORRECTING DEFECT 11 (vertices=13, convex hull=21, v0=20579) After retessellation of defect 11 (v0=20579), euler #=-45 (87813,262037,174179) : difference with theory (-44) = 1 CORRECTING DEFECT 12 (vertices=55, convex hull=71, v0=21902) After retessellation of defect 12 (v0=21902), euler #=-44 (87847,262173,174282) : difference with theory (-43) = 1 CORRECTING DEFECT 13 (vertices=45, convex hull=64, v0=25833) After retessellation of defect 13 (v0=25833), euler #=-43 (87866,262258,174349) : difference with theory (-42) = 1 CORRECTING DEFECT 14 (vertices=61, convex hull=86, v0=25971) After retessellation of defect 14 (v0=25971), euler #=-42 (87904,262413,174467) : difference with theory (-41) = 1 CORRECTING DEFECT 15 (vertices=24, convex hull=45, v0=28980) After retessellation of defect 15 (v0=28980), euler #=-41 (87913,262456,174502) : difference with theory (-40) = 1 CORRECTING DEFECT 16 (vertices=81, convex hull=109, v0=34147) After retessellation of defect 16 (v0=34147), euler #=-40 (87929,262553,174584) : difference with theory (-39) = 1 CORRECTING DEFECT 17 (vertices=87, convex hull=134, v0=34958) After retessellation of defect 17 (v0=34958), euler #=-39 (87955,262694,174700) : difference with theory (-38) = 1 CORRECTING DEFECT 18 (vertices=261, convex hull=200, v0=39053) After retessellation of defect 18 (v0=39053), euler #=-38 (88053,263090,174999) : difference with theory (-37) = 1 CORRECTING DEFECT 19 (vertices=37, convex hull=71, v0=42248) After retessellation of defect 19 (v0=42248), euler #=-37 (88066,263158,175055) : difference with theory (-36) = 1 CORRECTING DEFECT 20 (vertices=21, convex hull=32, v0=44419) After retessellation of defect 20 (v0=44419), euler #=-36 (88071,263183,175076) : difference with theory (-35) = 1 CORRECTING DEFECT 21 (vertices=51, convex hull=99, v0=45666) After retessellation of defect 21 (v0=45666), euler #=-35 (88098,263302,175169) : difference with theory (-34) = 1 CORRECTING DEFECT 22 (vertices=194, convex hull=148, v0=46502) After retessellation of defect 22 (v0=46502), euler #=-34 (88158,263551,175359) : difference with theory (-33) = 1 CORRECTING DEFECT 23 (vertices=7, convex hull=11, v0=49375) After retessellation of defect 23 (v0=49375), euler #=-33 (88159,263557,175365) : difference with theory (-32) = 1 CORRECTING DEFECT 24 (vertices=92, convex hull=93, v0=51148) After retessellation of defect 24 (v0=51148), euler #=-32 (88196,263708,175480) : difference with theory (-31) = 1 CORRECTING DEFECT 25 (vertices=62, convex hull=91, v0=51953) After retessellation of defect 25 (v0=51953), euler #=-31 (88223,263828,175574) : difference with theory (-30) = 1 CORRECTING DEFECT 26 (vertices=200, convex hull=169, v0=54668) After retessellation of defect 26 (v0=54668), euler #=-30 (88293,264121,175798) : difference with theory (-29) = 1 CORRECTING DEFECT 27 (vertices=58, convex hull=43, v0=54975) After retessellation of defect 27 (v0=54975), euler #=-29 (88308,264181,175844) : difference with theory (-28) = 1 CORRECTING DEFECT 28 (vertices=123, convex hull=130, v0=56599) After retessellation of defect 28 (v0=56599), euler #=-28 (88339,264334,175967) : difference with theory (-27) = 1 CORRECTING DEFECT 29 (vertices=29, convex hull=87, v0=56817) After retessellation of defect 29 (v0=56817), euler #=-27 (88355,264415,176033) : difference with theory (-26) = 1 CORRECTING DEFECT 30 (vertices=44, convex hull=28, v0=58721) After retessellation of defect 30 (v0=58721), euler #=-26 (88363,264445,176056) : difference with theory (-25) = 1 CORRECTING DEFECT 31 (vertices=5, convex hull=23, v0=59120) After retessellation of defect 31 (v0=59120), euler #=-25 (88363,264452,176064) : difference with theory (-24) = 1 CORRECTING DEFECT 32 (vertices=34, convex hull=25, v0=59165) After retessellation of defect 32 (v0=59165), euler #=-24 (88371,264487,176092) : difference with theory (-23) = 1 CORRECTING DEFECT 33 (vertices=9, convex hull=21, v0=59603) After retessellation of defect 33 (v0=59603), euler #=-23 (88374,264502,176105) : difference with theory (-22) = 1 CORRECTING DEFECT 34 (vertices=113, convex hull=34, v0=62976) After retessellation of defect 34 (v0=62976), euler #=-22 (88383,264541,176136) : difference with theory (-21) = 1 CORRECTING DEFECT 35 (vertices=75, convex hull=101, v0=63312) After retessellation of defect 35 (v0=63312), euler #=-21 (88422,264704,176261) : difference with theory (-20) = 1 CORRECTING DEFECT 36 (vertices=183, convex hull=163, v0=65545) After retessellation of defect 36 (v0=65545), euler #=-19 (88481,264970,176470) : difference with theory (-19) = 0 CORRECTING DEFECT 37 (vertices=169, convex hull=140, v0=67461) After retessellation of defect 37 (v0=67461), euler #=-18 (88537,265209,176654) : difference with theory (-18) = 0 CORRECTING DEFECT 38 (vertices=42, convex hull=73, v0=67724) After retessellation of defect 38 (v0=67724), euler #=-17 (88547,265265,176701) : difference with theory (-17) = 0 CORRECTING DEFECT 39 (vertices=51, convex hull=82, v0=68632) After retessellation of defect 39 (v0=68632), euler #=-16 (88565,265354,176773) : difference with theory (-16) = 0 CORRECTING DEFECT 40 (vertices=53, convex hull=74, v0=68814) After retessellation of defect 40 (v0=68814), euler #=-15 (88591,265463,176857) : difference with theory (-15) = 0 CORRECTING DEFECT 41 (vertices=67, convex hull=52, v0=73388) After retessellation of defect 41 (v0=73388), euler #=-14 (88600,265513,176899) : difference with theory (-14) = 0 CORRECTING DEFECT 42 (vertices=10, convex hull=22, v0=74370) After retessellation of defect 42 (v0=74370), euler #=-13 (88600,265518,176905) : difference with theory (-13) = 0 CORRECTING DEFECT 43 (vertices=19, convex hull=25, v0=75320) After retessellation of defect 43 (v0=75320), euler #=-12 (88604,265537,176921) : difference with theory (-12) = 0 CORRECTING DEFECT 44 (vertices=7, convex hull=27, v0=83823) After retessellation of defect 44 (v0=83823), euler #=-11 (88606,265552,176935) : difference with theory (-11) = 0 CORRECTING DEFECT 45 (vertices=45, convex hull=33, v0=84512) After retessellation of defect 45 (v0=84512), euler #=-10 (88613,265582,176959) : difference with theory (-10) = 0 CORRECTING DEFECT 46 (vertices=28, convex hull=34, v0=86781) After retessellation of defect 46 (v0=86781), euler #=-9 (88619,265611,176983) : difference with theory (-9) = 0 CORRECTING DEFECT 47 (vertices=50, convex hull=88, v0=86922) After retessellation of defect 47 (v0=86922), euler #=-8 (88645,265726,177073) : difference with theory (-8) = 0 CORRECTING DEFECT 48 (vertices=22, convex hull=47, v0=87648) After retessellation of defect 48 (v0=87648), euler #=-7 (88653,265766,177106) : difference with theory (-7) = 0 CORRECTING DEFECT 49 (vertices=51, convex hull=78, v0=88471) After retessellation of defect 49 (v0=88471), euler #=-6 (88683,265891,177202) : difference with theory (-6) = 0 CORRECTING DEFECT 50 (vertices=28, convex hull=29, v0=88580) After retessellation of defect 50 (v0=88580), euler #=-5 (88686,265908,177217) : difference with theory (-5) = 0 CORRECTING DEFECT 51 (vertices=17, convex hull=37, v0=88957) After retessellation of defect 51 (v0=88957), euler #=-4 (88691,265936,177241) : difference with theory (-4) = 0 CORRECTING DEFECT 52 (vertices=37, convex hull=57, v0=89151) After retessellation of defect 52 (v0=89151), euler #=-3 (88710,266017,177304) : difference with theory (-3) = 0 CORRECTING DEFECT 53 (vertices=39, convex hull=68, v0=89907) After retessellation of defect 53 (v0=89907), euler #=-2 (88734,266114,177378) : difference with theory (-2) = 0 CORRECTING DEFECT 54 (vertices=43, convex hull=74, v0=90259) After retessellation of defect 54 (v0=90259), euler #=-1 (88756,266209,177452) : difference with theory (-1) = 0 CORRECTING DEFECT 55 (vertices=43, convex hull=31, v0=90419) After retessellation of defect 55 (v0=90419), euler #=0 (88760,266232,177472) : difference with theory (0) = 0 CORRECTING DEFECT 56 (vertices=52, convex hull=78, v0=90605) After retessellation of defect 56 (v0=90605), euler #=1 (88787,266345,177559) : difference with theory (1) = 0 CORRECTING DEFECT 57 (vertices=33, convex hull=29, v0=91331) After retessellation of defect 57 (v0=91331), euler #=2 (88790,266364,177576) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.07-->10.13) (max @ vno 47869 --> 50888) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.07-->10.13) (max @ vno 47869 --> 50888) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 190 mutations (32.5%), 394 crossovers (67.5%), 143 vertices were eliminated building final representation... 2686 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=88790, nf=177576, ne=266364, g=0) writing corrected surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.1 minutes 0 defective edges removing intersecting faces 000: 361 intersecting 001: 6 intersecting mris_fix_topology utimesec 906.862567 mris_fix_topology stimesec 0.223992 mris_fix_topology ru_maxrss 319180 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 81611 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 11496 mris_fix_topology ru_oublock 8408 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 324 mris_fix_topology ru_nivcsw 1709 FSRUNTIME@ mris_fix_topology rh 0.2524 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 89800 - 269394 + 179596 = 2 --> 0 holes F =2V-4: 179596 = 179600-4 (0) 2E=3F: 538788 = 538788 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 88790 - 266364 + 177576 = 2 --> 0 holes F =2V-4: 177576 = 177580-4 (0) 2E=3F: 532728 = 532728 (0) total defect index = 0 /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 156 intersecting 001: 31 intersecting 002: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 20 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fri 15 Mar 2024 09:00:45 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs LS5K lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/filled.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/brain.finalsurfs.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/../mri/aseg.presurf.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... 11383 bright wm thresholded. 182280 bright non-wm voxels segmented. reading original surface position from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.orig... computing class statistics... border white: 178984 voxels (1.07%) border gray 266091 voxels (1.59%) WM (93.0): 93.2 +- 8.6 [70.0 --> 110.0] GM (67.0) : 67.3 +- 13.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.4 (was 70) setting MAX_BORDER_WHITE to 104.6 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 33.8 (was 40) setting MAX_GRAY to 87.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.24 (0.01-->4.18) (max @ vno 37955 --> 39869) face area 0.28 +- 0.13 (0.00-->2.86) mean absolute distance = 0.71 +- 0.79 2495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-7.8, GM=61+-8.7 mean inside = 88.1, mean outside = 70.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=72.5, 103 (103) missing vertices, mean dist 0.5 [0.4 (%23.3)->0.8 (%76.7))] %78 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.29 (0.10-->3.96) (max @ vno 75418 --> 89454) face area 0.28 +- 0.15 (0.00-->3.28) mean absolute distance = 0.31 +- 0.54 1806 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2480538.8, rms=11.200 001: dt: 0.5000, sse=1533603.5, rms=8.417 (24.853%) 002: dt: 0.5000, sse=1075731.5, rms=6.619 (21.358%) 003: dt: 0.5000, sse=838283.7, rms=5.444 (17.757%) 004: dt: 0.5000, sse=713111.9, rms=4.697 (13.710%) 005: dt: 0.5000, sse=644172.8, rms=4.238 (9.774%) 006: dt: 0.5000, sse=613271.9, rms=3.980 (6.084%) 007: dt: 0.5000, sse=590903.9, rms=3.828 (3.822%) 008: dt: 0.5000, sse=581162.5, rms=3.740 (2.293%) 009: dt: 0.5000, sse=575266.1, rms=3.685 (1.495%) rms = 3.65, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=571336.2, rms=3.648 (0.982%) 011: dt: 0.2500, sse=464026.6, rms=2.522 (30.868%) 012: dt: 0.2500, sse=442349.1, rms=2.259 (10.453%) 013: dt: 0.2500, sse=441101.8, rms=2.195 (2.814%) rms = 2.15, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=435745.4, rms=2.153 (1.917%) rms = 2.10, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=431967.9, rms=2.105 (2.230%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=74.4, 105 (23) missing vertices, mean dist -0.1 [0.3 (%64.1)->0.3 (%35.9))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.94 +- 0.29 (0.08-->3.96) (max @ vno 50207 --> 50221) face area 0.36 +- 0.19 (0.00-->4.51) mean absolute distance = 0.29 +- 0.45 1912 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=689562.4, rms=3.661 016: dt: 0.5000, sse=596753.5, rms=2.801 (23.490%) rms = 3.12, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=544790.9, rms=2.179 (22.208%) 018: dt: 0.2500, sse=534590.5, rms=1.930 (11.414%) 019: dt: 0.2500, sse=522871.4, rms=1.857 (3.810%) rms = 1.84, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=521387.3, rms=1.836 (1.146%) rms = 1.80, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=518770.8, rms=1.799 (2.018%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=75.8, 130 (15) missing vertices, mean dist -0.1 [0.3 (%58.9)->0.3 (%41.1))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.94 +- 0.28 (0.07-->3.97) (max @ vno 50207 --> 50221) face area 0.36 +- 0.19 (0.00-->4.53) mean absolute distance = 0.29 +- 0.41 1985 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=570451.1, rms=2.493 rms = 2.47, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=573446.1, rms=2.468 (1.036%) 023: dt: 0.2500, sse=519521.9, rms=1.762 (28.578%) 024: dt: 0.2500, sse=510786.2, rms=1.634 (7.281%) rms = 1.64, time step reduction 2 of 3 to 0.125... rms = 1.61, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=508632.5, rms=1.606 (1.709%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=76.5, 141 (11) missing vertices, mean dist -0.0 [0.3 (%51.8)->0.3 (%48.2))] %85 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=519671.4, rms=1.830 rms = 1.94, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=497992.8, rms=1.436 (21.507%) 027: dt: 0.2500, sse=488781.7, rms=1.239 (13.743%) rms = 1.24, time step reduction 2 of 3 to 0.125... rms = 1.22, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=487262.5, rms=1.225 (1.114%) positioning took 0.2 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6364 vertices erasing segment 1 (vno[0] = 27986) erasing segment 2 (vno[0] = 43651) erasing segment 3 (vno[0] = 56866) erasing segment 4 (vno[0] = 58754) erasing segment 5 (vno[0] = 59822) erasing segment 6 (vno[0] = 64966) erasing segment 7 (vno[0] = 68184) writing cortex label to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label... writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.area vertex spacing 0.93 +- 0.29 (0.04-->3.96) (max @ vno 50207 --> 50221) face area 0.36 +- 0.19 (0.00-->4.35) refinement took 1.9 minutes #-------------------------------------------- #@# Make White Surf rh Fri 15 Mar 2024 09:02:38 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs LS5K rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/filled.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/brain.finalsurfs.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/../mri/aseg.presurf.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... 11383 bright wm thresholded. 182280 bright non-wm voxels segmented. reading original surface position from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.orig... computing class statistics... border white: 178984 voxels (1.07%) border gray 266091 voxels (1.59%) WM (93.0): 93.2 +- 8.6 [70.0 --> 110.0] GM (67.0) : 67.3 +- 13.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.4 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 34.8 (was 40) setting MAX_GRAY to 89.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 48.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.04-->4.40) (max @ vno 59553 --> 88309) face area 0.28 +- 0.13 (0.00-->3.05) mean absolute distance = 0.69 +- 0.77 2436 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-7.8, GM=62+-7.0 mean inside = 88.6, mean outside = 70.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=73.4, 102 (102) missing vertices, mean dist 0.5 [0.4 (%25.9)->0.8 (%74.1))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.28 (0.10-->4.81) (max @ vno 54515 --> 59553) face area 0.28 +- 0.14 (0.00-->2.69) mean absolute distance = 0.30 +- 0.51 1787 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2399616.0, rms=11.016 001: dt: 0.5000, sse=1451825.2, rms=8.141 (26.091%) 002: dt: 0.5000, sse=1019372.2, rms=6.360 (21.880%) 003: dt: 0.5000, sse=801597.6, rms=5.233 (17.729%) 004: dt: 0.5000, sse=686985.1, rms=4.537 (13.286%) 005: dt: 0.5000, sse=630933.4, rms=4.144 (8.669%) 006: dt: 0.5000, sse=601482.1, rms=3.919 (5.424%) 007: dt: 0.5000, sse=587182.6, rms=3.800 (3.038%) 008: dt: 0.5000, sse=579933.7, rms=3.727 (1.937%) rms = 3.68, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=574064.9, rms=3.677 (1.325%) 010: dt: 0.2500, sse=463091.6, rms=2.541 (30.896%) 011: dt: 0.2500, sse=442473.4, rms=2.275 (10.485%) 012: dt: 0.2500, sse=437735.4, rms=2.205 (3.067%) rms = 2.17, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=436624.1, rms=2.174 (1.410%) 014: dt: 0.1250, sse=429236.5, rms=2.073 (4.627%) rms = 2.04, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=427651.3, rms=2.045 (1.361%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=75.6, 164 (52) missing vertices, mean dist -0.1 [0.3 (%67.3)->0.3 (%32.7))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.93 +- 0.28 (0.10-->4.60) (max @ vno 54515 --> 59553) face area 0.36 +- 0.18 (0.00-->3.31) mean absolute distance = 0.27 +- 0.43 2066 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=707074.7, rms=3.843 016: dt: 0.5000, sse=602981.0, rms=2.904 (24.449%) rms = 3.10, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=543827.8, rms=2.203 (24.145%) 018: dt: 0.2500, sse=524528.1, rms=1.947 (11.623%) 019: dt: 0.2500, sse=517456.6, rms=1.865 (4.189%) rms = 1.87, time step reduction 2 of 3 to 0.125... rms = 1.82, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=514570.6, rms=1.819 (2.484%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.0, 165 (42) missing vertices, mean dist -0.1 [0.3 (%59.5)->0.2 (%40.5))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.93 +- 0.28 (0.11-->4.45) (max @ vno 54515 --> 59553) face area 0.36 +- 0.18 (0.00-->3.30) mean absolute distance = 0.27 +- 0.39 2201 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=567212.2, rms=2.530 rms = 2.61, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=528031.6, rms=1.970 (22.111%) 022: dt: 0.2500, sse=514285.4, rms=1.711 (13.155%) rms = 1.74, time step reduction 2 of 3 to 0.125... 023: dt: 0.1250, sse=507095.6, rms=1.651 (3.492%) 024: dt: 0.1250, sse=501976.3, rms=1.581 (4.286%) rms = 1.56, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=501081.5, rms=1.558 (1.425%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.6, 160 (38) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.3 (%47.7))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=513806.9, rms=1.819 rms = 2.12, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=491807.3, rms=1.429 (21.464%) 027: dt: 0.2500, sse=505103.8, rms=1.365 (4.497%) rms = 1.43, time step reduction 2 of 3 to 0.125... 028: dt: 0.1250, sse=488586.5, rms=1.298 (4.890%) 029: dt: 0.1250, sse=482599.8, rms=1.231 (5.114%) rms = 1.20, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=479865.3, rms=1.199 (2.644%) positioning took 0.3 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6354 vertices erasing segment 1 (vno[0] = 42825) erasing segment 2 (vno[0] = 50042) erasing segment 3 (vno[0] = 50952) erasing segment 4 (vno[0] = 56353) erasing segment 5 (vno[0] = 58025) erasing segment 6 (vno[0] = 66695) writing cortex label to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label... writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.curv writing smoothed area to rh.area writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.area vertex spacing 0.93 +- 0.27 (0.04-->4.43) (max @ vno 54515 --> 59553) face area 0.36 +- 0.18 (0.00-->3.15) refinement took 2.0 minutes #-------------------------------------------- #@# Smooth2 lh Fri 15 Mar 2024 09:04:39 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Fri 15 Mar 2024 09:04:42 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri 15 Mar 2024 09:04:44 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 41.0 mm, total surface area = 57831 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.191 (target=0.015) step 005: RMS=0.135 (target=0.015) step 010: RMS=0.108 (target=0.015) step 015: RMS=0.090 (target=0.015) step 020: RMS=0.077 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.051 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.035 (target=0.015) step 060: RMS=0.034 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 22.132110 mris_inflate stimesec 0.067988 mris_inflate ru_maxrss 121844 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 15211 mris_inflate ru_majflt 2 mris_inflate ru_nswap 0 mris_inflate ru_inblock 56 mris_inflate ru_oublock 7024 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 139 mris_inflate ru_nivcsw 211 #-------------------------------------------- #@# Inflation2 rh Fri 15 Mar 2024 09:05:07 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_inflate -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 40.3 mm, total surface area = 57092 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.189 (target=0.015) step 005: RMS=0.134 (target=0.015) step 010: RMS=0.106 (target=0.015) step 015: RMS=0.088 (target=0.015) step 020: RMS=0.072 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.031 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 23.302365 mris_inflate stimesec 0.055996 mris_inflate ru_maxrss 120368 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 14830 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 6944 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 186 mris_inflate ru_nivcsw 437 #-------------------------------------------- #@# Curv .H and .K lh Fri 15 Mar 2024 09:05:31 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_curvature -w lh.white.preaparc total integrated curvature = 30.090*4pi (378.127) --> -29 handles ICI = 158.2, FI = 1178.3, variation=19733.797 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 55 vertices thresholded to be in k1 ~ [-0.36 1.82], k2 ~ [-0.17 0.23] total integrated curvature = 0.389*4pi (4.893) --> 1 handles ICI = 1.1, FI = 6.4, variation=114.472 78 vertices thresholded to be in [-0.12 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 63 vertices thresholded to be in [-0.19 0.56] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.020, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Fri 15 Mar 2024 09:06:24 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_curvature -w rh.white.preaparc total integrated curvature = 26.945*4pi (338.605) --> -26 handles ICI = 151.6, FI = 1222.6, variation=20086.329 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 95 vertices thresholded to be in k1 ~ [-0.20 2.90], k2 ~ [-0.17 0.08] total integrated curvature = 0.468*4pi (5.882) --> 1 handles ICI = 1.1, FI = 5.8, variation=105.301 82 vertices thresholded to be in [-0.27 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 59 vertices thresholded to be in [-0.13 0.75] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.019, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Fri 15 Mar 2024 09:07:15 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm LS5K lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ LS5K/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 153 ] Gb_filter = 0 WARN: S lookup min: -0.948898 WARN: S explicit min: 0.000000 vertex = 405 #----------------------------------------- #@# Curvature Stats rh Fri 15 Mar 2024 09:07:18 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm LS5K rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ LS5K/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 171 ] Gb_filter = 0 WARN: S lookup min: -0.045286 WARN: S explicit min: 0.000000 vertex = 163 #-------------------------------------------- #@# Sphere lh Fri 15 Mar 2024 09:07:23 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.342... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %22.23 pass 1: epoch 2 of 3 starting distance error %22.15 unfolding complete - removing small folds... starting distance error %21.90 removing remaining folds... final distance error %21.95 MRISunfold() return, current seed 1234 -01: dt=0.0000, 104 negative triangles 280: dt=0.9900, 104 negative triangles 281: dt=0.9900, 56 negative triangles 282: dt=0.9900, 50 negative triangles 283: dt=0.9900, 47 negative triangles 284: dt=0.9900, 46 negative triangles 285: dt=0.9900, 44 negative triangles 286: dt=0.9900, 47 negative triangles 287: dt=0.9900, 48 negative triangles 288: dt=0.9900, 34 negative triangles 289: dt=0.9900, 32 negative triangles 290: dt=0.9900, 27 negative triangles 291: dt=0.9900, 36 negative triangles 292: dt=0.9900, 30 negative triangles 293: dt=0.9900, 34 negative triangles 294: dt=0.9900, 28 negative triangles 295: dt=0.9900, 29 negative triangles 296: dt=0.9900, 23 negative triangles 297: dt=0.9900, 27 negative triangles 298: dt=0.9900, 27 negative triangles 299: dt=0.9900, 21 negative triangles 300: dt=0.9900, 20 negative triangles 301: dt=0.9900, 22 negative triangles 302: dt=0.9900, 20 negative triangles 303: dt=0.9900, 21 negative triangles 304: dt=0.9900, 17 negative triangles 305: dt=0.9900, 17 negative triangles 306: dt=0.9900, 14 negative triangles 307: dt=0.9900, 15 negative triangles 308: dt=0.9900, 15 negative triangles 309: dt=0.9900, 17 negative triangles 310: dt=0.9900, 16 negative triangles 311: dt=0.9900, 10 negative triangles 312: dt=0.9900, 8 negative triangles 313: dt=0.9900, 6 negative triangles 314: dt=0.9900, 10 negative triangles 315: dt=0.9900, 9 negative triangles 316: dt=0.9900, 11 negative triangles 317: dt=0.9900, 10 negative triangles 318: dt=0.9900, 9 negative triangles 319: dt=0.9900, 8 negative triangles 320: dt=0.9900, 13 negative triangles 321: dt=0.9900, 9 negative triangles 322: dt=0.9900, 8 negative triangles 323: dt=0.9405, 10 negative triangles 324: dt=0.9405, 10 negative triangles 325: dt=0.9405, 10 negative triangles 326: dt=0.9405, 8 negative triangles 327: dt=0.9405, 8 negative triangles 328: dt=0.9405, 9 negative triangles 329: dt=0.9405, 7 negative triangles 330: dt=0.9405, 7 negative triangles 331: dt=0.9405, 7 negative triangles 332: dt=0.9405, 4 negative triangles 333: dt=0.9405, 6 negative triangles 334: dt=0.9405, 5 negative triangles 335: dt=0.9405, 6 negative triangles 336: dt=0.9405, 5 negative triangles 337: dt=0.9405, 5 negative triangles 338: dt=0.9405, 4 negative triangles 339: dt=0.9405, 2 negative triangles 340: dt=0.9405, 2 negative triangles 341: dt=0.9405, 2 negative triangles 342: dt=0.9405, 3 negative triangles 343: dt=0.9405, 4 negative triangles 344: dt=0.9405, 2 negative triangles 345: dt=0.9405, 2 negative triangles 346: dt=0.9405, 1 negative triangles 347: dt=0.9405, 1 negative triangles 348: dt=0.9405, 1 negative triangles 349: dt=0.9405, 1 negative triangles 350: dt=0.9405, 1 negative triangles 351: dt=0.9405, 1 negative triangles 352: dt=0.9405, 1 negative triangles 353: dt=0.9405, 1 negative triangles 354: dt=0.9405, 1 negative triangles 355: dt=0.9405, 1 negative triangles 356: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.39 hours mris_sphere utimesec 1392.067390 mris_sphere stimesec 0.443920 mris_sphere ru_maxrss 165536 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 84730 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 6320 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 196 mris_sphere ru_nivcsw 13294 FSRUNTIME@ mris_sphere 0.3942 hours 1 threads #-------------------------------------------- #@# Sphere rh Fri 15 Mar 2024 09:31:02 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_sphere -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.361... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %40.26 pass 1: epoch 2 of 3 starting distance error %20.70 unfolding complete - removing small folds... starting distance error %20.51 removing remaining folds... final distance error %20.54 MRISunfold() return, current seed 1234 -01: dt=0.0000, 84 negative triangles 221: dt=0.9900, 84 negative triangles 222: dt=0.9900, 32 negative triangles 223: dt=0.9900, 22 negative triangles 224: dt=0.9900, 28 negative triangles 225: dt=0.9900, 23 negative triangles 226: dt=0.9900, 22 negative triangles 227: dt=0.9900, 18 negative triangles 228: dt=0.9900, 19 negative triangles 229: dt=0.9900, 16 negative triangles 230: dt=0.9900, 11 negative triangles 231: dt=0.9900, 13 negative triangles 232: dt=0.9900, 13 negative triangles 233: dt=0.9900, 14 negative triangles 234: dt=0.9900, 12 negative triangles 235: dt=0.9900, 16 negative triangles 236: dt=0.9900, 12 negative triangles 237: dt=0.9900, 9 negative triangles 238: dt=0.9900, 13 negative triangles 239: dt=0.9900, 6 negative triangles 240: dt=0.9900, 8 negative triangles 241: dt=0.9900, 5 negative triangles 242: dt=0.9900, 7 negative triangles 243: dt=0.9900, 9 negative triangles 244: dt=0.9900, 3 negative triangles 245: dt=0.9900, 8 negative triangles 246: dt=0.9900, 4 negative triangles 247: dt=0.9900, 3 negative triangles 248: dt=0.9900, 5 negative triangles 249: dt=0.9900, 2 negative triangles 250: dt=0.9900, 4 negative triangles 251: dt=0.9900, 3 negative triangles 252: dt=0.9900, 3 negative triangles 253: dt=0.9900, 1 negative triangles 254: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.22 hours mris_sphere utimesec 805.317923 mris_sphere stimesec 0.135993 mris_sphere ru_maxrss 163628 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 25973 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 24 mris_sphere ru_oublock 6256 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 239 mris_sphere ru_nivcsw 1853 FSRUNTIME@ mris_sphere 0.2238 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Fri 15 Mar 2024 09:44:28 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_register -curv -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cmdline mris_register -curv -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.588 curvature mean = 0.031, std = 0.805 curvature mean = 0.001, std = 0.896 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 165808.9, tmin=0.5592 d=32.00 min @ (0.00, 0.00, 8.00) sse = 158739.1, tmin=1.1154 d=16.00 min @ (-4.00, -4.00, -4.00) sse = 128101.2, tmin=1.7056 d=8.00 min @ (0.00, 0.00, 2.00) sse = 126365.2, tmin=2.3285 d=4.00 min @ (1.00, 1.00, -1.00) sse = 124576.4, tmin=2.8969 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 124168.3, tmin=3.4548 d=1.00 min @ (0.00, 0.00, 0.25) sse = 124084.4, tmin=3.8870 tol=1.0e+00, sigma=0.5, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 4.30 min curvature mean = 0.035, std = 0.853 curvature mean = 0.002, std = 0.962 curvature mean = 0.035, std = 0.866 curvature mean = 0.001, std = 0.985 curvature mean = 0.035, std = 0.870 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.036, std = 0.287 curvature mean = 0.047, std = 0.250 curvature mean = 0.059, std = 0.405 curvature mean = 0.036, std = 0.315 curvature mean = 0.054, std = 0.551 curvature mean = 0.034, std = 0.342 curvature mean = 0.030, std = 0.684 curvature mean = 0.032, std = 0.355 curvature mean = 0.012, std = 0.787 MRISregister() return, current seed 0 -01: dt=0.0000, 63 negative triangles 113: dt=0.9900, 63 negative triangles expanding nbhd size to 1 114: dt=0.9900, 95 negative triangles 115: dt=0.9900, 62 negative triangles 116: dt=0.9900, 71 negative triangles 117: dt=0.9900, 71 negative triangles 118: dt=0.9900, 69 negative triangles 119: dt=0.9900, 60 negative triangles 120: dt=0.9900, 52 negative triangles 121: dt=0.9900, 47 negative triangles 122: dt=0.9900, 42 negative triangles 123: dt=0.9900, 43 negative triangles 124: dt=0.9900, 34 negative triangles 125: dt=0.9900, 33 negative triangles 126: dt=0.9900, 31 negative triangles 127: dt=0.9900, 30 negative triangles 128: dt=0.9900, 28 negative triangles 129: dt=0.9900, 25 negative triangles 130: dt=0.9900, 23 negative triangles 131: dt=0.9900, 18 negative triangles 132: dt=0.9900, 19 negative triangles 133: dt=0.9900, 14 negative triangles 134: dt=0.9900, 14 negative triangles 135: dt=0.9900, 15 negative triangles 136: dt=0.9900, 14 negative triangles 137: dt=0.9900, 12 negative triangles 138: dt=0.9900, 12 negative triangles 139: dt=0.9900, 12 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 9 negative triangles 142: dt=0.9900, 8 negative triangles 143: dt=0.9900, 9 negative triangles 144: dt=0.9900, 8 negative triangles 145: dt=0.9900, 8 negative triangles 146: dt=0.9900, 8 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 5 negative triangles 149: dt=0.9900, 5 negative triangles 150: dt=0.9900, 4 negative triangles 151: dt=0.9900, 5 negative triangles 152: dt=0.9900, 2 negative triangles 153: dt=0.9900, 1 negative triangles 154: dt=0.9900, 1 negative triangles 155: dt=0.9900, 1 negative triangles 156: dt=0.9900, 1 negative triangles 157: dt=0.9900, 1 negative triangles 158: dt=0.9900, 1 negative triangles 159: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.39 hours mris_register utimesec 1364.431332 mris_register stimesec 0.327922 mris_register ru_maxrss 175484 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 29153 mris_register ru_majflt 4 mris_register ru_nswap 0 mris_register ru_inblock 624 mris_register ru_oublock 6328 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 129 mris_register ru_nivcsw 16818 FSRUNTIME@ mris_register 0.3871 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Fri 15 Mar 2024 10:07:41 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_register -curv -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts cmdline mris_register -curv -rusage /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 5.683 curvature mean = 0.059, std = 0.809 curvature mean = 0.004, std = 0.900 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 32.00) sse = 171414.7, tmin=0.3521 d=32.00 min @ (0.00, 0.00, -8.00) sse = 157207.9, tmin=0.7109 d=16.00 min @ (0.00, 4.00, 4.00) sse = 126997.9, tmin=1.0692 d=8.00 min @ (0.00, -2.00, 0.00) sse = 124211.9, tmin=1.4346 d=4.00 min @ (0.00, 1.00, 0.00) sse = 122868.1, tmin=1.8011 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 122233.9, tmin=2.1667 d=1.00 min @ (0.25, 0.00, 0.00) sse = 122163.8, tmin=2.5295 tol=1.0e+00, sigma=0.5, host=ramon, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 2.89 min curvature mean = 0.040, std = 0.842 curvature mean = 0.002, std = 0.964 curvature mean = 0.040, std = 0.855 curvature mean = 0.001, std = 0.986 curvature mean = 0.039, std = 0.859 curvature mean = 0.000, std = 0.994 2 Reading smoothwm curvature mean = -0.036, std = 0.296 curvature mean = 0.043, std = 0.242 curvature mean = 0.054, std = 0.402 curvature mean = 0.034, std = 0.303 curvature mean = 0.045, std = 0.551 curvature mean = 0.032, std = 0.331 curvature mean = 0.024, std = 0.675 curvature mean = 0.031, std = 0.343 curvature mean = 0.008, std = 0.776 MRISregister() return, current seed 0 -01: dt=0.0000, 45 negative triangles 108: dt=0.9900, 45 negative triangles expanding nbhd size to 1 109: dt=0.9900, 59 negative triangles 110: dt=0.9900, 40 negative triangles 111: dt=0.9900, 41 negative triangles 112: dt=0.9900, 40 negative triangles 113: dt=0.9900, 38 negative triangles 114: dt=0.9900, 31 negative triangles 115: dt=0.9900, 36 negative triangles 116: dt=0.9900, 27 negative triangles 117: dt=0.9900, 24 negative triangles 118: dt=0.9900, 27 negative triangles 119: dt=0.9900, 22 negative triangles 120: dt=0.9900, 24 negative triangles 121: dt=0.9900, 20 negative triangles 122: dt=0.9900, 15 negative triangles 123: dt=0.9900, 17 negative triangles 124: dt=0.9900, 15 negative triangles 125: dt=0.9900, 12 negative triangles 126: dt=0.9900, 10 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 7 negative triangles 129: dt=0.9900, 8 negative triangles 130: dt=0.9900, 6 negative triangles 131: dt=0.9900, 5 negative triangles 132: dt=0.9900, 5 negative triangles 133: dt=0.9900, 5 negative triangles 134: dt=0.9900, 4 negative triangles 135: dt=0.9900, 4 negative triangles 136: dt=0.9900, 3 negative triangles 137: dt=0.9900, 2 negative triangles 138: dt=0.9900, 2 negative triangles 139: dt=0.9900, 3 negative triangles 140: dt=0.9900, 1 negative triangles 141: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.28 hours mris_register utimesec 990.921016 mris_register stimesec 0.215997 mris_register ru_maxrss 174524 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 20939 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5032 mris_register ru_oublock 6256 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 229 mris_register ru_nivcsw 1620 FSRUNTIME@ mris_register 0.2753 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Fri 15 Mar 2024 10:24:13 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri 15 Mar 2024 10:24:14 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri 15 Mar 2024 10:24:14 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mrisp_paint -a 5 /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Fri 15 Mar 2024 10:24:15 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mrisp_paint -a 5 /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri 15 Mar 2024 10:24:16 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K lh ../surf/lh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 810 labels changed using aseg relabeling using gibbs priors... 000: 2145 changed, 89800 examined... 001: 507 changed, 9120 examined... 002: 116 changed, 2845 examined... 003: 39 changed, 679 examined... 004: 19 changed, 227 examined... 005: 12 changed, 110 examined... 006: 5 changed, 52 examined... 007: 2 changed, 26 examined... 008: 0 changed, 19 examined... 183 labels changed using aseg 000: 90 total segments, 49 labels (151 vertices) changed 001: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 435 vertices marked for relabeling... 435 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 5 seconds. #----------------------------------------- #@# Cortical Parc rh Fri 15 Mar 2024 10:24:21 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K rh ../surf/rh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 857 labels changed using aseg relabeling using gibbs priors... 000: 2034 changed, 88790 examined... 001: 447 changed, 8907 examined... 002: 99 changed, 2548 examined... 003: 29 changed, 603 examined... 004: 7 changed, 186 examined... 005: 1 changed, 42 examined... 006: 1 changed, 7 examined... 007: 0 changed, 9 examined... 148 labels changed using aseg 000: 81 total segments, 44 labels (195 vertices) changed 001: 38 total segments, 1 labels (1 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 426 vertices marked for relabeling... 426 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 5 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri 15 Mar 2024 10:24:27 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs LS5K lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/filled.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/brain.finalsurfs.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/../mri/aseg.presurf.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... 11383 bright wm thresholded. 182280 bright non-wm voxels segmented. reading original surface position from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.orig... computing class statistics... border white: 178984 voxels (1.07%) border gray 266091 voxels (1.59%) WM (93.0): 93.2 +- 8.6 [70.0 --> 110.0] GM (67.0) : 67.3 +- 13.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.4 (was 70) setting MAX_BORDER_WHITE to 104.6 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 33.8 (was 40) setting MAX_GRAY to 87.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 20.1 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=96+-7.8, GM=61+-8.7 mean inside = 88.1, mean outside = 70.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.93 +- 0.29 (0.04-->3.96) (max @ vno 50207 --> 50221) face area 0.36 +- 0.19 (0.00-->4.34) mean absolute distance = 0.44 +- 0.67 1467 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 136 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 49 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 5 with 28 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 769 points - only 0.00% unknown deleting segment 10 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 109 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 17 points - only 0.00% unknown deleting segment 16 with 18 points - only 0.00% unknown deleting segment 17 with 35 points - only 0.00% unknown deleting segment 18 with 9 points - only 0.00% unknown deleting segment 19 with 64 points - only 0.00% unknown mean border=71.7, 106 (105) missing vertices, mean dist 0.3 [0.5 (%16.4)->0.4 (%83.6))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.95 +- 0.30 (0.10-->4.34) (max @ vno 66993 --> 66316) face area 0.36 +- 0.20 (0.00-->4.50) mean absolute distance = 0.32 +- 0.55 1875 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1143766.9, rms=6.309 001: dt: 0.5000, sse=757567.5, rms=4.106 (34.915%) 002: dt: 0.5000, sse=689095.2, rms=3.578 (12.869%) rms = 3.62, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=615713.1, rms=2.910 (18.659%) 004: dt: 0.2500, sse=586912.1, rms=2.571 (11.659%) 005: dt: 0.2500, sse=572212.2, rms=2.426 (5.631%) 006: dt: 0.2500, sse=569030.7, rms=2.363 (2.581%) rms = 2.31, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=563525.5, rms=2.314 (2.077%) rms = 2.27, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=560170.0, rms=2.269 (1.949%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 128 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 202 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 60 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 17 points - only 0.00% unknown deleting segment 19 with 15 points - only 0.00% unknown deleting segment 20 with 30 points - only 0.00% unknown deleting segment 21 with 7 points - only 0.00% unknown deleting segment 22 with 52 points - only 0.00% unknown mean border=74.1, 147 (55) missing vertices, mean dist -0.1 [0.3 (%67.2)->0.3 (%32.8))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.95 +- 0.29 (0.09-->4.45) (max @ vno 66993 --> 66316) face area 0.37 +- 0.20 (0.00-->4.81) mean absolute distance = 0.29 +- 0.46 2028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=708273.3, rms=3.589 009: dt: 0.5000, sse=607156.9, rms=2.640 (26.431%) rms = 2.99, time step reduction 1 of 3 to 0.250... 010: dt: 0.2500, sse=558679.6, rms=2.032 (23.032%) 011: dt: 0.2500, sse=544369.0, rms=1.808 (11.011%) 012: dt: 0.2500, sse=543446.8, rms=1.756 (2.879%) rms = 1.76, time step reduction 2 of 3 to 0.125... rms = 1.74, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=540420.9, rms=1.740 (0.899%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 119 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 236 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 72 points - only 0.00% unknown deleting segment 13 with 29 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown deleting segment 16 with 17 points - only 0.00% unknown deleting segment 17 with 15 points - only 0.00% unknown deleting segment 18 with 31 points - only 0.00% unknown deleting segment 19 with 7 points - only 0.00% unknown deleting segment 20 with 54 points - only 0.00% unknown mean border=75.6, 154 (44) missing vertices, mean dist -0.1 [0.3 (%58.8)->0.3 (%41.2))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.94 +- 0.29 (0.07-->4.46) (max @ vno 66993 --> 66316) face area 0.37 +- 0.20 (0.00-->4.76) mean absolute distance = 0.29 +- 0.41 2012 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=588737.8, rms=2.491 rms = 2.44, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=585200.2, rms=2.441 (1.986%) 015: dt: 0.2500, sse=534585.2, rms=1.747 (28.435%) 016: dt: 0.2500, sse=526395.1, rms=1.618 (7.368%) rms = 1.62, time step reduction 2 of 3 to 0.125... rms = 1.59, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=524396.8, rms=1.588 (1.848%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 23 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 267 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 71 points - only 0.00% unknown deleting segment 13 with 21 points - only 0.00% unknown deleting segment 14 with 54 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 17 points - only 0.00% unknown deleting segment 17 with 15 points - only 0.00% unknown deleting segment 18 with 31 points - only 0.00% unknown deleting segment 19 with 9 points - only 0.00% unknown deleting segment 20 with 55 points - only 0.00% unknown mean border=76.3, 167 (35) missing vertices, mean dist -0.0 [0.3 (%51.8)->0.3 (%48.2))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=534587.8, rms=1.823 rms = 1.97, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=512604.7, rms=1.425 (21.831%) 019: dt: 0.2500, sse=504174.4, rms=1.237 (13.208%) rms = 1.24, time step reduction 2 of 3 to 0.125... rms = 1.22, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=502343.1, rms=1.223 (1.161%) positioning took 0.2 minutes generating cortex label... 6 non-cortical segments detected only using segment with 6350 vertices erasing segment 1 (vno[0] = 48347) erasing segment 2 (vno[0] = 55411) erasing segment 3 (vno[0] = 58754) erasing segment 4 (vno[0] = 58845) erasing segment 5 (vno[0] = 68184) writing cortex label to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label... writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.area vertex spacing 0.94 +- 0.29 (0.04-->4.52) (max @ vno 66316 --> 66993) face area 0.37 +- 0.19 (0.00-->4.49) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=46.8, 98 (98) missing vertices, mean dist 1.2 [0.6 (%0.0)->3.2 (%100.0))] % 5 local maxima, %31 large gradients and %59 min vals, 1331 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=16031530.0, rms=30.249 001: dt: 0.0500, sse=14203161.0, rms=28.416 (6.061%) 002: dt: 0.0500, sse=12869874.0, rms=27.000 (4.982%) 003: dt: 0.0500, sse=11835943.0, rms=25.849 (4.264%) 004: dt: 0.0500, sse=10991314.0, rms=24.869 (3.792%) 005: dt: 0.0500, sse=10276431.0, rms=24.008 (3.462%) 006: dt: 0.0500, sse=9653986.0, rms=23.232 (3.231%) 007: dt: 0.0500, sse=9100936.0, rms=22.521 (3.063%) 008: dt: 0.0500, sse=8602201.0, rms=21.859 (2.938%) 009: dt: 0.0500, sse=8148083.0, rms=21.238 (2.839%) 010: dt: 0.0500, sse=7731147.0, rms=20.652 (2.760%) positioning took 0.4 minutes mean border=46.4, 82 (42) missing vertices, mean dist 1.0 [0.3 (%0.1)->2.7 (%99.9))] % 5 local maxima, %31 large gradients and %59 min vals, 1350 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8398568.0, rms=21.583 011: dt: 0.0500, sse=8004223.5, rms=21.038 (2.524%) 012: dt: 0.0500, sse=7639477.0, rms=20.521 (2.457%) 013: dt: 0.0500, sse=7300981.5, rms=20.030 (2.396%) 014: dt: 0.0500, sse=6985583.0, rms=19.560 (2.343%) 015: dt: 0.0500, sse=6692049.5, rms=19.113 (2.287%) 016: dt: 0.0500, sse=6418596.5, rms=18.687 (2.231%) 017: dt: 0.0500, sse=6163874.5, rms=18.280 (2.174%) 018: dt: 0.0500, sse=5926635.0, rms=17.893 (2.116%) 019: dt: 0.0500, sse=5705197.0, rms=17.525 (2.062%) 020: dt: 0.0500, sse=5498473.5, rms=17.173 (2.007%) positioning took 0.4 minutes mean border=46.3, 103 (36) missing vertices, mean dist 0.9 [0.1 (%1.1)->2.5 (%98.9))] % 6 local maxima, %31 large gradients and %58 min vals, 1307 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=5540804.5, rms=17.252 021: dt: 0.0500, sse=5343169.0, rms=16.910 (1.980%) 022: dt: 0.0500, sse=5159439.5, rms=16.586 (1.916%) 023: dt: 0.0500, sse=4987499.0, rms=16.277 (1.864%) 024: dt: 0.0500, sse=4827376.5, rms=15.984 (1.802%) 025: dt: 0.0500, sse=4677961.5, rms=15.705 (1.745%) 026: dt: 0.0500, sse=4538225.0, rms=15.439 (1.690%) 027: dt: 0.0500, sse=4406975.0, rms=15.186 (1.643%) 028: dt: 0.0500, sse=4282928.5, rms=14.942 (1.606%) 029: dt: 0.0500, sse=4165798.5, rms=14.708 (1.567%) 030: dt: 0.0500, sse=4055053.5, rms=14.483 (1.530%) positioning took 0.4 minutes mean border=46.3, 112 (30) missing vertices, mean dist 0.8 [0.1 (%9.3)->2.3 (%90.7))] % 6 local maxima, %31 large gradients and %58 min vals, 1241 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4093424.8, rms=14.562 031: dt: 0.5000, sse=3333500.8, rms=12.922 (11.258%) 032: dt: 0.5000, sse=2839967.8, rms=11.727 (9.251%) 033: dt: 0.5000, sse=2478729.5, rms=10.766 (8.189%) 034: dt: 0.5000, sse=2244698.5, rms=10.088 (6.305%) 035: dt: 0.5000, sse=2055016.6, rms=9.502 (5.804%) 036: dt: 0.5000, sse=1919154.0, rms=9.055 (4.706%) 037: dt: 0.5000, sse=1789421.4, rms=8.610 (4.917%) 038: dt: 0.5000, sse=1688346.6, rms=8.244 (4.244%) 039: dt: 0.5000, sse=1594562.8, rms=7.894 (4.253%) 040: dt: 0.5000, sse=1534061.0, rms=7.656 (3.005%) 041: dt: 0.5000, sse=1478834.5, rms=7.435 (2.899%) 042: dt: 0.5000, sse=1445278.9, rms=7.298 (1.842%) 043: dt: 0.5000, sse=1413478.6, rms=7.163 (1.841%) 044: dt: 0.5000, sse=1394745.5, rms=7.083 (1.114%) 045: dt: 0.5000, sse=1371511.0, rms=6.984 (1.405%) 046: dt: 0.5000, sse=1357698.1, rms=6.923 (0.877%) 047: dt: 0.5000, sse=1340162.5, rms=6.847 (1.095%) rms = 6.82, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1335112.1, rms=6.824 (0.335%) 049: dt: 0.2500, sse=1315356.1, rms=6.714 (1.615%) rms = 6.68, time step reduction 2 of 3 to 0.125... 050: dt: 0.2500, sse=1307760.1, rms=6.680 (0.504%) 051: dt: 0.1250, sse=1297307.1, rms=6.629 (0.762%) rms = 6.61, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1294119.0, rms=6.614 (0.226%) positioning took 2.2 minutes mean border=46.5, 2510 (14) missing vertices, mean dist 0.1 [0.3 (%52.9)->1.0 (%47.1))] %13 local maxima, %24 large gradients and %55 min vals, 672 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1242960.1, rms=5.388 053: dt: 0.5000, sse=1207413.8, rms=5.197 (3.549%) 054: dt: 0.5000, sse=1174264.8, rms=5.032 (3.164%) rms = 5.07, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1154384.2, rms=4.886 (2.895%) rms = 4.88, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1155130.4, rms=4.880 (0.132%) 057: dt: 0.1250, sse=1145782.0, rms=4.815 (1.324%) rms = 4.79, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1141675.4, rms=4.792 (0.493%) positioning took 0.8 minutes mean border=46.0, 3060 (14) missing vertices, mean dist 0.1 [0.2 (%49.5)->0.8 (%50.5))] %21 local maxima, %17 large gradients and %54 min vals, 847 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1165287.2, rms=4.858 rms = 4.97, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1153017.2, rms=4.780 (1.594%) rms = 4.76, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1148404.9, rms=4.761 (0.401%) 061: dt: 0.1250, sse=1139988.8, rms=4.704 (1.192%) rms = 4.68, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1134840.8, rms=4.677 (0.591%) positioning took 0.7 minutes mean border=45.4, 6130 (13) missing vertices, mean dist 0.1 [0.2 (%46.4)->0.7 (%53.6))] %24 local maxima, %14 large gradients and %51 min vals, 944 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1164040.1, rms=4.797 rms = 4.80, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1148335.1, rms=4.702 (1.970%) 064: dt: 0.2500, sse=1129191.4, rms=4.606 (2.040%) rms = 4.57, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1121414.6, rms=4.572 (0.745%) 066: dt: 0.1250, sse=1103086.8, rms=4.448 (2.707%) 067: dt: 0.1250, sse=1094055.8, rms=4.395 (1.201%) rms = 4.37, time step reduction 3 of 3 to 0.062... 068: dt: 0.1250, sse=1089039.5, rms=4.367 (0.637%) positioning took 0.7 minutes writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.area.pial vertex spacing 1.13 +- 0.57 (0.06-->7.44) (max @ vno 55255 --> 54370) face area 0.50 +- 0.46 (0.00-->6.98) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 89800 vertices processed 25000 of 89800 vertices processed 50000 of 89800 vertices processed 75000 of 89800 vertices processed 0 of 89800 vertices processed 25000 of 89800 vertices processed 50000 of 89800 vertices processed 75000 of 89800 vertices processed thickness calculation complete, 1065:3691 truncations. 13316 vertices at 0 distance 47071 vertices at 1 distance 55708 vertices at 2 distance 32300 vertices at 3 distance 13280 vertices at 4 distance 4923 vertices at 5 distance 1860 vertices at 6 distance 788 vertices at 7 distance 376 vertices at 8 distance 173 vertices at 9 distance 94 vertices at 10 distance 68 vertices at 11 distance 63 vertices at 12 distance 61 vertices at 13 distance 43 vertices at 14 distance 29 vertices at 15 distance 29 vertices at 16 distance 14 vertices at 17 distance 13 vertices at 18 distance 11 vertices at 19 distance 16 vertices at 20 distance writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.thickness positioning took 8.3 minutes #-------------------------------------------- #@# Make Pial Surf rh Fri 15 Mar 2024 10:32:44 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs LS5K rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/filled.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/brain.finalsurfs.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/../mri/aseg.presurf.mgz... reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... 11383 bright wm thresholded. 182280 bright non-wm voxels segmented. reading original surface position from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.orig... computing class statistics... border white: 178984 voxels (1.07%) border gray 266091 voxels (1.59%) WM (93.0): 93.2 +- 8.6 [70.0 --> 110.0] GM (67.0) : 67.3 +- 13.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.4 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 34.8 (was 40) setting MAX_GRAY to 89.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 48.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=98+-7.8, GM=62+-7.0 mean inside = 88.6, mean outside = 70.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.93 +- 0.27 (0.04-->4.43) (max @ vno 54515 --> 59553) face area 0.36 +- 0.18 (0.00-->3.14) mean absolute distance = 0.45 +- 0.68 1442 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 5 with 467 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 10 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown deleting segment 14 with 9 points - only 0.00% unknown deleting segment 15 with 36 points - only 0.00% unknown mean border=72.7, 129 (126) missing vertices, mean dist 0.3 [0.5 (%15.8)->0.4 (%84.2))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.95 +- 0.29 (0.05-->4.58) (max @ vno 54515 --> 59553) face area 0.36 +- 0.19 (0.00-->3.33) mean absolute distance = 0.31 +- 0.52 1590 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1138578.0, rms=6.370 001: dt: 0.5000, sse=743540.9, rms=4.096 (35.694%) 002: dt: 0.5000, sse=664611.8, rms=3.487 (14.864%) rms = 3.62, time step reduction 1 of 3 to 0.250... 003: dt: 0.2500, sse=590701.9, rms=2.789 (20.030%) 004: dt: 0.2500, sse=564307.2, rms=2.476 (11.215%) 005: dt: 0.2500, sse=561446.9, rms=2.425 (2.057%) 006: dt: 0.2500, sse=551214.2, rms=2.304 (4.976%) rms = 2.32, time step reduction 2 of 3 to 0.125... rms = 2.27, time step reduction 3 of 3 to 0.062... 007: dt: 0.1250, sse=549406.9, rms=2.266 (1.669%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 240 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 30 points - only 0.00% unknown mean border=75.4, 125 (63) missing vertices, mean dist -0.1 [0.3 (%70.4)->0.3 (%29.6))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.94 +- 0.28 (0.05-->4.30) (max @ vno 54515 --> 59553) face area 0.37 +- 0.19 (0.00-->3.99) mean absolute distance = 0.27 +- 0.42 1986 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=731093.2, rms=3.885 008: dt: 0.5000, sse=610957.9, rms=2.808 (27.726%) rms = 3.06, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=572329.9, rms=2.133 (24.028%) 010: dt: 0.2500, sse=537225.2, rms=1.882 (11.760%) rms = 1.84, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=533569.9, rms=1.840 (2.264%) 012: dt: 0.1250, sse=526942.4, rms=1.730 (5.989%) rms = 1.70, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=525113.4, rms=1.704 (1.509%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 287 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 29 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 17 points - only 0.00% unknown deleting segment 14 with 9 points - only 0.00% unknown deleting segment 15 with 31 points - only 0.00% unknown mean border=76.8, 152 (48) missing vertices, mean dist -0.1 [0.3 (%60.2)->0.2 (%39.8))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.94 +- 0.28 (0.07-->4.19) (max @ vno 54515 --> 59553) face area 0.37 +- 0.19 (0.00-->3.96) mean absolute distance = 0.27 +- 0.39 1759 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=572621.9, rms=2.467 rms = 2.61, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=531840.3, rms=1.911 (22.514%) 015: dt: 0.2500, sse=518693.2, rms=1.666 (12.830%) rms = 1.68, time step reduction 2 of 3 to 0.125... 016: dt: 0.1250, sse=514350.0, rms=1.612 (3.257%) 017: dt: 0.1250, sse=511674.8, rms=1.546 (4.096%) rms = 1.53, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=509735.0, rms=1.533 (0.802%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 297 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 29 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 17 points - only 0.00% unknown deleting segment 12 with 9 points - only 0.00% unknown deleting segment 13 with 32 points - only 0.00% unknown mean border=77.4, 162 (44) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.2 (%47.7))] %88 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=522268.1, rms=1.799 rms = 2.08, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=501120.0, rms=1.415 (21.338%) 020: dt: 0.2500, sse=497220.9, rms=1.337 (5.493%) rms = 1.44, time step reduction 2 of 3 to 0.125... 021: dt: 0.1250, sse=493860.4, rms=1.275 (4.606%) rms = 1.23, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=491464.1, rms=1.226 (3.883%) positioning took 0.5 minutes generating cortex label... 7 non-cortical segments detected only using segment with 6359 vertices erasing segment 1 (vno[0] = 41675) erasing segment 2 (vno[0] = 42825) erasing segment 3 (vno[0] = 50042) erasing segment 4 (vno[0] = 50952) erasing segment 5 (vno[0] = 57261) erasing segment 6 (vno[0] = 66695) writing cortex label to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label... writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.curv writing smoothed area to rh.area writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.area vertex spacing 0.93 +- 0.28 (0.04-->4.17) (max @ vno 54515 --> 59553) face area 0.37 +- 0.19 (0.00-->3.95) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=47.7, 90 (90) missing vertices, mean dist 1.2 [2.4 (%0.1)->3.3 (%99.9))] % 5 local maxima, %29 large gradients and %60 min vals, 1386 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=16111049.0, rms=30.526 001: dt: 0.0500, sse=14225636.0, rms=28.628 (6.219%) 002: dt: 0.0500, sse=12856711.0, rms=27.166 (5.105%) 003: dt: 0.0500, sse=11799632.0, rms=25.981 (4.362%) 004: dt: 0.0500, sse=10938591.0, rms=24.974 (3.875%) 005: dt: 0.0500, sse=10211625.0, rms=24.092 (3.535%) 006: dt: 0.0500, sse=9581626.0, rms=23.299 (3.289%) 007: dt: 0.0500, sse=9024911.0, rms=22.576 (3.105%) 008: dt: 0.0500, sse=8524839.0, rms=21.906 (2.969%) 009: dt: 0.0500, sse=8071316.0, rms=21.279 (2.859%) 010: dt: 0.0500, sse=7657849.0, rms=20.692 (2.761%) positioning took 0.8 minutes mean border=47.3, 88 (52) missing vertices, mean dist 1.1 [1.4 (%0.1)->2.9 (%99.9))] % 6 local maxima, %29 large gradients and %59 min vals, 1293 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8387407.5, rms=21.719 011: dt: 0.0500, sse=7993313.0, rms=21.172 (2.522%) 012: dt: 0.0500, sse=7630467.5, rms=20.654 (2.443%) 013: dt: 0.0500, sse=7293691.5, rms=20.162 (2.382%) 014: dt: 0.0500, sse=6981030.5, rms=19.694 (2.321%) 015: dt: 0.0500, sse=6690249.0, rms=19.249 (2.262%) 016: dt: 0.0500, sse=6419997.0, rms=18.825 (2.201%) 017: dt: 0.0500, sse=6167581.5, rms=18.420 (2.149%) 018: dt: 0.0500, sse=5933094.0, rms=18.036 (2.085%) 019: dt: 0.0500, sse=5714183.0, rms=17.670 (2.031%) 020: dt: 0.0500, sse=5509876.0, rms=17.321 (1.975%) positioning took 0.8 minutes mean border=47.2, 123 (44) missing vertices, mean dist 1.0 [0.2 (%0.9)->2.6 (%99.1))] % 6 local maxima, %30 large gradients and %59 min vals, 1271 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=5588725.5, rms=17.462 021: dt: 0.0500, sse=5387625.0, rms=17.115 (1.990%) 022: dt: 0.0500, sse=5202591.0, rms=16.789 (1.907%) 023: dt: 0.0500, sse=5029167.0, rms=16.477 (1.857%) 024: dt: 0.0500, sse=4868456.0, rms=16.182 (1.787%) 025: dt: 0.0500, sse=4718436.0, rms=15.902 (1.730%) 026: dt: 0.0500, sse=4578964.0, rms=15.638 (1.666%) 027: dt: 0.0500, sse=4448199.0, rms=15.385 (1.615%) 028: dt: 0.0500, sse=4325213.0, rms=15.143 (1.570%) 029: dt: 0.0500, sse=4209336.5, rms=14.912 (1.527%) 030: dt: 0.0500, sse=4099810.5, rms=14.690 (1.490%) positioning took 0.8 minutes mean border=47.2, 144 (39) missing vertices, mean dist 0.8 [0.1 (%6.7)->2.4 (%93.3))] % 6 local maxima, %30 large gradients and %59 min vals, 1251 gradients ignored tol=1.0e-04, sigma=2.0, host=ramon, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4139656.8, rms=14.772 031: dt: 0.5000, sse=3391873.5, rms=13.165 (10.878%) 032: dt: 0.5000, sse=2900634.2, rms=11.984 (8.972%) 033: dt: 0.5000, sse=2535091.5, rms=11.022 (8.030%) 034: dt: 0.5000, sse=2283792.0, rms=10.301 (6.544%) 035: dt: 0.5000, sse=2080472.0, rms=9.678 (6.044%) 036: dt: 0.5000, sse=1939308.4, rms=9.216 (4.777%) 037: dt: 0.5000, sse=1813230.0, rms=8.786 (4.658%) 038: dt: 0.5000, sse=1727246.5, rms=8.477 (3.525%) 039: dt: 0.5000, sse=1639266.0, rms=8.154 (3.809%) 040: dt: 0.5000, sse=1583764.2, rms=7.940 (2.622%) 041: dt: 0.5000, sse=1524705.2, rms=7.710 (2.900%) 042: dt: 0.5000, sse=1495038.4, rms=7.587 (1.594%) 043: dt: 0.5000, sse=1458041.1, rms=7.438 (1.960%) 044: dt: 0.5000, sse=1436468.9, rms=7.346 (1.234%) 045: dt: 0.5000, sse=1404905.0, rms=7.215 (1.788%) 046: dt: 0.5000, sse=1386795.8, rms=7.137 (1.080%) 047: dt: 0.5000, sse=1363087.2, rms=7.035 (1.426%) rms = 7.00, time step reduction 1 of 3 to 0.250... 048: dt: 0.5000, sse=1354448.9, rms=6.996 (0.554%) 049: dt: 0.2500, sse=1322780.2, rms=6.838 (2.269%) rms = 6.80, time step reduction 2 of 3 to 0.125... 050: dt: 0.2500, sse=1314539.8, rms=6.800 (0.546%) 051: dt: 0.1250, sse=1294969.8, rms=6.709 (1.342%) rms = 6.68, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1289437.8, rms=6.684 (0.374%) positioning took 2.1 minutes mean border=47.3, 2897 (27) missing vertices, mean dist 0.1 [0.3 (%51.0)->1.0 (%49.0))] %14 local maxima, %22 large gradients and %56 min vals, 642 gradients ignored tol=1.0e-04, sigma=1.0, host=ramon, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1243675.1, rms=5.494 053: dt: 0.5000, sse=1222419.0, rms=5.383 (2.026%) 054: dt: 0.5000, sse=1166397.5, rms=5.085 (5.526%) rms = 5.22, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=1134219.2, rms=4.867 (4.294%) rms = 4.91, time step reduction 2 of 3 to 0.125... rms = 4.82, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1128151.6, rms=4.824 (0.869%) positioning took 0.4 minutes mean border=46.7, 3308 (26) missing vertices, mean dist 0.1 [0.2 (%45.0)->0.8 (%55.0))] %21 local maxima, %15 large gradients and %55 min vals, 820 gradients ignored tol=1.0e-04, sigma=0.5, host=ramon, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1160793.6, rms=4.970 rms = 5.16, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1137047.6, rms=4.817 (3.081%) rms = 4.82, time step reduction 2 of 3 to 0.125... rms = 4.79, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1132504.5, rms=4.787 (0.635%) positioning took 0.2 minutes mean border=46.2, 6096 (25) missing vertices, mean dist 0.1 [0.2 (%40.3)->0.7 (%59.7))] %24 local maxima, %11 large gradients and %52 min vals, 915 gradients ignored tol=1.0e-04, sigma=0.2, host=ramon, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1157406.8, rms=4.939 rms = 5.08, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1131483.2, rms=4.781 (3.204%) 060: dt: 0.2500, sse=1112854.9, rms=4.686 (1.986%) rms = 4.72, time step reduction 2 of 3 to 0.125... 061: dt: 0.1250, sse=1103856.2, rms=4.626 (1.279%) 062: dt: 0.1250, sse=1088861.5, rms=4.531 (2.072%) 063: dt: 0.1250, sse=1078407.1, rms=4.467 (1.391%) rms = 4.43, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1071594.1, rms=4.429 (0.854%) positioning took 0.5 minutes writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.area.pial vertex spacing 1.12 +- 0.56 (0.07-->7.91) (max @ vno 54517 --> 53599) face area 0.49 +- 0.45 (0.00-->6.96) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 88790 vertices processed 25000 of 88790 vertices processed 50000 of 88790 vertices processed 75000 of 88790 vertices processed 0 of 88790 vertices processed 25000 of 88790 vertices processed 50000 of 88790 vertices processed 75000 of 88790 vertices processed thickness calculation complete, 1020:3441 truncations. 13620 vertices at 0 distance 47575 vertices at 1 distance 55397 vertices at 2 distance 31301 vertices at 3 distance 12531 vertices at 4 distance 4489 vertices at 5 distance 1657 vertices at 6 distance 733 vertices at 7 distance 299 vertices at 8 distance 167 vertices at 9 distance 108 vertices at 10 distance 62 vertices at 11 distance 40 vertices at 12 distance 37 vertices at 13 distance 24 vertices at 14 distance 21 vertices at 15 distance 10 vertices at 16 distance 10 vertices at 17 distance 24 vertices at 18 distance 10 vertices at 19 distance 25 vertices at 20 distance writing curvature file /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.thickness positioning took 11.0 minutes #-------------------------------------------- #@# Surf Volume lh Fri 15 Mar 2024 10:43:42 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume LS5K lh /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.volume masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label Total face volume 214802 Total vertex volume 210500 (mask=0) #@# LS5K lh 210500 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri 15 Mar 2024 10:43:43 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume LS5K rh /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.volume masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label Total face volume 211837 Total vertex volume 207260 (mask=0) #@# LS5K rh 207260 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri 15 Mar 2024 10:43:45 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon LS5K SUBJECTS_DIR is /data/pt_02321/1_Analysen/2_CROSSING/FS loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 251 writing volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz mris_volmask took 3.31 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri 15 Mar 2024 10:47:03 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab LS5K lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 1023 740 2147 2.976 0.694 0.101 0.024 6 0.9 bankssts 628 430 1535 3.362 0.543 0.145 0.035 10 0.8 caudalanteriorcingulate 2562 1861 6167 2.782 0.747 0.143 0.044 36 4.6 caudalmiddlefrontal 1422 1057 3016 2.349 0.683 0.168 0.044 24 3.1 cuneus 358 275 1219 2.674 0.934 0.154 0.050 5 0.9 entorhinal 2714 2100 7547 2.968 0.715 0.161 0.048 43 6.5 fusiform 4667 3654 11435 2.681 0.658 0.154 0.044 79 9.1 inferiorparietal 2691 1968 7593 2.905 0.759 0.157 0.049 44 5.8 inferiortemporal 1064 756 2732 3.080 0.822 0.148 0.046 15 2.2 isthmuscingulate 5418 3813 10042 2.341 0.667 0.151 0.042 83 9.9 lateraloccipital 1737 1265 4504 3.082 0.740 0.136 0.048 21 3.5 lateralorbitofrontal 2847 2172 6685 2.495 0.700 0.168 0.042 54 5.6 lingual 1258 929 4263 3.690 0.881 0.151 0.049 25 2.5 medialorbitofrontal 2901 2271 8639 2.976 0.795 0.169 0.058 49 8.0 middletemporal 693 513 1671 2.724 0.743 0.114 0.029 5 0.8 parahippocampal 1598 1164 3670 2.769 0.636 0.117 0.027 13 1.6 paracentral 1477 1131 4286 3.019 0.716 0.132 0.035 18 2.0 parsopercularis 546 452 1907 2.911 0.819 0.185 0.054 12 1.5 parsorbitalis 1336 935 2930 2.727 0.593 0.136 0.046 13 2.5 parstriangularis 1112 814 1626 2.123 0.532 0.148 0.034 13 1.9 pericalcarine 4335 3095 8617 2.307 0.691 0.121 0.030 46 5.6 postcentral 1255 887 3083 3.016 0.739 0.137 0.035 15 1.9 posteriorcingulate 5161 3828 11085 2.594 0.643 0.134 0.032 54 7.3 precentral 4091 2983 10754 2.969 0.733 0.133 0.033 56 5.8 precuneus 548 369 1652 3.909 0.766 0.122 0.033 6 0.7 rostralanteriorcingulate 5143 3754 14834 3.125 0.766 0.151 0.052 70 11.7 rostralmiddlefrontal 7379 5479 23791 3.386 0.808 0.141 0.043 89 12.9 superiorfrontal 5789 4359 12393 2.383 0.629 0.136 0.033 83 9.1 superiorparietal 3892 2872 10995 3.021 0.761 0.121 0.032 41 5.5 superiortemporal 4158 3156 10061 2.641 0.824 0.156 0.046 76 9.0 supramarginal 270 220 1375 3.696 0.783 0.207 0.082 6 0.9 frontalpole 374 344 1700 3.029 1.106 0.181 0.069 9 1.2 temporalpole 441 324 919 2.894 0.567 0.153 0.043 5 0.8 transversetemporal 1993 1409 5522 3.529 0.921 0.106 0.027 11 2.2 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab LS5K lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 1023 697 2147 2.976 0.694 0.143 0.039 17 1.8 bankssts 628 546 1535 3.362 0.543 0.208 0.077 51 2.1 caudalanteriorcingulate 2562 2561 6167 2.782 0.747 0.195 0.049 49 6.3 caudalmiddlefrontal 1422 1562 3016 2.349 0.683 0.200 0.046 23 3.3 cuneus 358 613 1219 2.674 0.934 0.276 0.074 6 1.4 entorhinal 2714 2937 7547 2.968 0.715 0.206 0.054 49 6.9 fusiform 4667 4947 11435 2.681 0.658 0.198 0.059 103 14.8 inferiorparietal 2691 3113 7593 2.905 0.759 0.222 0.058 51 7.6 inferiortemporal 1064 1064 2732 3.080 0.822 0.230 0.071 32 3.5 isthmuscingulate 5418 4849 10042 2.341 0.667 0.165 0.045 93 11.9 lateraloccipital 1737 1709 4504 3.082 0.740 0.213 0.065 33 5.5 lateralorbitofrontal 2847 3226 6685 2.495 0.700 0.207 0.047 49 6.6 lingual 1258 1353 4263 3.690 0.881 0.234 0.069 28 4.2 medialorbitofrontal 2901 3626 8639 2.976 0.795 0.228 0.057 54 8.1 middletemporal 693 765 1671 2.724 0.743 0.204 0.058 10 1.9 parahippocampal 1598 1512 3670 2.769 0.636 0.155 0.036 24 2.5 paracentral 1477 1602 4286 3.019 0.716 0.185 0.042 18 2.9 parsopercularis 546 881 1907 2.911 0.819 0.276 0.058 8 1.7 parsorbitalis 1336 1209 2930 2.727 0.593 0.179 0.050 25 2.8 parstriangularis 1112 746 1626 2.123 0.532 0.152 0.053 34 2.8 pericalcarine 4335 4336 8617 2.307 0.691 0.169 0.039 50 8.4 postcentral 1255 1101 3083 3.016 0.739 0.185 0.055 44 2.7 posteriorcingulate 5161 4741 11085 2.594 0.643 0.164 0.042 99 10.5 precentral 4091 4228 10754 2.969 0.733 0.195 0.051 71 10.0 precuneus 548 558 1652 3.909 0.766 0.213 0.080 19 2.5 rostralanteriorcingulate 5143 5430 14834 3.125 0.766 0.216 0.068 115 18.2 rostralmiddlefrontal 7379 7940 23791 3.386 0.808 0.198 0.052 153 18.5 superiorfrontal 5789 5881 12393 2.383 0.629 0.177 0.040 82 11.6 superiorparietal 3892 4186 10995 3.021 0.761 0.197 0.051 64 9.9 superiortemporal 4158 4375 10061 2.641 0.824 0.192 0.052 85 11.4 supramarginal 270 537 1375 3.696 0.783 0.285 0.056 3 0.7 frontalpole 374 744 1700 3.029 1.106 0.266 0.053 5 0.9 temporalpole 441 369 919 2.894 0.567 0.152 0.040 4 0.9 transversetemporal 1993 1441 5522 3.529 0.921 0.158 0.044 37 3.9 insula #----------------------------------------- #@# Parcellation Stats rh Fri 15 Mar 2024 10:47:29 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab LS5K rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 1023 745 2078 2.854 0.489 0.110 0.019 8 0.7 bankssts 629 441 1605 3.017 0.588 0.148 0.033 10 1.0 caudalanteriorcingulate 2271 1744 5463 2.739 0.562 0.144 0.038 28 3.7 caudalmiddlefrontal 1257 932 2807 2.691 0.595 0.159 0.037 16 2.0 cuneus 295 207 1037 3.324 0.786 0.152 0.052 3 0.8 entorhinal 2571 1867 6403 2.904 0.738 0.151 0.044 42 5.1 fusiform 5539 4104 13700 2.759 0.687 0.136 0.032 80 7.8 inferiorparietal 2922 2147 8014 3.007 0.795 0.144 0.038 49 4.8 inferiortemporal 1016 702 2459 3.013 0.879 0.136 0.046 13 1.5 isthmuscingulate 4059 2670 6734 2.223 0.877 0.137 0.038 58 6.5 lateraloccipital 1948 1391 4983 3.091 0.746 0.143 0.046 28 3.8 lateralorbitofrontal 2595 1960 6342 2.590 0.737 0.167 0.049 46 6.0 lingual 1581 1155 4905 3.236 0.825 0.153 0.054 30 3.7 medialorbitofrontal 3484 2719 10392 3.008 0.712 0.150 0.038 51 6.0 middletemporal 638 458 1611 2.857 0.851 0.109 0.028 4 0.5 parahippocampal 1775 1286 3820 2.636 0.714 0.125 0.030 18 2.3 paracentral 1384 1022 4020 3.208 0.619 0.123 0.032 16 2.0 parsopercularis 646 479 1848 3.020 0.785 0.164 0.061 20 2.1 parsorbitalis 1527 1103 4570 3.223 0.588 0.118 0.030 14 1.7 parstriangularis 1072 769 1548 2.047 0.828 0.166 0.054 19 2.6 pericalcarine 4046 3144 8438 2.325 0.707 0.147 0.041 60 7.8 postcentral 1317 1009 3389 2.859 0.916 0.152 0.039 21 2.1 posteriorcingulate 4854 3572 10403 2.627 0.653 0.128 0.028 51 6.2 precentral 4197 3066 10155 2.752 0.866 0.136 0.034 53 6.6 precuneus 426 282 1028 3.407 0.634 0.118 0.027 4 0.5 rostralanteriorcingulate 5297 3879 14364 2.888 0.765 0.150 0.051 84 10.9 rostralmiddlefrontal 6957 5201 21097 3.189 0.832 0.139 0.044 84 12.6 superiorfrontal 5242 3933 11410 2.464 0.683 0.153 0.040 86 9.6 superiorparietal 4245 3083 12747 3.329 0.786 0.125 0.034 48 6.5 superiortemporal 3906 2901 10922 3.010 0.675 0.145 0.038 52 6.5 supramarginal 369 267 1328 3.178 0.681 0.182 0.089 8 1.4 frontalpole 336 246 1037 2.920 1.131 0.146 0.051 5 0.7 temporalpole 439 304 948 2.946 0.624 0.144 0.029 6 0.5 transversetemporal 1985 1386 5631 3.710 0.840 0.116 0.039 38 3.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab LS5K rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 1023 700 2078 2.854 0.489 0.127 0.032 16 1.3 bankssts 629 651 1605 3.017 0.588 0.207 0.050 20 1.4 caudalanteriorcingulate 2271 2296 5463 2.739 0.562 0.179 0.040 34 4.5 caudalmiddlefrontal 1257 1198 2807 2.691 0.595 0.159 0.036 18 2.1 cuneus 295 407 1037 3.324 0.786 0.230 0.059 4 0.9 entorhinal 2571 2535 6403 2.904 0.738 0.183 0.051 49 6.4 fusiform 5539 5710 13700 2.759 0.687 0.173 0.039 76 10.4 inferiorparietal 2922 3162 8014 3.007 0.795 0.191 0.048 46 6.9 inferiortemporal 1016 933 2459 3.013 0.879 0.199 0.064 42 2.7 isthmuscingulate 4059 3306 6734 2.223 0.877 0.138 0.036 227 6.6 lateraloccipital 1948 1887 4983 3.091 0.746 0.200 0.054 39 5.1 lateralorbitofrontal 2595 2908 6342 2.590 0.737 0.201 0.050 45 6.2 lingual 1581 1730 4905 3.236 0.825 0.223 0.067 35 4.8 medialorbitofrontal 3484 4056 10392 3.008 0.712 0.196 0.045 70 7.8 middletemporal 638 625 1611 2.857 0.851 0.176 0.046 9 1.3 parahippocampal 1775 1592 3820 2.636 0.714 0.157 0.041 24 3.2 paracentral 1384 1482 4020 3.208 0.619 0.184 0.042 20 2.9 parsopercularis 646 763 1848 3.020 0.785 0.222 0.072 16 2.3 parsorbitalis 1527 1680 4570 3.223 0.588 0.187 0.046 24 2.9 parstriangularis 1072 777 1548 2.047 0.828 0.165 0.056 25 2.8 pericalcarine 4046 4230 8438 2.325 0.707 0.175 0.044 63 8.5 postcentral 1317 1273 3389 2.859 0.916 0.179 0.042 37 2.4 posteriorcingulate 4854 4300 10403 2.627 0.653 0.154 0.037 66 8.2 precentral 4197 4051 10155 2.752 0.866 0.185 0.045 76 9.0 precuneus 426 390 1028 3.407 0.634 0.143 0.033 3 0.6 rostralanteriorcingulate 5297 5704 14364 2.888 0.765 0.213 0.054 108 14.1 rostralmiddlefrontal 6957 7619 21097 3.189 0.832 0.201 0.051 117 17.0 superiorfrontal 5242 5283 11410 2.464 0.683 0.182 0.044 82 10.7 superiorparietal 4245 4383 12747 3.329 0.786 0.176 0.045 62 8.7 superiortemporal 3906 4183 10922 3.010 0.675 0.184 0.042 72 7.9 supramarginal 369 521 1328 3.178 0.681 0.269 0.069 6 1.3 frontalpole 336 504 1037 2.920 1.131 0.249 0.066 8 0.8 temporalpole 439 376 948 2.946 0.624 0.153 0.044 6 0.9 transversetemporal 1985 1449 5631 3.710 0.840 0.166 0.062 70 5.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri 15 Mar 2024 10:47:57 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K lh ../surf/lh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 36 labels changed using aseg relabeling using gibbs priors... 000: 5909 changed, 89800 examined... 001: 1215 changed, 23252 examined... 002: 325 changed, 6599 examined... 003: 121 changed, 1845 examined... 004: 45 changed, 706 examined... 005: 18 changed, 273 examined... 006: 7 changed, 95 examined... 007: 2 changed, 40 examined... 008: 1 changed, 14 examined... 009: 1 changed, 6 examined... 010: 2 changed, 8 examined... 011: 1 changed, 13 examined... 012: 1 changed, 7 examined... 013: 0 changed, 6 examined... 7 labels changed using aseg 000: 158 total segments, 76 labels (677 vertices) changed 001: 83 total segments, 1 labels (2 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 355 vertices marked for relabeling... 355 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 7 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Fri 15 Mar 2024 10:48:05 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K rh ../surf/rh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 28 labels changed using aseg relabeling using gibbs priors... 000: 5838 changed, 88790 examined... 001: 1282 changed, 22793 examined... 002: 364 changed, 6901 examined... 003: 155 changed, 2083 examined... 004: 63 changed, 913 examined... 005: 21 changed, 334 examined... 006: 2 changed, 121 examined... 007: 1 changed, 11 examined... 008: 0 changed, 7 examined... 29 labels changed using aseg 000: 182 total segments, 96 labels (1012 vertices) changed 001: 87 total segments, 3 labels (8 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 20 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 354 vertices marked for relabeling... 354 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 7 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri 15 Mar 2024 10:48:12 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab LS5K lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 668 501 2072 3.234 0.727 0.162 0.056 10 1.7 G&S_frontomargin 1195 896 2927 2.637 0.629 0.153 0.041 19 2.1 G&S_occipital_inf 1251 967 3201 2.514 0.683 0.147 0.034 18 1.8 G&S_paracentral 1008 731 2864 2.907 0.733 0.153 0.049 16 2.1 G&S_subcentral 530 410 2441 3.716 0.613 0.199 0.089 12 2.0 G&S_transv_frontopol 1305 894 3509 3.425 0.826 0.121 0.032 12 1.7 G&S_cingul-Ant 952 671 2373 3.444 0.665 0.115 0.026 7 1.0 G&S_cingul-Mid-Ant 931 679 2276 2.974 0.713 0.115 0.027 7 1.1 G&S_cingul-Mid-Post 384 275 1422 3.543 0.740 0.175 0.056 7 1.0 G_cingul-Post-dorsal 222 173 756 3.242 0.815 0.200 0.070 5 0.7 G_cingul-Post-ventral 1222 970 2920 2.395 0.720 0.190 0.056 25 3.4 G_cuneus 900 741 3593 3.370 0.704 0.168 0.049 18 1.8 G_front_inf-Opercular 283 217 1062 3.164 0.667 0.166 0.053 4 0.7 G_front_inf-Orbital 729 551 2036 2.758 0.597 0.159 0.056 9 1.7 G_front_inf-Triangul 3226 2453 10781 2.943 0.795 0.177 0.067 66 9.1 G_front_middle 4854 3703 18733 3.647 0.744 0.161 0.052 78 10.2 G_front_sup 399 308 1435 4.114 0.744 0.113 0.035 3 0.4 G_Ins_lg&S_cent_ins 379 276 1876 4.327 0.549 0.105 0.027 2 0.4 G_insular_short 1946 1554 4916 2.496 0.699 0.192 0.061 47 5.3 G_occipital_middle 888 673 1796 2.292 0.647 0.184 0.056 20 2.4 G_occipital_sup 1172 972 3977 3.164 0.535 0.197 0.069 27 4.4 G_oc-temp_lat-fusifor 1954 1536 5323 2.579 0.738 0.193 0.052 46 4.9 G_oc-temp_med-Lingual 837 631 2392 2.839 0.780 0.142 0.039 9 1.3 G_oc-temp_med-Parahip 1197 975 4107 2.986 0.781 0.179 0.069 25 3.6 G_orbital 1870 1583 5785 2.756 0.686 0.198 0.062 52 5.6 G_pariet_inf-Angular 1969 1622 6080 2.713 0.993 0.187 0.062 48 6.0 G_pariet_inf-Supramar 2094 1762 6241 2.537 0.700 0.172 0.047 47 4.7 G_parietal_sup 1614 1211 3622 2.314 0.578 0.145 0.034 23 2.5 G_postcentral 1789 1473 4769 2.526 0.553 0.166 0.049 29 3.9 G_precentral 2068 1618 7394 3.130 0.787 0.171 0.051 49 4.8 G_precuneus 568 446 2230 3.433 0.925 0.195 0.069 18 1.7 G_rectus 10 5 14 2.432 0.209 0.070 0.015 0 0.0 G_subcallosal 339 250 834 2.790 0.466 0.154 0.046 4 0.7 G_temp_sup-G_T_transv 1237 1050 5194 3.169 0.699 0.183 0.062 25 3.4 G_temp_sup-Lateral 392 271 1287 3.442 0.864 0.065 0.013 1 0.2 G_temp_sup-Plan_polar 618 479 2046 3.271 0.915 0.115 0.025 6 0.5 G_temp_sup-Plan_tempo 1311 1007 4833 3.115 0.760 0.169 0.061 27 3.7 G_temporal_inf 1822 1520 6361 2.957 0.799 0.204 0.077 43 6.7 G_temporal_middle 164 112 280 2.810 0.360 0.099 0.031 1 0.2 Lat_Fis-ant-Horizont 173 127 330 2.573 0.554 0.107 0.023 1 0.1 Lat_Fis-ant-Vertical 808 541 1274 2.906 0.743 0.102 0.021 4 0.7 Lat_Fis-post 1209 741 1583 1.948 0.679 0.151 0.047 20 2.4 Pole_occipital 928 794 3830 2.963 0.949 0.196 0.072 22 3.4 Pole_temporal 1451 1046 2283 2.294 0.699 0.120 0.027 12 1.7 S_calcarine 2122 1426 2632 2.059 0.500 0.096 0.020 10 1.7 S_central 871 605 1429 2.553 0.527 0.100 0.015 4 0.6 S_cingul-Marginalis 312 200 611 3.344 0.621 0.087 0.020 1 0.2 S_circular_insula_ant 977 668 1748 2.925 0.839 0.093 0.021 4 0.9 S_circular_insula_inf 1227 788 1921 2.824 0.633 0.093 0.020 5 1.1 S_circular_insula_sup 654 452 1089 2.403 0.620 0.121 0.025 4 0.8 S_collat_transv_ant 320 217 609 2.759 0.869 0.146 0.041 4 0.5 S_collat_transv_post 1437 967 2806 2.904 0.856 0.099 0.026 7 1.4 S_front_inf 889 608 1433 2.974 0.689 0.126 0.039 6 1.5 S_front_middle 2201 1611 4813 2.826 0.595 0.120 0.028 16 2.7 S_front_sup 138 109 322 3.217 0.539 0.173 0.028 2 0.2 S_interm_prim-Jensen 2487 1680 3797 2.460 0.521 0.089 0.014 12 1.4 S_intrapariet&P_trans 806 545 1117 2.360 0.451 0.116 0.026 5 0.9 S_oc_middle&Lunatus 921 647 1538 2.462 0.593 0.116 0.023 7 0.9 S_oc_sup&transversal 678 468 1100 2.614 0.606 0.135 0.036 8 1.1 S_occipital_ant 564 400 1063 2.738 0.494 0.150 0.037 8 0.8 S_oc-temp_lat 1320 938 2334 2.499 0.719 0.113 0.022 10 1.1 S_oc-temp_med&Lingual 104 78 261 3.656 0.789 0.165 0.061 1 0.4 S_orbital_lateral 157 129 485 3.529 0.693 0.137 0.022 1 0.1 S_orbital_med-olfact 598 392 1078 3.009 0.776 0.111 0.031 3 0.8 S_orbital-H_Shaped 1520 1013 2466 2.434 0.677 0.098 0.016 8 1.1 S_parieto_occipital 942 581 1172 2.845 0.750 0.125 0.032 14 1.1 S_pericallosal 2183 1470 3056 2.300 0.506 0.097 0.019 13 1.6 S_postcentral 1225 831 2166 2.938 0.625 0.096 0.018 6 0.9 S_precentral-inf-part 1066 749 1949 2.703 0.637 0.111 0.021 7 1.0 S_precentral-sup-part 505 353 1505 3.888 0.805 0.124 0.038 4 0.8 S_suborbital 825 586 1667 3.164 0.536 0.116 0.024 5 0.8 S_subparietal 811 565 1330 2.715 0.632 0.127 0.028 6 0.9 S_temporal_inf 3972 2763 7436 2.734 0.722 0.101 0.022 26 3.4 S_temporal_sup 226 161 508 3.642 0.616 0.127 0.023 2 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Fri 15 Mar 2024 10:48:25 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab LS5K rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 536 375 1650 3.189 0.801 0.155 0.065 9 1.3 G&S_frontomargin 645 396 796 2.049 0.971 0.120 0.032 7 0.8 G&S_occipital_inf 1130 907 2922 2.551 0.700 0.171 0.044 17 2.3 G&S_paracentral 954 721 2832 3.166 0.558 0.144 0.035 13 1.4 G&S_subcentral 851 607 2557 2.970 0.773 0.169 0.079 20 2.7 G&S_transv_frontopol 1894 1286 4796 3.291 0.724 0.115 0.031 14 2.4 G&S_cingul-Ant 987 721 2422 2.854 0.720 0.126 0.031 10 1.7 G&S_cingul-Mid-Ant 1093 811 2741 2.998 0.717 0.125 0.032 10 1.3 G&S_cingul-Mid-Post 364 298 1415 3.441 0.859 0.200 0.069 9 1.1 G_cingul-Post-dorsal 242 185 770 2.917 0.862 0.185 0.073 5 0.7 G_cingul-Post-ventral 1132 882 2820 2.691 0.651 0.189 0.052 20 2.6 G_cuneus 910 714 3414 3.303 0.615 0.146 0.043 16 1.8 G_front_inf-Opercular 218 162 698 2.974 0.589 0.157 0.052 4 0.4 G_front_inf-Orbital 505 380 2094 3.449 0.637 0.149 0.040 7 0.8 G_front_inf-Triangul 3067 2424 10692 3.048 0.766 0.182 0.062 66 7.9 G_front_middle 4694 3597 16315 3.259 0.908 0.163 0.056 79 11.2 G_front_sup 369 290 1410 4.073 0.769 0.124 0.038 3 0.5 G_Ins_lg&S_cent_ins 429 276 1794 4.248 0.707 0.127 0.070 28 1.6 G_insular_short 1431 1040 3884 2.627 0.749 0.160 0.042 28 2.7 G_occipital_middle 1045 767 2286 2.308 0.597 0.161 0.035 21 1.8 G_occipital_sup 1126 810 3540 3.058 0.790 0.171 0.052 26 2.7 G_oc-temp_lat-fusifor 1653 1306 4731 2.709 0.723 0.194 0.063 36 4.9 G_oc-temp_med-Lingual 742 522 2337 3.212 0.781 0.133 0.042 8 1.2 G_oc-temp_med-Parahip 1560 1149 5105 3.188 0.793 0.169 0.065 33 4.4 G_orbital 2009 1628 7454 3.115 0.750 0.188 0.060 48 5.5 G_pariet_inf-Angular 1869 1477 6909 3.183 0.766 0.169 0.048 35 3.8 G_pariet_inf-Supramar 1808 1491 5436 2.634 0.852 0.197 0.064 46 5.4 G_parietal_sup 1433 1207 3599 2.266 0.701 0.189 0.060 35 4.4 G_postcentral 1744 1416 4920 2.641 0.669 0.153 0.037 30 3.0 G_precentral 1679 1361 6162 3.040 0.823 0.182 0.052 37 4.1 G_precuneus 483 403 2232 3.551 0.838 0.222 0.093 20 2.0 G_rectus 18 11 47 3.521 0.267 0.042 0.007 0 0.0 G_subcallosal 363 250 934 2.909 0.602 0.142 0.034 5 0.4 G_temp_sup-G_T_transv 1318 1062 6076 3.805 0.710 0.167 0.050 27 3.1 G_temp_sup-Lateral 466 323 1285 3.466 0.839 0.104 0.026 2 0.5 G_temp_sup-Plan_polar 662 482 1778 2.951 0.624 0.096 0.023 4 0.6 G_temp_sup-Plan_tempo 1656 1266 5626 3.177 0.875 0.173 0.047 40 3.6 G_temporal_inf 1835 1543 7088 3.206 0.726 0.176 0.048 38 4.2 G_temporal_middle 317 227 807 3.192 0.531 0.081 0.013 1 0.2 Lat_Fis-ant-Horizont 226 164 433 2.998 0.669 0.095 0.017 1 0.2 Lat_Fis-ant-Vertical 1099 729 1811 3.223 0.472 0.102 0.021 6 0.9 Lat_Fis-post 1708 1132 3078 2.164 1.034 0.160 0.049 32 3.7 Pole_occipital 948 734 2924 2.753 0.942 0.168 0.067 18 2.6 Pole_temporal 1282 883 1763 2.218 1.007 0.127 0.035 15 2.2 S_calcarine 1936 1379 2519 2.110 0.447 0.105 0.022 11 1.7 S_central 1079 747 1838 2.416 0.605 0.094 0.015 5 0.7 S_cingul-Marginalis 453 300 833 3.261 0.573 0.089 0.018 2 0.3 S_circular_insula_ant 827 559 1356 2.708 0.643 0.100 0.025 4 0.9 S_circular_insula_inf 836 567 1598 3.414 0.641 0.095 0.021 4 0.7 S_circular_insula_sup 556 415 1094 2.603 0.603 0.121 0.027 5 0.6 S_collat_transv_ant 211 139 336 2.632 0.424 0.089 0.017 1 0.1 S_collat_transv_post 1285 888 2245 2.709 0.546 0.104 0.021 6 1.1 S_front_inf 1322 969 2447 2.596 0.566 0.125 0.031 10 1.7 S_front_middle 1579 1134 2719 2.620 0.517 0.099 0.022 7 1.3 S_front_sup 335 227 461 2.513 0.509 0.113 0.023 2 0.3 S_interm_prim-Jensen 2343 1701 4082 2.486 0.555 0.126 0.027 25 2.8 S_intrapariet&P_trans 584 399 984 2.450 0.594 0.118 0.030 6 0.6 S_oc_middle&Lunatus 1059 693 1529 2.435 0.459 0.097 0.017 6 0.7 S_oc_sup&transversal 330 243 422 2.121 0.459 0.128 0.032 4 0.3 S_occipital_ant 841 561 1343 2.820 0.530 0.114 0.025 6 0.9 S_oc-temp_lat 1063 756 1867 2.709 0.608 0.102 0.018 6 0.8 S_oc-temp_med&Lingual 267 185 515 2.668 0.589 0.119 0.036 2 0.3 S_orbital_lateral 318 237 800 2.890 1.083 0.133 0.031 3 0.3 S_orbital_med-olfact 672 455 1419 3.056 0.669 0.130 0.044 14 1.5 S_orbital-H_Shaped 1787 1202 2669 2.407 0.766 0.107 0.020 12 1.6 S_parieto_occipital 984 616 1106 2.429 0.714 0.128 0.027 14 0.8 S_pericallosal 1605 1087 2264 2.430 0.536 0.111 0.024 11 1.5 S_postcentral 1151 788 1992 2.872 0.559 0.095 0.017 5 0.8 S_precentral-inf-part 925 644 1475 2.658 0.541 0.117 0.020 6 0.9 S_precentral-sup-part 41 28 114 3.420 0.610 0.132 0.063 0 0.0 S_suborbital 845 596 1613 2.943 0.879 0.116 0.028 4 1.0 S_subparietal 865 601 1430 2.724 0.500 0.108 0.020 5 0.7 S_temporal_inf 4997 3467 9301 2.796 0.641 0.103 0.019 36 4.1 S_temporal_sup 263 185 505 3.804 0.617 0.121 0.018 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri 15 Mar 2024 10:48:38 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K lh ../surf/lh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1008 labels changed using aseg relabeling using gibbs priors... 000: 1399 changed, 89800 examined... 001: 288 changed, 6685 examined... 002: 71 changed, 1663 examined... 003: 26 changed, 436 examined... 004: 18 changed, 161 examined... 005: 10 changed, 110 examined... 006: 6 changed, 61 examined... 007: 6 changed, 43 examined... 008: 5 changed, 37 examined... 009: 6 changed, 39 examined... 010: 4 changed, 32 examined... 011: 4 changed, 20 examined... 012: 6 changed, 20 examined... 013: 5 changed, 34 examined... 014: 5 changed, 30 examined... 015: 5 changed, 29 examined... 016: 5 changed, 30 examined... 017: 3 changed, 31 examined... 018: 3 changed, 19 examined... 019: 4 changed, 21 examined... 020: 2 changed, 23 examined... 021: 2 changed, 10 examined... 022: 1 changed, 12 examined... 023: 0 changed, 7 examined... 206 labels changed using aseg 000: 45 total segments, 12 labels (89 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 309 vertices marked for relabeling... 309 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Fri 15 Mar 2024 10:48:44 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 LS5K rh ../surf/rh.sphere.reg /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1077 labels changed using aseg relabeling using gibbs priors... 000: 1396 changed, 88790 examined... 001: 327 changed, 6517 examined... 002: 80 changed, 1820 examined... 003: 41 changed, 492 examined... 004: 29 changed, 231 examined... 005: 16 changed, 168 examined... 006: 6 changed, 69 examined... 007: 4 changed, 33 examined... 008: 3 changed, 25 examined... 009: 4 changed, 21 examined... 010: 4 changed, 24 examined... 011: 5 changed, 30 examined... 012: 2 changed, 29 examined... 013: 5 changed, 18 examined... 014: 3 changed, 24 examined... 015: 3 changed, 17 examined... 016: 3 changed, 22 examined... 017: 2 changed, 14 examined... 018: 3 changed, 10 examined... 019: 2 changed, 13 examined... 020: 0 changed, 14 examined... 196 labels changed using aseg 000: 47 total segments, 14 labels (78 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 304 vertices marked for relabeling... 304 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 6 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri 15 Mar 2024 10:48:50 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab LS5K lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 1027 704 2417 3.353 0.659 0.133 0.032 12 1.3 caudalanteriorcingulate 2712 1981 6492 2.757 0.748 0.143 0.044 37 4.8 caudalmiddlefrontal 1912 1408 4019 2.391 0.659 0.155 0.042 28 4.0 cuneus 323 235 907 2.530 0.880 0.143 0.047 5 0.6 entorhinal 2497 1931 6737 2.955 0.697 0.162 0.050 41 6.2 fusiform 4619 3623 11426 2.685 0.662 0.158 0.044 86 8.9 inferiorparietal 2761 2071 8581 2.957 0.787 0.162 0.052 48 6.5 inferiortemporal 1041 738 2662 3.085 0.819 0.148 0.047 14 2.1 isthmuscingulate 5535 3894 10142 2.336 0.654 0.152 0.042 85 10.2 lateraloccipital 1784 1339 5227 3.146 0.771 0.148 0.054 24 3.9 lateralorbitofrontal 2845 2172 6668 2.485 0.702 0.168 0.042 53 5.5 lingual 1051 793 3739 3.664 0.919 0.166 0.055 22 2.4 medialorbitofrontal 3928 3004 10610 2.951 0.774 0.155 0.050 56 9.1 middletemporal 738 542 1750 2.701 0.751 0.116 0.030 6 0.8 parahippocampal 1911 1398 4560 2.853 0.736 0.120 0.028 17 2.1 paracentral 1399 1043 4013 3.070 0.702 0.131 0.035 17 1.9 parsopercularis 593 448 1694 3.020 0.607 0.134 0.038 9 0.8 parsorbitalis 1529 1094 3421 2.739 0.678 0.136 0.044 14 2.9 parstriangularis 1085 798 1578 2.111 0.512 0.147 0.033 13 1.7 pericalcarine 4919 3509 9714 2.330 0.687 0.123 0.031 55 6.6 postcentral 1347 949 3201 2.994 0.724 0.133 0.035 15 2.0 posteriorcingulate 5093 3756 10924 2.603 0.635 0.133 0.032 54 7.2 precentral 4004 2982 10810 2.959 0.759 0.140 0.035 60 6.1 precuneus 825 555 2299 3.702 0.815 0.120 0.032 9 1.1 rostralanteriorcingulate 3651 2720 10471 3.041 0.778 0.156 0.054 52 8.9 rostralmiddlefrontal 8053 5969 26797 3.401 0.788 0.146 0.047 106 15.4 superiorfrontal 4875 3616 10202 2.379 0.620 0.129 0.030 65 7.1 superiorparietal 4924 3688 14122 3.008 0.792 0.124 0.034 54 7.3 superiortemporal 3752 2855 9198 2.657 0.852 0.153 0.047 64 8.2 supramarginal 439 324 925 2.900 0.566 0.153 0.043 5 0.8 transversetemporal 1752 1272 5194 3.616 0.903 0.108 0.027 9 2.0 insula #----------------------------------------- #@# Parcellation Stats 3 rh Fri 15 Mar 2024 10:49:03 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab LS5K rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 691 489 1731 2.991 0.599 0.147 0.032 11 1.1 caudalanteriorcingulate 2373 1829 5666 2.725 0.572 0.146 0.039 32 3.9 caudalmiddlefrontal 1672 1219 3710 2.665 0.609 0.149 0.034 21 2.4 cuneus 287 193 976 3.329 0.788 0.160 0.053 4 0.8 entorhinal 2319 1693 5912 2.988 0.664 0.148 0.039 36 3.9 fusiform 5544 4098 13580 2.744 0.703 0.138 0.033 80 8.3 inferiorparietal 3144 2298 8373 2.916 0.846 0.146 0.043 54 6.0 inferiortemporal 1018 708 2426 2.956 0.838 0.142 0.047 14 1.7 isthmuscingulate 4073 2665 6755 2.226 0.862 0.137 0.037 59 6.2 lateraloccipital 2106 1491 5935 3.211 0.791 0.151 0.053 32 4.3 lateralorbitofrontal 2553 1920 6226 2.594 0.737 0.163 0.046 44 5.4 lingual 1133 872 4170 3.326 0.830 0.172 0.063 27 3.1 medialorbitofrontal 4313 3324 12123 2.997 0.676 0.143 0.034 58 6.7 middletemporal 698 504 1746 2.844 0.824 0.122 0.038 6 1.1 parahippocampal 1941 1435 4514 2.661 0.722 0.135 0.033 23 3.1 paracentral 1589 1167 4415 3.158 0.636 0.119 0.031 17 2.2 parsopercularis 618 446 1352 2.766 0.616 0.148 0.057 19 1.9 parsorbitalis 1537 1113 4580 3.206 0.581 0.124 0.032 15 2.0 parstriangularis 1020 747 1532 2.113 0.787 0.164 0.050 17 2.4 pericalcarine 4467 3445 9236 2.357 0.701 0.148 0.041 65 8.5 postcentral 1431 1102 3842 2.881 0.910 0.154 0.040 22 2.5 posteriorcingulate 4626 3396 10171 2.657 0.653 0.127 0.028 46 5.7 precentral 4144 3023 9908 2.709 0.922 0.137 0.035 54 6.8 precuneus 530 342 1210 3.446 0.644 0.108 0.024 4 0.5 rostralanteriorcingulate 3764 2774 10544 2.915 0.795 0.153 0.050 59 8.0 rostralmiddlefrontal 8685 6409 24969 3.107 0.829 0.138 0.046 110 15.6 superiorfrontal 4423 3346 9885 2.496 0.688 0.154 0.042 75 8.4 superiorparietal 5160 3758 15033 3.259 0.823 0.126 0.034 60 7.7 superiortemporal 3721 2794 10541 3.006 0.678 0.143 0.037 49 6.1 supramarginal 417 289 914 2.908 0.605 0.143 0.029 5 0.5 transversetemporal 1862 1294 5285 3.676 0.835 0.112 0.037 36 3.2 insula #----------------------------------------- #@# WM/GM Contrast lh Fri 15 Mar 2024 10:49:16 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts pctsurfcon --s LS5K --lh-only Log file is /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts/pctsurfcon.log Fri 15 Mar 2024 10:49:16 PM CET setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS cd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 mri_vol2surf --mov /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.wm.mgh --regheader LS5K --cortex srcvol = /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99678 0.00000 -0.08020 0.00002; -0.08020 0.00000 0.99678 0.00001; 0.00000 -1.00000 0.00000 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label Reading surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 52327 Masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.wm.mgh Dim: 89800 1 1 mri_vol2surf --mov /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.gm.mgh --projfrac 0.3 --regheader LS5K --cortex srcvol = /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99678 0.00000 -0.08020 0.00002; -0.08020 0.00000 0.99678 0.00001; 0.00000 -1.00000 0.00000 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label Reading surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Done reading source surface Reading thickness /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 59545 Masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.cortex.label Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.gm.mgh Dim: 89800 1 1 mri_concat /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.wm.mgh /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217071/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.w-g.pct.mgh mri_segstats --in /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.w-g.pct.mgh --annot LS5K lh aparc --sum /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.w-g.pct.mgh --annot LS5K lh aparc --sum /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/stats/lh.w-g.pct.stats --snr sysname Linux hostname ramones machine x86_64 user yangc UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.w-g.pct.mgh Vertex Area is 0.733448 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Fri 15 Mar 2024 10:49:18 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts pctsurfcon --s LS5K --rh-only Log file is /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts/pctsurfcon.log Fri 15 Mar 2024 10:49:19 PM CET setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS cd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/scripts /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 mri_vol2surf --mov /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.wm.mgh --regheader LS5K --cortex srcvol = /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99678 0.00000 -0.08020 0.00002; -0.08020 0.00000 0.99678 0.00001; 0.00000 -1.00000 0.00000 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label Reading surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 51593 Masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.wm.mgh Dim: 88790 1 1 mri_vol2surf --mov /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.gm.mgh --projfrac 0.3 --regheader LS5K --cortex srcvol = /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99678 0.00000 -0.08020 0.00002; -0.08020 0.00000 0.99678 0.00001; 0.00000 -1.00000 0.00000 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label Reading surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Done reading source surface Reading thickness /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 58977 Masking with /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.cortex.label Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.gm.mgh Dim: 88790 1 1 mri_concat /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.wm.mgh /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/tmp.pctsurfcon.217157/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.w-g.pct.mgh mri_segstats --in /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.w-g.pct.mgh --annot LS5K rh aparc --sum /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.w-g.pct.mgh --annot LS5K rh aparc --sum /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/stats/rh.w-g.pct.stats --snr sysname Linux hostname ramones machine x86_64 user yangc UseRobust 0 Constructing seg from annotation Reading annotation /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.w-g.pct.mgh Vertex Area is 0.727225 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Fri 15 Mar 2024 10:49:21 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1823 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1354 voxels changed to hypointensity... 3520 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri 15 Mar 2024 10:49:31 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_aparc2aseg --s LS5K --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt freadInt: fread failed relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS subject LS5K outvol /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white freadInt: fread failed Reading lh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial Loading lh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) freadInt: fread failed Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white freadInt: fread failed Reading rh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial Loading rh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) znzreadInt: znzread failed Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz znzreadInt: znzread failed Loading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; znzreadInt: znzread failed ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Numerical argument out of domain setting orig areas to linear transform determinant scaled 4.56 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 110 rescaling Left_Cerebral_Cortex from 61 --> 51 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 54 rescaling Left_Thalamus from 94 --> 86 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 73 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 22 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 54 rescaling Left_Amygdala from 56 --> 56 rescaling CSF from 32 --> 31 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 52 rescaling Right_Lateral_Ventricle from 13 --> 6 rescaling Right_Inf_Lat_Vent from 25 --> 21 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 28 rescaling from 22 --> 28 rescaling from 22 --> 28 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 57 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 znzreadInt: znzread failed nctx = 412885 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter Numerical argument out of domain average std[0] = 7.3 pass 1: 96 changed. pass 2: 12 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Fri 15 Mar 2024 10:51:54 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_aparc2aseg --s LS5K --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s freadInt: fread failed relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS subject LS5K outvol /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white freadInt: fread failed Reading lh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial Loading lh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) freadInt: fread failed Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white freadInt: fread failed Reading rh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial Loading rh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) znzreadInt: znzread failed Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz znzreadInt: znzread failed Loading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; znzreadInt: znzread failed ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Numerical argument out of domain setting orig areas to linear transform determinant scaled 4.56 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 110 rescaling Left_Cerebral_Cortex from 61 --> 51 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 54 rescaling Left_Thalamus from 94 --> 86 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 73 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 22 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 54 rescaling Left_Amygdala from 56 --> 56 rescaling CSF from 32 --> 31 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 52 rescaling Right_Lateral_Ventricle from 13 --> 6 rescaling Right_Inf_Lat_Vent from 25 --> 21 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 28 rescaling from 22 --> 28 rescaling from 22 --> 28 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 57 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 znzreadInt: znzread failed nctx = 412988 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter Numerical argument out of domain average std[0] = 7.3 pass 1: 96 changed. pass 2: 12 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri 15 Mar 2024 10:54:17 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_aparc2aseg --s LS5K --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz freadInt: fread failed relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS subject LS5K outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white freadInt: fread failed Reading lh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial Loading lh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) freadInt: fread failed Have color table for lh white annotation Building hash of lh white Building hash of lh pial Reading rh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white freadInt: fread failed Reading rh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial Loading rh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) znzreadInt: znzread failed Have color table for rh white annotation Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz znzreadInt: znzread failed Loading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; znzreadInt: znzread failed ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Numerical argument out of domain setting orig areas to linear transform determinant scaled 4.56 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 110 rescaling Left_Cerebral_Cortex from 61 --> 51 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 25 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 54 rescaling Left_Thalamus from 94 --> 86 rescaling Left_Thalamus_Proper from 84 --> 87 rescaling Left_Caudate from 75 --> 72 rescaling Left_Putamen from 80 --> 73 rescaling Left_Pallidum from 98 --> 89 rescaling Third_Ventricle from 25 --> 22 rescaling Fourth_Ventricle from 22 --> 13 rescaling Brain_Stem from 81 --> 83 rescaling Left_Hippocampus from 57 --> 54 rescaling Left_Amygdala from 56 --> 56 rescaling CSF from 32 --> 31 rescaling Left_Accumbens_area from 62 --> 57 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 107 rescaling Right_Cerebral_Cortex from 58 --> 52 rescaling Right_Lateral_Ventricle from 13 --> 6 rescaling Right_Inf_Lat_Vent from 25 --> 21 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 53 rescaling Right_Thalamus_Proper from 85 --> 83 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 72 rescaling Right_Pallidum from 97 --> 87 rescaling Right_Hippocampus from 53 --> 54 rescaling Right_Amygdala from 55 --> 51 rescaling Right_Accumbens_area from 65 --> 65 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 28 rescaling from 22 --> 28 rescaling from 22 --> 28 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 57 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 znzreadInt: znzread failed nctx = 412988 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter Numerical argument out of domain average std[0] = 7.3 pass 1: 96 changed. pass 2: 12 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Fri 15 Mar 2024 10:56:35 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Fri 15 Mar 2024 10:56:35 PM CET setenv SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS cd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname ramones machine x86_64 user yangc input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Fri 15 Mar 2024 10:56:35 PM CET Ended at Fri 15 Mar 2024 10:56:39 PM CET Apas2aseg-Run-Time-Sec 4 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Fri 15 Mar 2024 10:56:40 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/ASegStatsLUT.txt --subject LS5K $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/ASegStatsLUT.txt --subject LS5K sysname Linux hostname ramones machine x86_64 user yangc UseRobust 0 atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) Computing euler number orig.nofix lheno = -144, rheno = -92 orig.nofix lhholes = 73, rhholes = 47 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Fri 15 Mar 2024 10:58:05 PM CET /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K mri_aparc2aseg --s LS5K --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz freadInt: fread failed SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS subject LS5K outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc+aseg.mgz Reading lh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white freadInt: fread failed Reading lh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial Loading lh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) freadInt: fread failed Have color table for lh white annotation Ripping vertices labeled as unkown Ripped 6919 vertices from left hemi Building hash of lh white Building hash of lh pial Reading rh white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white freadInt: fread failed Reading rh pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial Loading rh annotations from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) znzreadInt: znzread failed Have color table for rh white annotation Ripping vertices labeled as unkown Ripped 6942 vertices from right hemi Building hash of rh white Building hash of rh pial Loading ribbon segmentation from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz znzreadInt: znzread failed Loading filled from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/ribbon.mgz znzreadInt: znzread failed Loading aseg from /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aseg.mgz znzreadInt: znzread failed Loading Ctx Seg File /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/aparc+aseg.mgz Numerical argument out of domain ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 715467 Used brute-force search on 418 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 946.000000 Fixing Parahip RH WM Found 3 clusters 0 k 992.000000 1 k 3.000000 2 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject LS5K --surf-wm-vol --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject LS5K --surf-wm-vol --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/WMParcStatsLUT.txt --etiv sysname Linux hostname ramones machine x86_64 user yangc UseRobust 0 atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri 15 Mar 2024 11:03:59 PM CET mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA1_exvivo.label --trgsubject LS5K --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA2_exvivo.label --trgsubject LS5K --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8079 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3a_exvivo.label --trgsubject LS5K --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3b_exvivo.label --trgsubject LS5K --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6114 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4a_exvivo.label --trgsubject LS5K --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5894 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4p_exvivo.label --trgsubject LS5K --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA6_exvivo.label --trgsubject LS5K --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 446 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14035 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA44_exvivo.label --trgsubject LS5K --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4253 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA45_exvivo.label --trgsubject LS5K --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3595 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V1_exvivo.label --trgsubject LS5K --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 419 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5060 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V2_exvivo.label --trgsubject LS5K --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 844 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 8958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.MT_exvivo.label --trgsubject LS5K --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2330 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject LS5K --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject LS5K --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2133 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1516 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 207 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7242 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1948 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1223 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 243 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3648 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 378 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 620 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 501 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject LS5K --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 89800 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 478 mri_label2label: Done mris_label2annot --s LS5K --hemi lh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label cmdline mris_label2annot --s LS5K --hemi lh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname ramones machine x86_64 user yangc subject LS5K hemi lh SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS ColorTable /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 61613 unhit vertices Writing annot to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.BA_exvivo.annot mris_label2annot --s LS5K --hemi lh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label cmdline mris_label2annot --s LS5K --hemi lh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname ramones machine x86_64 user yangc subject LS5K hemi lh SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS ColorTable /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 73565 unhit vertices Writing annot to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab LS5K lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 787 602 2146 2.550 0.648 0.178 0.043 15 1.5 BA1_exvivo 2916 2077 5452 2.359 0.603 0.109 0.023 27 2.6 BA2_exvivo 777 504 832 1.906 0.522 0.120 0.030 6 0.8 BA3a_exvivo 1676 1184 3214 2.264 0.675 0.127 0.043 22 3.2 BA3b_exvivo 1156 897 2881 2.687 0.540 0.135 0.028 12 1.2 BA4a_exvivo 818 565 1288 2.281 0.420 0.106 0.021 5 0.8 BA4p_exvivo 6682 5165 19414 3.037 0.825 0.150 0.042 92 12.0 BA6_exvivo 1562 1172 4502 3.038 0.701 0.124 0.031 18 1.8 BA44_exvivo 1805 1322 4794 2.937 0.813 0.141 0.046 18 3.5 BA45_exvivo 2044 1436 3175 2.070 0.679 0.156 0.044 31 4.4 V1_exvivo 5202 3828 11008 2.417 0.717 0.165 0.043 85 10.1 V2_exvivo 1805 1316 3623 2.529 0.566 0.143 0.037 26 3.0 MT_exvivo 499 348 1168 2.506 0.867 0.161 0.167 13 5.4 perirhinal_exvivo 458 356 1624 3.160 0.888 0.139 0.043 6 0.9 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab LS5K lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 214802 Total vertex volume 210500 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 482 355 1107 2.325 0.575 0.187 0.044 10 0.9 BA1_exvivo 1154 808 1943 2.150 0.452 0.088 0.016 6 0.8 BA2_exvivo 639 406 604 1.926 0.513 0.124 0.030 5 0.7 BA3a_exvivo 1009 721 1588 2.039 0.615 0.089 0.017 5 0.7 BA3b_exvivo 1043 811 2406 2.534 0.552 0.129 0.027 9 1.2 BA4a_exvivo 706 487 1035 2.242 0.417 0.107 0.024 5 0.6 BA4p_exvivo 3702 2931 11321 3.091 0.871 0.155 0.042 51 6.7 BA6_exvivo 970 759 3082 3.095 0.636 0.145 0.039 15 1.5 BA44_exvivo 725 569 1935 2.669 0.670 0.156 0.051 8 1.5 BA45_exvivo 2172 1549 3534 2.070 0.684 0.151 0.042 32 4.4 V1_exvivo 2595 1947 5542 2.371 0.696 0.181 0.048 50 5.9 V2_exvivo 510 358 1076 2.502 0.600 0.157 0.058 9 1.4 MT_exvivo 247 179 635 2.523 0.711 0.132 0.034 2 0.3 perirhinal_exvivo 281 192 714 2.910 0.798 0.113 0.040 3 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fri 15 Mar 2024 11:06:12 PM CET mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA1_exvivo.label --trgsubject LS5K --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4182 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA2_exvivo.label --trgsubject LS5K --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6890 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3a_exvivo.label --trgsubject LS5K --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3b_exvivo.label --trgsubject LS5K --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4708 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4a_exvivo.label --trgsubject LS5K --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 5879 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4p_exvivo.label --trgsubject LS5K --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA6_exvivo.label --trgsubject LS5K --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA44_exvivo.label --trgsubject LS5K --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7110 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA45_exvivo.label --trgsubject LS5K --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 271 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5626 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V1_exvivo.label --trgsubject LS5K --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5071 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V2_exvivo.label --trgsubject LS5K --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 571 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 8587 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.MT_exvivo.label --trgsubject LS5K --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject LS5K --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1082 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject LS5K --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 780 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 927 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2716 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1713 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7101 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1062 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1234 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3437 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 3709 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 720 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject LS5K --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = LS5K trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /data/pt_02321/1_Analysen/2_CROSSING/FS/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white Reading target registration /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 88790 Number of reverse mapping hits = 16 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 307 mri_label2label: Done mris_label2annot --s LS5K --hemi rh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label cmdline mris_label2annot --s LS5K --hemi rh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname ramones machine x86_64 user yangc subject LS5K hemi rh SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS ColorTable /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 63184 unhit vertices Writing annot to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.BA_exvivo.annot mris_label2annot --s LS5K --hemi rh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label cmdline mris_label2annot --s LS5K --hemi rh --ctab /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname ramones machine x86_64 user yangc subject LS5K hemi rh SUBJECTS_DIR /data/pt_02321/1_Analysen/2_CROSSING/FS ColorTable /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 74344 unhit vertices Writing annot to /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab LS5K rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 659 572 1845 2.431 0.762 0.234 0.070 19 2.0 BA1_exvivo 1956 1446 3525 2.354 0.570 0.126 0.033 22 3.2 BA2_exvivo 782 496 774 2.118 0.479 0.135 0.032 8 1.0 BA3a_exvivo 1374 1133 3027 2.130 0.667 0.149 0.041 19 2.8 BA3b_exvivo 1062 818 2688 2.662 0.672 0.117 0.028 8 1.4 BA4a_exvivo 787 569 1289 2.324 0.480 0.101 0.019 5 0.6 BA4p_exvivo 5387 4166 14627 2.864 0.759 0.148 0.039 78 9.3 BA6_exvivo 2465 1792 6057 3.010 0.637 0.114 0.025 22 2.7 BA44_exvivo 2698 1956 7216 2.983 0.626 0.130 0.036 30 4.3 BA45_exvivo 1969 1485 3903 2.190 0.876 0.171 0.050 34 4.6 V1_exvivo 4467 3133 9267 2.485 0.844 0.156 0.045 75 9.0 V2_exvivo 1351 969 2599 2.503 0.656 0.140 0.036 17 2.0 MT_exvivo 408 279 1314 3.228 0.918 0.149 0.059 9 0.8 perirhinal_exvivo 241 183 690 2.943 0.691 0.149 0.045 3 0.6 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab LS5K rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/mri/wm.mgz... reading input surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... reading input pial surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.pial... reading input white surface /data/pt_02321/1_Analysen/2_CROSSING/FS/LS5K/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 211837 Total vertex volume 207260 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /afs/cbs.mpg.de/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1285721 mm^3 (det: 1.515185 ) lhCtxGM: 209736.774 209594.000 diff= 142.8 pctdiff= 0.068 rhCtxGM: 206172.488 205750.000 diff= 422.5 pctdiff= 0.205 lhCtxWM: 151350.089 151572.000 diff= -221.9 pctdiff=-0.147 rhCtxWM: 149457.891 150056.000 diff= -598.1 pctdiff=-0.400 SubCortGMVol 49212.000 SupraTentVol 775208.241 (772378.000) diff=2830.241 pctdiff=0.365 SupraTentVolNotVent 769035.241 (766205.000) diff=2830.241 pctdiff=0.368 BrainSegVol 864668.000 (862045.000) diff=2623.000 pctdiff=0.303 BrainSegVolNotVent 855344.000 (854933.241) diff=410.759 pctdiff=0.048 BrainSegVolNotVent 855344.000 CerebellumVol 88983.000 VentChorVol 6173.000 3rd4th5thCSF 3151.000 CSFVol 528.000, OptChiasmVol 156.000 MaskVol 3935601.000 409 343 1124 2.352 0.807 0.236 0.072 14 1.2 BA1_exvivo 1133 860 2162 2.250 0.497 0.106 0.022 7 1.1 BA2_exvivo 705 431 583 2.054 0.385 0.132 0.032 7 0.9 BA3a_exvivo 1037 858 1946 2.017 0.546 0.135 0.036 12 1.8 BA3b_exvivo 700 537 1696 2.564 0.798 0.156 0.044 11 1.5 BA4a_exvivo 669 468 982 2.273 0.465 0.087 0.015 3 0.4 BA4p_exvivo 3532 2770 9627 2.815 0.738 0.154 0.039 52 6.1 BA6_exvivo 623 505 2317 3.332 0.573 0.143 0.041 10 1.2 BA44_exvivo 708 541 2632 3.235 0.677 0.144 0.041 10 1.1 BA45_exvivo 1883 1387 3543 2.143 0.895 0.169 0.050 35 4.5 V1_exvivo 2430 1786 5553 2.518 0.855 0.175 0.052 45 5.8 V2_exvivo 215 159 582 2.475 0.796 0.163 0.047 5 0.4 MT_exvivo 224 159 803 3.425 0.744 0.142 0.055 6 0.3 perirhinal_exvivo 178 126 563 3.277 0.674 0.136 0.038 2 0.3 entorhinal_exvivo Started at Fri 15 Mar 2024 05:21:46 PM CET Ended at Fri 15 Mar 2024 11:08:19 PM CET #@#%# recon-all-run-time-hours 5.776 recon-all -s LS5K finished without error at Fri 15 Mar 2024 11:08:19 PM CET